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Chen Z, Huang Y, Shen Y, Zhang J, Deng J, Chen X. Denitrification shifted autotroph-heterotroph interactions in Microcystis aggregates. ENVIRONMENTAL RESEARCH 2023; 231:116269. [PMID: 37257745 DOI: 10.1016/j.envres.2023.116269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/13/2023] [Accepted: 05/27/2023] [Indexed: 06/02/2023]
Abstract
Denitrification is the most important process for nitrogen removal in eutrophic lakes and was mostly investigated in lake sediment. Denitrification could also be mediated by cyanobacterial aggregates, yet how this process impacts nitrogen (N) availability and the associated autotroph-heterotroph relationships within cyanobacterial aggregates has not been investigated. In this study, incubation experiments with nitrate amendment were conducted with Microcystis aggregates (MAs). Measurement of nitrogen contents, 16S rRNA-based microbial community profiling and metatranscriptomic sequencing were used to jointly assess nitrogen turnover dynamics, as well as changes in microbial composition and gene expression. Strong denitrification potential was revealed, and maximal N removal was achieved within two days, after which the communities entered a state of severe N limitation. Changes of active microbial communities were further promoted both with regard to taxonomic composition and transcriptive activities. Expression of transportation-related genes confirmed competition for N sources by Microcystis and phycospheric communities. Strong stress response to reactive oxygen species by Microcystis was revealed. Notably, interspecific relationships among Microcystis and phycospheric communities exhibited a shift toward antagonistic interactions, particularly evidenced by overall increased expression of genes related to cell lysis and utilization of cellular materials. Patterns of fatty acid and starch metabolism also suggested changes in carbon metabolism and cross-feeding patterns within MAs. Taken together, this study demonstrated substantial denitrification potential of MAs, which, importantly, further induced changes in both metabolic activities and autotroph-heterotroph interactions. These findings also highlight the key role of nutrient condition in shaping autotroph-heterotroph relationships.
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Affiliation(s)
- Zhijie Chen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yingying Huang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai, China.
| | - Yingshi Shen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Junyi Zhang
- Jiangsu Wuxi Environmental Monitoring Center, Jiangsu, China
| | - Jie Deng
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai, China.
| | - Xuechu Chen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai, China
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Li Z, Fan Y, Bai H, Zhang J, Mao S, Jin W. Live yeast supplementation altered the bacterial community's composition and function in rumen and hindgut and alleviated the detrimental effects of heat stress on dairy cows. J Anim Sci 2023; 101:skac410. [PMID: 36534956 PMCID: PMC9841158 DOI: 10.1093/jas/skac410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The objective of this study was to investigate the effects of live yeast (LY, Saccharomyces cerevisiae) on the lactation performance, bacterial community, and functions in the rumen and hindgut of dairy cows under heat stress. Thirty-three multiparous (parity 3.9 ± 0.8) Holstein dairy cows (189.1 ± 6.6 d in milk at the beginning of the experiment) were randomly assigned to three groups (11 cows per treatment). Cows in the three groups were fed a diet without yeast (CON), with 10 g yeast/d/head (LY-10), and with 20 g yeast/d/head (LY-20). The yeast product contained 2.0 × 1010 CFU/g. Supplementing LY decreased the rectal temperature and respiratory rate of cows, and increased dry matter intake, milk yield, milk fat yield, milk protein yield, and milk lactose yield (P < 0.001), yet decreased milk urea nitrogen concentration (P = 0.035). Interaction effects of treatment × week were observed for rectal temperature (P < 0.05), respiratory rate (P < 0.05), milk yield (P = 0.015), milk urea nitrogen (P = 0.001), milk protein yield (P = 0.008), and milk lactose yield (P = 0.030). In rumen, LY increased the concentrations of acetate, isobutyrate, isovaterate, valerate, total volatile fatty acids (VFAs), and NH3-N (P < 0.05). Miseq sequencing of the 16S rRNA genes showed that LY increased the relative abundance of Prevotella and Prevotellaceae UCG-003 at the genus level with a series of enriched pathways in the metabolism of carbohydrates and protein. In fecal samples, LY did not affect the profile of VFAs (P > 0.05). Clostridium sensu stricto 1 (P = 0.013) and Actinobacillus (P = 0.011) increased in the relative abundance by LY, whereas Bacteroides (P = 0.016) and Oscillospirales UCG-010 (P = 0.005) decreased with a series of enriched pathways in carbohydrate metabolism, secondary bile acid biosynthesis. In summary, LY supplementation altered the bacterial community's composition and function in rumen and hindgut, and simultaneously alleviated the detrimental effects of heat stress on dairy cows. These findings provide extended insight into the effects of LY in the rumen and hindgut of dairy cows exposed to heat stress.
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Affiliation(s)
- Zihao Li
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Fan
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Bai
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiyou Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Jin
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Sohail M, Barzkar N, Michaud P, Tamadoni Jahromi S, Babich O, Sukhikh S, Das R, Nahavandi R. Cellulolytic and Xylanolytic Enzymes from Yeasts: Properties and Industrial Applications. Molecules 2022; 27:3783. [PMID: 35744909 PMCID: PMC9229053 DOI: 10.3390/molecules27123783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Lignocellulose, the main component of plant cell walls, comprises polyaromatic lignin and fermentable materials, cellulose and hemicellulose. It is a plentiful and renewable feedstock for chemicals and energy. It can serve as a raw material for the production of various value-added products, including cellulase and xylanase. Cellulase is essentially required in lignocellulose-based biorefineries and is applied in many commercial processes. Likewise, xylanases are industrially important enzymes applied in papermaking and in the manufacture of prebiotics and pharmaceuticals. Owing to the widespread application of these enzymes, many prokaryotes and eukaryotes have been exploited to produce cellulase and xylanases in good yields, yet yeasts have rarely been explored for their plant-cell-wall-degrading activities. This review is focused on summarizing reports about cellulolytic and xylanolytic yeasts, their properties, and their biotechnological applications.
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Affiliation(s)
- Muhammad Sohail
- Department of Microbiology, University of Karachi, Karachi 75270, Pakistan;
| | - Noora Barzkar
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas 3995, Iran
| | - Philippe Michaud
- Institute Pascal, Université Clermont Auvergne, CNRS, Clermont Auvergne INP, F-63000 Clermont-Ferrand, France;
| | - Saeid Tamadoni Jahromi
- Persian Gulf and Oman Sea Ecology Research Center, Iranian Fisheries Sciences Research Institute, Agricultural Research Education and Extension Organization (AREEO), Bandar Abbas 3995, Iran
| | - Olga Babich
- Institute of Living Systems, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia; (O.B.); (S.S.)
| | - Stanislav Sukhikh
- Institute of Living Systems, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia; (O.B.); (S.S.)
| | - Rakesh Das
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), 1433 Aas, Norway;
| | - Reza Nahavandi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj 8361, Iran;
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Fang J, Bai XT, Qi L, Vukanti R, Ge Y. Rare-earth metal oxide nanoparticles decouple the linkage between soil bacterial community structure and function by selectively influencing potential keystone taxa. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 298:118863. [PMID: 35063538 DOI: 10.1016/j.envpol.2022.118863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Excessive production and application of rare-earth metal oxide nanoparticles warrants assessment of their environmental risks. Little is known about the impact of these nanoparticles on soil bacterial communities. We quantified the effects of nano-Gd2O3 and nano-La2O3, at the different concentrations and exposure regimes, on soil bacterial community structure and function as well as the structure-function relationship. Further, we constructed and analyzed a co-occurrence network to identify and characterize potential keystone taxa that were related to the enzyme activities and responded to the increasing concentrations of nanoparticles. Both nano-Gd2O3 and nano-La2O3 significantly altered the bacterial community structure and function in a concentration-dependent manner; however, these negative effects were observed on day 1 or day 7 but not on day 60, indicating that these effects were transient and the bacterial communities can mitigate the effect of these nanoparticles over time. Interestingly, the nanoparticle exposure decoupled the relationship between the structure and function of the soil bacterial communities. The decoupling was due to changes in the composition and relative abundances of potential keystone taxa related to bacterial community functions. Altogether, we provide insights into the interactions between the rare-earth metal oxide nanoparticles and soil bacterial communities. Our results facilitate the environmental risk assessment and safe usage of rare-earth metal oxide nanoparticles.
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Affiliation(s)
- Junnan Fang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xue-Ting Bai
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Qi
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Raja Vukanti
- Department of Microbiology, Bhavan's Vivekananda College, Secunderabad, 500094, India
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Lu S, Mikkelsen D, Flanagan BM, Williams BA, Gidley MJ. Interaction of cellulose and xyloglucan influences in vitro fermentation outcomes. Carbohydr Polym 2021; 258:117698. [PMID: 33593569 DOI: 10.1016/j.carbpol.2021.117698] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/12/2021] [Accepted: 01/22/2021] [Indexed: 01/08/2023]
Abstract
To investigate the effects of interactions between cellulose and xyloglucan (XG) on in vitro fermentation, a composite of bacterial cellulose (BC) incorporating XG during pellicle formation (BCXG), was fermented using a human faecal inoculum, and compared with BC, XG and a mixture (BC&XG) physically blended to have the same BC to XG ratio of BCXG. Compared to individual polysaccharides, the fermentation extent of BC and fermentation rate of XG were promoted in BC&XG. XG embedded in the BCXG composite was degraded less than in BC&XG, while more cellulose in BCXG was fermented than in BC&XG. This combination explains the similar amount of short chain fatty acid production noted throughout the fermentation process for BCXG and BC&XG. Microbial community dynamics for each substrate were consistent with the corresponding polysaccharide degradation. Thus, interactions between cellulose and XG are shown to influence their fermentability in multiple ways.
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Affiliation(s)
- Shiyi Lu
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Deirdre Mikkelsen
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia; School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Bernadine M Flanagan
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Barbara A Williams
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Michael J Gidley
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
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A novel D-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae. Sci Rep 2021; 11:4766. [PMID: 33637780 PMCID: PMC7910561 DOI: 10.1038/s41598-021-83937-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/09/2021] [Indexed: 11/25/2022] Open
Abstract
Carbohydrate rich substrates such as lignocellulosic hydrolysates remain one of the primary sources of potentially renewable fuel and bulk chemicals. The pentose sugar d-xylose is often present in significant amounts along with hexoses. Saccharomyces cerevisiae can acquire the ability to metabolize d-xylose through expression of heterologous d-xylose isomerase (XI). This enzyme is notoriously difficult to express in S. cerevisiae and only fourteen XIs have been reported to be active so far. We cloned a new d-xylose isomerase derived from microorganisms in the gut of the wood-feeding beetle Odontotaenius disjunctus. Although somewhat homologous to the XI from Piromyces sp. E2, the new gene was identified as bacterial in origin and the host as a Parabacteroides sp. Expression of the new XI in S. cerevisiae resulted in faster aerobic growth than the XI from Piromyces on d-xylose media. The d-xylose isomerization rate conferred by the new XI was also 72% higher, while absolute xylitol production was identical in both strains. Interestingly, increasing concentrations of xylitol (up to 8 g L−1) appeared not to inhibit d-xylose consumption. The newly described XI displayed 2.6 times higher specific activity, 37% lower KM for d-xylose, and exhibited higher activity over a broader temperature range, retaining 51% of maximal activity at 30 °C compared with only 29% activity for the Piromyces XI.
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Usai G, Cirrincione S, Re A, Manfredi M, Pagnani A, Pessione E, Mazzoli R. Clostridium cellulovorans metabolism of cellulose as studied by comparative proteomic approach. J Proteomics 2020; 216:103667. [DOI: 10.1016/j.jprot.2020.103667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/31/2019] [Accepted: 01/22/2020] [Indexed: 12/15/2022]
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Kozaki R, Miyake H. Enzymatic and molecular characterization of an endoglucanase E from Clostridium cellulovorans 743B. J Biosci Bioeng 2019; 128:398-404. [DOI: 10.1016/j.jbiosc.2019.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/08/2019] [Accepted: 03/15/2019] [Indexed: 10/27/2022]
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Aburaya S, Aoki W, Kuroda K, Minakuchi H, Ueda M. Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides. BMC Microbiol 2019; 19:118. [PMID: 31159733 PMCID: PMC6547498 DOI: 10.1186/s12866-019-1480-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 05/07/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clostridium cellulovorans is a mesophilic, cellulosome-producing bacterium containing 57 genomic cellulosomal enzyme-encoding genes. In addition to cellulosomal proteins, C. cellulovorans also secretes non-cellulosomal proteins to degrade plant cell wall polysaccharides. Unlike other cellulosome-producing Clostridium species, C. cellulovorans can metabolize all major plant cell wall polysaccharides (cellulose, hemicelluloses, and pectins). In this study, we performed a temporal proteome analysis of C. cellulovorans to reveal strategies underlying plant cell wall polysaccharide degradation. RESULTS We cultured C. cellulovorans with five different carbon sources (glucose, cellulose, xylan, galactomannan, and pectin) and performed proteome analysis on cellular and secreted proteins. In total, we identified 1895 cellular proteins and 875 secreted proteins. The identified unique carbohydrate-degrading enzymes corresponding to each carbon source were annotated to have specific activity against each carbon source. However, we identified pectate lyase as a unique enzyme in C. cellulovorans cultivated on xylan, which was not previously associated with xylan degradation. We performed k-means clustering analysis for elucidation of temporal changes of the cellular and secreted proteins in each carbon sources. We found that cellular proteins in most of the k-means clusters are involved in carbohydrate metabolism, amino acid metabolism, translation, or membrane transport. When xylan and pectin were used as the carbon sources, the most increasing k-means cluster contained proteins involved in the metabolism of cofactors and vitamins. In case of secreted proteins of C. cellulovorans cultured either on cellulose or xylan, galactomannan, and pectin, the clusters with the most increasing trend contained either 25 cellulosomal proteins and five non-cellulosomal proteins or 8-19 cellulosomal proteins and 9-16 non-cellulosomal proteins, respectively. These differences might reflect mechanisms for degrading cellulose of other carbon source. Co-abundance analysis of the secreted proteins revealed that proteases and protease inhibitors accumulated coordinately. This observation implies that the secreted protease inhibitors and proteases protect carbohydrate-degrading enzymes from an attack from the plant. CONCLUSION In this study, we clarified, for the first time, the temporal proteome dynamics of cellular and secreted proteins in C. cellulovorans. This data will be valuable in understanding strategies employed by C. cellulovorans for degrading major plant cell wall polysaccharides.
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Affiliation(s)
- Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.,Research Fellow of the Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.,Kyoto Integrated Science and Technology Bio-Analysis Center, Shimogyo-ku, Kyoto, Japan.,JST-PRESTO, Chiyoda-ku, Tokyo, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hiroshi Minakuchi
- Kyoto-monotech, 1095, Shuzei-cho, Kamigyo-ku, Kyoto-shi, Kyoto, 602-8155, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan. .,Kyoto Integrated Science and Technology Bio-Analysis Center, Shimogyo-ku, Kyoto, Japan. .,JST-PRESTO, Chiyoda-ku, Tokyo, Japan.
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Jeong DW, Hyeon JE, Joo YC, Shin SK, Han SO. Integration of Bacterial Expansin on Agarolytic Complexes to Enhance the Degrading Activity of Red Algae by Control of Gelling Properties. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:1-9. [PMID: 29151139 DOI: 10.1007/s10126-017-9782-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
Expansin act by loosening hydrogen bonds in densely packed polysaccharides. This work characterizes the biological functions of expansin in the gelling and degradation of algal polysaccharides. In this study, the bacterial expansin BpEX from Bacillus pumilus was fused with the dockerin module of a cellulosome system for assembly with agarolytic complexes. The assembly of chimeric expansin caused an indicative enhancement in agarase activity. The enzymatic activities on agar substrate and natural biomass were 3.7-fold and 3.3-fold higher respectively than that of agarase as a single enzyme. To validate the effect on the agar degradation, the regulation potential of parameters related to gel rheology by bacterial expansin was experimentally investigated to indicate that the bacterial expansin lowered the gelling temperature and viscosity of agar. Thus, these results demonstrated the possibility of advancing more efficient strategies for utilizing agar as oligo sugar source in the biorefinery field that uses marine biomass as feedstocks.
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Affiliation(s)
- Da Woon Jeong
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Jeong Eun Hyeon
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19702, USA
| | - Young-Chul Joo
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Sang Kyu Shin
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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Nakajima D, Nagano A, Shibata T, Tanaka R, Kuroda K, Ueda M, Miyake H. Xylanase B from Clostridium cellulovorans 743B: overexpression, purification, crystallization and X-ray diffraction analysis. Acta Crystallogr F Struct Biol Commun 2018; 74:113-116. [PMID: 29400321 PMCID: PMC5947682 DOI: 10.1107/s2053230x18000341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 01/06/2018] [Indexed: 11/11/2022] Open
Abstract
Clostridium cellulovorans produces multi-enzyme complexes called cellulosomes capable of efficiently degrading cellulosic biomass. There are three xylanase genes containing a sequence corresponding to a dockerin domain that are necessary for constructing cellulosomes in the genome. Among the xylanases encoded by these genes, xylanase B (XynB) contains a catalytic domain belonging to glycoside hydrolase family 10 and a carbohydrate-binding module (CBM) at the N-terminus, making it a member of CBM family 22. In this study, XynB was cloned, overexpressed, purified and crystallized. XynB was crystallized using the hanging-drop vapour-diffusion method in the presence of 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl pH 8.5, 32%(w/v) PEG 4000 at 293 K. X-ray diffraction analysis revealed that the crystal diffracted to 1.95 Å resolution and belonged to space group P212121, with unit-cell parameters a = 74.28, b = 77.55, c = 88.20 Å, α = β = γ = 90°. The data-evaluation statistics revealed high quality of the collected data, thereby establishing a solid basis for determination of the structure of cellulosomal xylanase from C. cellulovorans.
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Affiliation(s)
- Daichi Nakajima
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Akihiko Nagano
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Toshiyuki Shibata
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
- Seaweed Biorefinery Research Center, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Reiji Tanaka
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
- Seaweed Biorefinery Research Center, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Kouichi Kuroda
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mitsuyoshi Ueda
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideo Miyake
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
- Seaweed Biorefinery Research Center, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
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Nakajima D, Shibata T, Tanaka R, Kuroda K, Ueda M, Miyake H. Characterization of the cellulosomal scaffolding protein CbpC from Clostridium cellulovorans 743B. J Biosci Bioeng 2017; 124:376-380. [PMID: 28533157 DOI: 10.1016/j.jbiosc.2017.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 12/15/2022]
Abstract
Clostridium cellulovorans 743B, an anaerobic and mesophilic bacterium, produces an extracellular enzyme complex called the cellulosome on the cell surface. Recently, we have reported the whole genome sequence of C. cellulovorans, which revealed that a total of 4 cellulosomal scaffolding proteins: CbpA, HbpA, CbpB, and CbpC were encoded in the C. cellulovorans genome. In particular, cbpC encoded a 429-residue polypeptide that includes a carbohydrate-binding module (CBM), an S-layer homology module, and a cohesin. CbpC was also detected in the culture supernatant of C. cellulovorans. Genomic DNA coding for CbpC was subcloned into a pET-22b+ vector in order to express and produce the recombinant protein in Escherichia coli BL21(DE3). Measurement of CbpC adsorption to crystalline cellulose indicated a dissociation constant of 0.60 μM, which is a similar to that of CBM from CbpA. We also subcloned the region encoding xylanase B (XynB) with the dockerin from C. cellulovorans and analyzed the interaction between XynB and CbpC by GST pull-down assay. It was observed that GST-CbpC assembles with XynB to form a minimal cellulosome. The activity of XynB against rice straw tended to be increased in the presence of CbpC. These results showed a synergistic effect on rice straw as a representative cellulosic biomass through the formation of a minimal cellulosome containing XynB bound to CbpC. Thus, our findings provide a foundation for the development of cellulosic biomass saccharification using a minimal cellulosome.
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Affiliation(s)
- Daichi Nakajima
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Toshiyuki Shibata
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Reiji Tanaka
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideo Miyake
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan; Life Science Research Center, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan.
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13
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Singh G, Chandoha-Lee C, Zhang W, Renneckar S, Vikesland PJ, Pruden A. Biodegradation of nanocrystalline cellulose by two environmentally-relevant consortia. WATER RESEARCH 2016; 104:137-146. [PMID: 27522024 DOI: 10.1016/j.watres.2016.07.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/12/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Nanocellulose is growing in popularity due to its versatile properties and applications. However, there is a void of knowledge regarding the environmental fate of nanocellulose and the response of environmental microbial communities that are historically adapted to non-nano cellulose forms. Given its distinction in terms of size and chemical and physical properties, nanocellulose could potentially resist biodegradation and/or pose a xenobiotic influence on microbial communities during wastewater treatment or in receiving environments. In this study, biodegradation of H2SO4 hydrolyzed nanocrystalline cellulose (HNC) was compared with that of microcrystalline cellulose using two distinct anaerobic cellulose-degrading microbial consortia initially sourced from anaerobic digester (AD) and wetland (W) inocula. Equivalent cellulose masses were dosed and monitored with time by measurement of liberated glucose. HNC biodegraded at slightly faster rate than microcrystalline cellulose (1st order decay constants: 0.62 ± 0.08 wk-1 for HNC versus 0.39 ± 0.05 wk-1 for microcrystalline cellulose for the AD consortium; 0.69 ± 0.04 wk-1for HNCversus 0.58 ± 0.05 wk-1 for microcrystalline cellulose for the W consortium). 16S rRNA (total bacteria) and cel48 (glycoside hydrolase gene family 48, indicative of cellulose-degrading potential) genes were observed to be more enriched in the HNC condition for both consortia. According to Illumina amplicon sequencing of 16S rRNA genes, the composition of the consortia underwent distinct shifts in concert with HNC versus microcrystalline cellulose degradation. This study demonstrates that the biodegradation of cellulose is not inhibited in the nano-size range, particularly in the crystalline form, though the microbes and pathways involved likely differ.
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Affiliation(s)
- Gargi Singh
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | | | - Wei Zhang
- Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, VA 24060, USA; Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, VA 24060, USA
| | - Scott Renneckar
- Department of Wood Science, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA.
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Hyeon JE, Shin SK, Han SO. Design of nanoscale enzyme complexes based on various scaffolding materials for biomass conversion and immobilization. Biotechnol J 2016; 11:1386-1396. [PMID: 27783468 PMCID: PMC5132044 DOI: 10.1002/biot.201600039] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 09/26/2016] [Accepted: 10/07/2016] [Indexed: 12/14/2022]
Abstract
The utilization of scaffolds for enzyme immobilization involves advanced bionanotechnology applications in biorefinery fields, which can be achieved by optimizing the function of various enzymes. This review presents various current scaffolding techniques based on proteins, microbes and nanomaterials for enzyme immobilization, as well as the impact of these techniques on the biorefinery of lignocellulosic materials. Among them, architectural scaffolds have applied to useful strategies for protein engineering to improve the performance of immobilized enzymes in several industrial and research fields. In complexed enzyme systems that have critical roles in carbon metabolism, scaffolding proteins assemble different proteins in relatively durable configurations and facilitate collaborative protein interactions and functions. Additionally, a microbial strain, combined with designer enzyme complexes, can be applied to the immobilizing scaffold because the in vivo immobilizing technique has several benefits in enzymatic reaction systems related to both synthetic biology and metabolic engineering. Furthermore, with the advent of nanotechnology, nanomaterials possessing ideal physicochemical characteristics, such as mass transfer resistance, specific surface area and efficient enzyme loading, can be applied as novel and interesting scaffolds for enzyme immobilization. Intelligent application of various scaffolds to couple with nanoscale engineering tools and metabolic engineering technology may offer particular benefits in research.
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Affiliation(s)
- Jeong Eun Hyeon
- Department of BiotechnologyKorea University02841SeoulRepublic of Korea
| | - Sang Kyu Shin
- Department of BiotechnologyKorea University02841SeoulRepublic of Korea
| | - Sung Ok Han
- Department of BiotechnologyKorea University02841SeoulRepublic of Korea
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15
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Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
Abstract
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.
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Affiliation(s)
- Melissabye Gunnoo
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Pierre-André Cazade
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique, de Roscoff, CS 90074, F-29688, Roscoff cedex, Bretagne, France
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Beatriz Alvarez
- Biopolis S.L., Parc Científic de la Universitat de Valencia, Edificio 2, C/Catedrático Agustín Escardino 9, 46980, Paterna (Valencia), Spain
| | - Marina Aguilar
- Abengoa, S.A., Palmas Altas, Calle Energía Solar nº 1, 41014, Seville, Spain
| | - Alon Karpol
- Designer Energy Ltd., 2 Bergman St., Tamar Science Park, Rehovot, 7670504, Israel
| | - Hermann Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
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16
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Munir RI, Spicer V, Krokhin OV, Shamshurin D, Zhang X, Taillefer M, Blunt W, Cicek N, Sparling R, Levin DB. Transcriptomic and proteomic analyses of core metabolism in Clostridium termitidis CT1112 during growth on α-cellulose, xylan, cellobiose and xylose. BMC Microbiol 2016; 16:91. [PMID: 27215540 PMCID: PMC4877739 DOI: 10.1186/s12866-016-0711-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 05/16/2016] [Indexed: 01/15/2023] Open
Abstract
Background Clostridium termitidis CT1112 is an anaerobic, Gram-positive, mesophilic, spore-forming, cellulolytic bacterium, originally isolated from the gut of a wood feeding termite Nasusitermes lujae. It has the ability to hydrolyze both cellulose and hemicellulose, and ferment the degradation products to acetate, formate, ethanol, lactate, H2, and CO2. It is therefore ges in gene and gene product expression during growth of C. termitidis on cellobiose, xylose, xylan, and α–cellulose. Results Correlation of transcriptome and proteome data with growth and fermentation profiles identified putative carbon-catabolism pathways in C. termitidis. The majority of the proteins associated with central metabolism were detected in high abundance. While major differences were not observed in gene and gene-product expression for enzymes associated with metabolic pathways under the different substrate conditions, xylulokinase and xylose isomerase of the pentose phosphate pathway were found to be highly up-regulated on five carbon sugars compared to hexoses. In addition, genes and gene-products associated with a variety of cellulosome and non-cellulosome associated CAZymes were found to be differentially expressed. Specifically, genes for cellulosomal enzymes and components were highly expressed on α–cellulose, while xylanases and glucosidases were up-regulated on 5 carbon sugars with respect to cellobiose. Chitinase and cellobiophosphorylases were the predominant CAZymes expressed on cellobiose. In addition to growth on xylan, the simultaneous consumption of two important lignocellulose constituents, cellobiose and xylose was also demonstrated. Conclusion There are little changes in core-metabolic pathways under the different carbon sources compared. The most significant differences were found to be associated with the CAZymes, as well as specific up regulation of some key components of the pentose phosphate pathway in the presence of xylose and xylan. This study has enhanced our understanding of the physiology and metabolism of C. termitidis, and provides a foundation for future studies on metabolic engineering to optimize biofuel production from natural biomass. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0711-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Riffat I Munir
- Department of Biosystems Engineering, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Victor Spicer
- Department of Physics and Astronomy, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada.,Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Dmitry Shamshurin
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - XiangLi Zhang
- Department of Plant Science, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Marcel Taillefer
- Department of Microbiology, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Warren Blunt
- Department of Biosystems Engineering, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Nazim Cicek
- Department of Biosystems Engineering, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada.
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Miyake H, Maeda Y, Ishikawa T, Tanaka A. Calorimetric studies of the growth of anaerobic microbes. J Biosci Bioeng 2016; 122:364-9. [PMID: 27012376 DOI: 10.1016/j.jbiosc.2016.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/23/2016] [Accepted: 02/12/2016] [Indexed: 11/27/2022]
Abstract
This article aims to validate the use of calorimetry to measure the growth of anaerobic microbes. It has been difficult to monitor the growth of strict anaerobes while maintaining optimal growth conditions. Traditionally, optical density and ATP concentration are usually used as measures of the growth of anaerobic microbes. However, to take these measurements it is necessary to extract an aliquot of the culture, which can be difficult while maintaining anaerobic conditions. In this study, calorimetry was used to continuously and nondestructively measure the heat generated by the growth of anaerobic microbes as a function of time. Clostridium acetobutylicum, Clostridium beijerinckii, and Clostridium cellulovorans were used as representative anaerobic microbes. Using a multiplex isothermal calorimeter, we observed that peak time (tp) of C. acetobutylicum heat evolution increased as the inoculation rate decreased. This strong correlation between the inoculation rate and tp showed that it was possible to measure the growth rate of anaerobic microbes by calorimetry. Overall, our results showed that there is a very good correlation between heat evolution and optical density/ATP concentration, validating the use of the method.
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Affiliation(s)
- Hideo Miyake
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan; Life Science Research Center, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan.
| | - Yukiko Maeda
- Faculty of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Takashi Ishikawa
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Akiyoshi Tanaka
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
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18
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Yamamoto K, Tamaru Y. Synergistic properties of cellulases from Clostridium cellulovorans in the presence of cellobiose. AMB Express 2016; 6:1. [PMID: 26728466 PMCID: PMC4700033 DOI: 10.1186/s13568-015-0169-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/11/2015] [Indexed: 11/10/2022] Open
Abstract
An anaerobic mesophile, Clostridium cellulovorans, produces a multienzyme complex called the cellulosome and actively degrades polysaccharides in the plant cell wall. C. cellulovorans also changes cellulosomal subunits to form highly active combinations dependent on the carbon substrate. A previous study reported on the synergistic effects of exoglucanase S (ExgS) and endoglucanase H (EngH) that are classified into the glycosyl hydrolase (GH) families 48, and 9, respectively. In this study, we investigated synergistic effects of ExgS and EngK, a GH9 cellulase different from EngH. In addition, since EngK was known to produce cellobiose as its main product, the inhibition on cellulase activity of EngK with cellobiose was examined. As a result, the effect of cellobiose inhibition on EngK coexistent with ExgS was found to be much lower than that with EngH. Thus, although EngH and EngK are in the same GH9 family, enzymatic activity in the presence of cellobiose was significantly different.
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19
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Esaka K, Aburaya S, Morisaka H, Kuroda K, Ueda M. Exoproteome analysis of Clostridium cellulovorans in natural soft-biomass degradation. AMB Express 2015; 5:2. [PMID: 25642399 PMCID: PMC4305082 DOI: 10.1186/s13568-014-0089-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 12/23/2014] [Indexed: 02/03/2023] Open
Abstract
Clostridium cellulovorans is an anaerobic, cellulolytic bacterium, capable of effectively degrading various types of soft biomass. Its excellent capacity for degradation results from optimization of the composition of the protein complex (cellulosome) and production of non-cellulosomal proteins according to the type of substrates. In this study, we performed a quantitative proteome analysis to determine changes in the extracellular proteins produced by C. cellulovorans for degradation of several types of natural soft biomass. C. cellulovorans was cultured in media containing bagasse, corn germ, rice straw (natural soft biomass), or cellobiose (control). Using an isobaric tag method and a liquid chromatograph equipped with a long monolithic silica capillary column/mass spectrometer, we identified 372 proteins in the culture supernatant. Of these, we focused on 77 saccharification-related proteins of both cellulosomal and non-cellulosomal origins. Statistical analysis showed that 18 of the proteins were specifically produced during degradation of types of natural soft biomass. Interestingly, the protein Clocel_3197 was found and commonly involved in the degradation of every natural soft biomass studied. This protein may perform functions, in addition to its known metabolic functions, that contribute to effective degradation of natural soft biomass.
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20
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Jeon SD, Kim SJ, Park SH, Choi GW, Han SO. Hydrolytic effects of scaffolding proteins CbpB and CbpC on crystalline cellulose mediated by the major cellulolytic complex from Clostridium cellulovorans. BIORESOURCE TECHNOLOGY 2015; 191:505-511. [PMID: 25748018 DOI: 10.1016/j.biortech.2015.02.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 06/04/2023]
Abstract
The role of the scaffolding proteins, cellulose binding protein B and C (CbpB and CbpC, respectively) were identified in cellulolytic complex (cellulosome) of Clostridium cellulovorans for efficient degradation of cellulose. Recombinant CbpB and CbpC directly anchored to the cell surface of C. cellulovorans. In addition, CbpB and CbpC showed increased hydrolytic activity on crystalline cellulose incubated with exoglucanase S (ExgS) and endoglucanase Z (EngZ) compared with the activity of free enzymes. Moreover, the results showed synergistic effects of crystalline cellulose hydrolytic activity (1.8- to 2.2-fold) when CbpB and CbpC complex with ExgS and EngZ are incubated with cellulolytic complex containing mini-CbpA. The results suggest C. cellulovorans critically uses CbpB and CbpC, which can directly anchor cells for the hydrolysis of cellulosic material with the major cellulosome complex.
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Affiliation(s)
- Sang Duck Jeon
- Department of Biotechnology, Korea University, Seoul 136-701, Republic of Korea
| | - Su Jung Kim
- Department of Biotechnology, Korea University, Seoul 136-701, Republic of Korea
| | - Sung Hyun Park
- Department of Biotechnology, Korea University, Seoul 136-701, Republic of Korea
| | - Gi-Wook Choi
- Changhae Advanced Institute of Technology, Changhae Ethanol Co., Ltd., Jeonju 561-203, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 136-701, Republic of Korea.
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Kognole AA, Payne CM. Cello-oligomer-binding dynamics and directionality in family 4 carbohydrate-binding modules. Glycobiology 2015; 25:1100-11. [DOI: 10.1093/glycob/cwv048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/04/2015] [Indexed: 12/11/2022] Open
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Čater M, Fanedl L, Malovrh Š, Marinšek Logar R. Biogas production from brewery spent grain enhanced by bioaugmentation with hydrolytic anaerobic bacteria. BIORESOURCE TECHNOLOGY 2015; 186:261-269. [PMID: 25836034 DOI: 10.1016/j.biortech.2015.03.029] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 05/19/2023]
Abstract
Lignocellulosic substrates are widely available but not easily applied in biogas production due to their poor anaerobic degradation. The effect of bioaugmentation by anaerobic hydrolytic bacteria on biogas production was determined by the biochemical methane potential assay. Microbial biomass from full scale upflow anaerobic sludge blanket reactor treating brewery wastewater was a source of active microorganisms and brewery spent grain a model lignocellulosic substrate. Ruminococcus flavefaciens 007C, Pseudobutyrivibrio xylanivorans Mz5(T), Fibrobacter succinogenes S85 and Clostridium cellulovorans as pure and mixed cultures were used to enhance the lignocellulose degradation and elevate the biogas production. P. xylanivorans Mz5(T) was the most successful in elevating methane production (+17.8%), followed by the coculture of P. xylanivorans Mz5(T) and F. succinogenes S85 (+6.9%) and the coculture of C. cellulovorans and F. succinogenes S85 (+4.9%). Changes in microbial community structure were detected by fingerprinting techniques.
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Affiliation(s)
- Maša Čater
- Division of Microbiology and Microbial Biotechnology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - Lijana Fanedl
- Division of Microbiology and Microbial Biotechnology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - Špela Malovrh
- Division of Animal Breeding Sciences, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - Romana Marinšek Logar
- Division of Microbiology and Microbial Biotechnology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia.
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23
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Matsumoto T, Shimada S, Hata Y, Tanaka T, Kondo A. Multi-functional glycoside hydrolase: Blon_0625 from Bifidobacterium longum subsp. infantis ATCC 15697. Enzyme Microb Technol 2014; 68:10-4. [PMID: 25435500 DOI: 10.1016/j.enzmictec.2014.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 10/14/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
We here describe a unique β-D-glucosidase (BGL; Blon_0625) derived from Bifidobacterium longum subsp. infantis ATCC 15697. The Blon_0625 gene was expressed by recombinant Escherichia coli. Purified recombinant Blon_0625 retains hydrolyzing activity against both p-nitrophenyl-β-D-glucopyranoside (pNPG; 17.3±0.24Umg(-1)) and p-nitrophenyl-β-D-xylopyranoside (pNPX; 16.7±0.32Umg(-1)) at pH 6.0, 30°C. To best of our knowledge, no previously described BGL retains the same level of both pNPGase and pNPXase activity. Furthermore, Blon_0625 also retains the activity against 4-nitrophenyl-α-l-arabinofranoside (pNPAf; 5.6±0.09Umg(-1)). In addition, the results of the degradation of phosphoric acid swollen cellulose (PASC) or xylan using endoglucanase from Thermobifida fusca YX (Tfu_0901) or xylanase from Kitasatospora setae KM-6054 (KSE_59480) show that Blon_0625 acts as a BGL and as a β-D-xylosidase (XYL) for hydrolyzing oligosaccharides. These results clearly indicate that Blon_0625 is a multi-functional glycoside hydrolase which retains the activity of BGL, XYL, and also α-l-arabinofuranosidase. Therefore, the utilization of multi-functional Blon_0625 may contribute to facilitating the efficient degradation of lignocellulosic materials and help enhance bioconversion processes.
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Affiliation(s)
- Takuya Matsumoto
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Shota Shimada
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Yuto Hata
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
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Wen Z, Wu M, Lin Y, Yang L, Lin J, Cen P. Artificial symbiosis for acetone-butanol-ethanol (ABE) fermentation from alkali extracted deshelled corn cobs by co-culture of Clostridium beijerinckii and Clostridium cellulovorans. Microb Cell Fact 2014; 13:92. [PMID: 25023325 PMCID: PMC4223388 DOI: 10.1186/s12934-014-0092-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/17/2014] [Indexed: 02/02/2023] Open
Abstract
Background Butanol is an industrial commodity and also considered to be a more promising gasoline substitute compared to ethanol. Renewed attention has been paid to solvents (acetone, butanol and ethanol) production from the renewable and inexpensive substrates, for example, lignocellulose, on account of the depletion of oil resources, increasing gasoline prices and deteriorating environment. Limited to current tools for genetic manipulation, it is difficult to develop a genetically engineered microorganism with combined ability of lignocellulose utilization and solvents production. Mixed culture of cellulolytic microorganisms and solventogenic bacteria provides a more convenient and feasible approach for ABE fermentation due to the potential for synergistic utilization of the metabolic pathways of two organisms. But few bacteria pairs succeeded in producing biobutanol of high titer or high productivity without adding butyrate. The aim of this work was to use Clostridium cellulovorans 743B to saccharify lignocellulose and produce butyric acid, instead of adding cellulase and butyric acid to the medium, so that the soluble sugars and butyric acid generated can be subsequently utilized by Clostridium beijerinckii NCIMB 8052 to produce butanol in one pot reaction. Results A stable artificial symbiotic system was constructed by co-culturing a celluloytic, anaerobic, butyrate-producing mesophile (C. cellulovorans 743B) and a non-celluloytic, solventogenic bacterium (C. beijerinckii NCIMB 8052) to produce solvents by consolidated bioprocessing (CBP) with alkali extracted deshelled corn cobs (AECC), a low-cost renewable feedstock, as the sole carbon source. Under optimized conditions, the co-culture degraded 68.6 g/L AECC and produced 11.8 g/L solvents (2.64 g/L acetone, 8.30 g/L butanol and 0.87 g/L ethanol) in less than 80 h. Besides, a real-time PCR assay based on the 16S rRNA gene sequence was performed to study the dynamics of the abundance of each strain during the co-culturing process, which figured out the roles of each strain at different periods in the symbiosis. Conclusion Our work illustrated the great potential of artificial symbiosis in biofuel production from lignocellulosic biomass by CBP. The dynamics of the abundance of C. beijerinckii and C. cellulovorans revealed mechanisms of cooperation and competition between the two strains during the co-culture process.
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A noncellulosomal mannanase26E contains a CBM59 in Clostridium cellulovorans. BIOMED RESEARCH INTERNATIONAL 2014; 2014:438787. [PMID: 24795881 PMCID: PMC3985142 DOI: 10.1155/2014/438787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/18/2014] [Indexed: 11/17/2022]
Abstract
A multicomponent enzyme-complex prevents efficient degradation of the plant cell wall for biorefinery. In this study, the method of identifying glycoside hydrolases (GHs) to degrade hemicelluloses was demonstrated. The competence of C. cellulovorans, which changes to be suitable for degradation of each carbon source, was used for the method. C. cellulovorans was cultivated into locust bean gum (LBG) that is composed of galactomannan. The proteins produced by C. cellulovorans were separated into either fractions binding to crystalline cellulose or not. Proteins obtained from each fraction were further separated by SDS-PAGE and were stained with Coomassie Brilliant Blue and were detected for mannanase activity. The proteins having the enzymatic activity for LBG were cut out and were identified by mass spectrometry. As a result, four protein bands were classified into glycosyl hydrolase family 26 (GH26) mannanases. One of the identified mannanases, Man26E, contains a carbohydrate-binding module (CBM) family 59, which binds to xylan, mannan, and Avicel. Although mannose and galactose are the same as a hexose, the expression patterns of the proteins from C. cellulovorans were quite different. More interestingly, zymogram for mannanase activity showed that Man26E was detected in only LBG medium.
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Borne R, Bayer EA, Pagès S, Perret S, Fierobe HP. Unraveling enzyme discrimination during cellulosome assembly independent of cohesin-dockerin affinity. FEBS J 2013; 280:5764-79. [PMID: 24033928 DOI: 10.1111/febs.12497] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/08/2013] [Accepted: 08/21/2013] [Indexed: 01/24/2023]
Abstract
Bacterial cellulosomes are generally believed to assemble at random, like those produced by Clostridium cellulolyticum. They are composed of one scaffolding protein bearing eight homologous type I cohesins that bind to any of the type I dockerins borne by the 62 cellulosomal subunits, thus generating highly heterogeneous complexes. In the present study, the heterogeneity and random assembly of the cellulosomes were evaluated with a simpler model: a miniscaffoldin containing three C. cellulolyticum cohesins and three cellulases of the same bacterium bearing the cognate dockerin (Cel5A, Cel48F, and Cel9G). Surprisingly, rather than the expected randomized integration of enzymes, the assembly of the minicellulosome generated only three distinct types of complex out of the 10 possible combinations, thus indicating preferential integration of enzymes upon binding to the scaffoldin. A hybrid scaffoldin that displays one cohesin from C. cellulolyticum and one from C. thermocellum, thus allowing sequential integration of enzymes, was exploited to further characterize this phenomenon. The initial binding of a given enzyme to the C. thermocellum cohesin was found to influence the type of enzyme that subsequently bound to the C. cellulolyticum cohesin. The preferential integration appears to be related to the length of the inter-cohesin linker. The data indicate that the binding of a cellulosomal enzyme to a cohesin has a direct influence on the dockerin-bearing proteins that will subsequently interact with adjacent cohesins. Thus, despite the general lack of specificity of the cohesin-dockerin interaction within a given species and type, bacterial cellulosomes are not necessarily assembled at random.
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Affiliation(s)
- Romain Borne
- Aix-Marseille Université-CNRS, LCB UMR7283, IMM, Marseille, France
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Exoproteome profiles of Clostridium cellulovorans grown on various carbon sources. Appl Environ Microbiol 2013; 79:6576-84. [PMID: 23956399 DOI: 10.1128/aem.02137-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The cellulosome is a complex of cellulosomal proteins bound to scaffolding proteins. This complex is considered the most efficient system for cellulose degradation. Clostridium cellulovorans, which is known to produce cellulosomes, changes the composition of its cellulosomes depending on the growth substrates. However, studies have investigated only cellulosomal proteins; profile changes in noncellulosomal proteins have rarely been examined. In this study, we performed a quantitative proteome analysis of the whole exoproteome of C. cellulovorans, including cellulosomal and noncellulosomal proteins, to illustrate how various substrates are efficiently degraded. C. cellulovorans was cultured with cellobiose, xylan, pectin, or phosphoric acid-swollen cellulose (PASC) as the sole carbon source. PASC was used as a cellulose substrate for more accurate quantitative analysis. Using an isobaric tag method and a liquid chromatography mass spectrometer equipped with a long monolithic silica capillary column, 639 proteins were identified and quantified in all 4 samples. Among these, 79 proteins were involved in saccharification, including 35 cellulosomal and 44 noncellulosomal proteins. We compared protein abundance by spectral count and found that cellulosomal proteins were more abundant than noncellulosomal proteins. Next, we focused on the fold change of the proteins depending on the growth substrates. Drastic changes were observed mainly among the noncellulosomal proteins. These results indicate that cellulosomal proteins were primarily produced to efficiently degrade any substrate and that noncellulosomal proteins were specifically produced to optimize the degradation of a particular substrate. This study highlights the importance of noncellulosomal proteins as well as cellulosomes for the efficient degradation of various substrates.
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Unique contribution of the cell wall-binding endoglucanase G to the cellulolytic complex in Clostridium cellulovorans. Appl Environ Microbiol 2013; 79:5942-8. [PMID: 23872560 DOI: 10.1128/aem.01400-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cellulosomes produced by Clostridium cellulovorans are organized by the specific interactions between the cohesins in the scaffolding proteins and the dockerins of the catalytic components. Using a cohesin biomarker, we identified a cellulosomal enzyme which belongs to the glycosyl hydrolase family 5 and has a domain of unknown function 291 (DUF291) with functions similar to those of the surface layer homology domain in C. cellulovorans. The purified endoglucanase G (EngG) had the highest synergistic degree with exoglucanase (ExgS) in the hydrolysis of crystalline cellulose (EngG/ExgS ratio = 3:1; 1.71-fold). To measure the binding affinity of the dockerins in EngG for the cohesins of the main scaffolding protein, a competitive enzyme-linked interaction assay was performed. Competitors, such as ExgS, reduced the percentage of EngG that were bound to the cohesins to less than 20%; the results demonstrated that the cohesins prefer to bind to the common cellulosomal enzymes rather than to EngG. Additionally, in surface plasmon resonance analysis, the dockerin in EngG had a relatively weak affinity (30- to 123-fold) for cohesins compared with the other cellulosomal enzymes. In the cell wall affinity assay, EngG anchored to the cell surfaces of C. cellulovorans using its DUF291 domain. Immunofluorescence microscopy confirmed the cell surface display of the EngG complex. These results indicated that in C. cellulovorans, EngG assemble into both the cellulolytic complex and the cell wall complex to aid in the hydrolysis of cellulose substrates.
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Morisaka H, Matsui K, Tatsukami Y, Kuroda K, Miyake H, Tamaru Y, Ueda M. Profile of native cellulosomal proteins of Clostridium cellulovorans adapted to various carbon sources. AMB Express 2012; 2:37. [PMID: 22839966 PMCID: PMC3444338 DOI: 10.1186/2191-0855-2-37] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 07/20/2012] [Indexed: 12/04/2022] Open
Abstract
We performed a focused proteome analysis of cellulosomal proteins predicted by a genome analysis of Clostridium cellulovorans [Tamaru, Y., et al.. 2010. J. Bacteriol. 192:901–902]. Our system employed a long monolithic column (300 cm), which provides better performance and higher resolution than conventional systems. Twenty-three cellulosomal proteins were, without purification, identified by direct analysis of the culture medium. Proteome analysis of the C. cellulovorans cellulosome after culture in various carbon sources demonstrated the production of carbon source-adapted cellulosome components.
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Hasunuma T, Kondo A. Development of yeast cell factories for consolidated bioprocessing of lignocellulose to bioethanol through cell surface engineering. Biotechnol Adv 2011; 30:1207-18. [PMID: 22085593 DOI: 10.1016/j.biotechadv.2011.10.011] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 10/12/2011] [Accepted: 10/30/2011] [Indexed: 10/15/2022]
Abstract
To build an energy and material secure future, a next generation of renewable fuels produced from lignocellulosic biomass is required. Although lignocellulosic biomass, which represents an abundant, inexpensive and renewable source for bioethanol production, is of great interest as a feedstock, the complicated ethanol production processes involved make the cost of producing bioethanol from it higher compared to corn starch and cane juice. Therefore, consolidated bioprocessing (CBP), which combines enzyme production, saccharification and fermentation in a single step, has gained increased recognition as a potential bioethanol production system. CBP requires a highly engineered microorganism developed for several different process-specific characteristics. The dominant strategy for engineering a CBP biocatalyst is to express multiple components of a cellulolytic system from either fungi or bacteria in the yeast Saccharomyces cerevisiae. The development of recombinant yeast strains displaying cellulases and hemicellulases on the cell surface represents significant progress toward realization of CBP. Regardless of the process used for biomass hydrolysis, CBP-enabling microorganisms encounter a variety of toxic compounds produced during biomass pretreatment that inhibit microbial growth and ethanol yield. Systems biology approaches including disruptome screening, transcriptomics, and metabolomics have been recently exploited to gain insight into the molecular and genetic traits involved in tolerance and adaptation to the fermentation inhibitors. In this review, we focus on recent advances in development of yeast strains with both the ability to directly convert lignocellulosic material to ethanol and tolerance in the harsh environments containing toxic compounds in the presence of ethanol.
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Affiliation(s)
- Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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Putative role of cellulosomal protease inhibitors in Clostridium cellulovorans based on gene expression and measurement of activities. J Bacteriol 2011; 193:5527-30. [PMID: 21784939 DOI: 10.1128/jb.05022-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study is the first to demonstrate the activity of putative cellulosomal protease/peptidase inhibitors (named cyspins) of Clostridium cellulovorans, using the Saccharomyces cerevisiae display system. Cyspins exhibited inhibitory activities against several representative plant proteases. This suggests that these inhibitors protect their microbe and cellulosome from external attack by plant proteases.
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Butanol production from crystalline cellulose by cocultured Clostridium thermocellum and Clostridium saccharoperbutylacetonicum N1-4. Appl Environ Microbiol 2011; 77:6470-5. [PMID: 21764954 DOI: 10.1128/aem.00706-11] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated butanol production from crystalline cellulose by cocultured cellulolytic Clostridium thermocellum and the butanol-producing strain, Clostridium saccharoperbutylacetonicum (strain N1-4). Butanol was produced from Avicel cellulose after it was incubated with C. thermocellum for at least 24 h at 60°C before the addition of strain N1-4. Butanol produced by strain N1-4 on 4% Avicel cellulose peaked (7.9 g/liter) after 9 days of incubation at 30°C, and acetone was undetectable in this coculture system. Less butanol was produced by cocultured Clostridium acetobutylicum and Clostridium beijerinckii than by strain N1-4, indicating that strain N1-4 was the optimal strain for producing butanol from crystalline cellulose in this coculture system.
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Wilson DB. Microbial diversity of cellulose hydrolysis. Curr Opin Microbiol 2011; 14:259-63. [PMID: 21531609 DOI: 10.1016/j.mib.2011.04.004] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 03/31/2011] [Accepted: 04/06/2011] [Indexed: 01/10/2023]
Abstract
Enzymatic hydrolysis of cellulose by microorganisms is a key step in the global carbon cycle. Despite its abundance only a small percentage of microorganisms can degrade cellulose, probably because it is present in recalcitrant cell walls. There are at least five distinct mechanisms used by different microorganisms to degrade cellulose all of which involve cellulases. Cellulolytic organisms and cellulases are extremely diverse possibly because their natural substrates, plant cell walls, are very diverse. At this time the microbial ecology of cellulose degradation in any environment is still not clearly understood even though there is a great deal of information available about the bovine rumen. Two major problems that limit our understanding of this area are the vast diversity of organisms present in most cellulose degrading environments and the inability to culture most of them.
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Affiliation(s)
- David B Wilson
- Department of Molecular Biology & Genetics, 458 Biotechnology Building, Cornell University, Ithaca, NY 14853, United States.
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van Dyk JS, Sakka M, Sakka K, Pletschke BI. Identification of endoglucanases, xylanases, pectinases and mannanases in the multi-enzyme complex of Bacillus licheniformis SVD1. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2010.05.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Pinheiro BA, Gilbert HJ, Sakka K, Sakka K, Fernandes VO, Prates JAM, Alves VD, Bolam DN, Ferreira LMA, Fontes CMGA. Functional insights into the role of novel type I cohesin and dockerin domains from Clostridium thermocellum. Biochem J 2009; 424:375-84. [PMID: 19758121 DOI: 10.1042/bj20091152] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Cellulosomes, synthesized by anaerobic microorganisms such as Clostridium thermocellum, are remarkably complex nanomachines that efficiently degrade plant cell wall polysaccharides. Cellulosome assembly results from the interaction of type I dockerin domains, present on the catalytic subunits, and the cohesin domains of a large non-catalytic integrating protein that acts as a molecular scaffold. In general, type I dockerins contain two distinct cohesin-binding interfaces that appear to display identical ligand specificities. Inspection of the C. thermocellum genome reveals 72 dockerin-containing proteins. In four of these proteins, Cthe_0258, Cthe_0435, Cthe_0624 and Cthe_0918, there are significant differences in the residues that comprise the two cohesin-binding sites of the type I dockerin domains. In addition, a protein of unknown function (Cthe_0452), containing a C-terminal cohesin highly similar to the equivalent domains present in C. thermocellum-integrating protein (CipA), was also identified. In the present study, the ligand specificities of the newly identified cohesin and dockerin domains are described. The results revealed that Cthe_0452 is located at the C. thermocellum cell surface and thus the protein was renamed as OlpC. The dockerins of Cthe_0258 and Cthe_0435 recognize, preferentially, the OlpC cohesin and thus these enzymes are believed to be predominantly located at the surface of the bacterium. By contrast, the dockerin domains of Cthe_0624 and Cthe_0918 are primarily cellulosomal since they bind preferentially to the cohesins of CipA. OlpC, which is a relatively abundant protein, may also adopt a 'warehouse' function by transiently retaining cellulosomal enzymes at the cell surface before they are assembled on to the multienzyme complex.
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Affiliation(s)
- Benedita A Pinheiro
- CIISA-Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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van Dyk JS, Sakka M, Sakka K, Pletschke BI. The cellulolytic and hemi-cellulolytic system of Bacillus licheniformis SVD1 and the evidence for production of a large multi-enzyme complex. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2009.06.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Nazir A, Soni R, Saini HS, Kaur A, Chadha BS. Profiling differential expression of cellulases and metabolite footprints in Aspergillus terreus. Appl Biochem Biotechnol 2009; 162:538-47. [PMID: 19779865 DOI: 10.1007/s12010-009-8775-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Accepted: 09/09/2009] [Indexed: 11/30/2022]
Abstract
This study reports differential expression of endoglucanase (EG) and beta-glucosidase (betaG) isoforms of Aspergillus terreus. Expression of multiple isoforms was observed, in presence of different carbon sources and culture conditions, by activity staining of poly acrylamide gel electrophoresis gels. Maximal expression of four EG isoforms was observed in presence of rice straw (28 U/g DW substrate) and corn cobs (1.147 U/ml) under solid substrate and shake flask culture, respectively. Furthermore, the sequential induction of EG isoforms was found to be associated with the presence of distinct metabolites (monosaccharides/oligosaccharides) i.e., xylose (X), G(1), G(3) and G(4) as well as putative positional isomers (G(1)/G(2), G(2)/G(3)) in the culture extracts sampled at different time intervals, indicating specific role of these metabolites in the sequential expression of multiple EGs. Addition of fructose and cellobiose to corn cobs containing medium during shake flask culture resulted in up-regulation of EG activity, whereas addition of mannitol, ethanol and glycerol selectively repressed the expression of three EG isoforms (Ia, Ic and Id). The observed regulation profile of betaG isoforms was distinct when compared to EG isoforms, and addition of glucose, fructose, sucrose, cellobiose, mannitol and glycerol resulted in down-regulation of one or more of the four betaG isoforms.
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Affiliation(s)
- Asiya Nazir
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143 005, India
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Fukuda H, Kondo A, Tamalampudi S. Bioenergy: Sustainable fuels from biomass by yeast and fungal whole-cell biocatalysts. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2008.11.016] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Lavan LM, Van Dyk JS, Chan H, Doi RH, Pletschke BI. Effect of physical conditions and chemicals on the binding of a mini-CbpA from Clostridium cellulovorans to a semi-crystalline cellulose ligand. Lett Appl Microbiol 2009; 48:419-25. [PMID: 19187497 DOI: 10.1111/j.1472-765x.2008.02545.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To investigate the effect that environmental factors have on Clostridium cellulovorans cellulose binding domain (CBD) binding to a semi-crystalline cellulose ligand, namely Avicel. METHODS AND RESULTS The behaviour of a 58 kDa mini-CbpA protein containing the CBD from the scaffoldin protein of C. cellulovorans was studied in the presence of various environmental factors, in order to determine whether such factors promote or reduce CBD binding to its ligand, thus potentially affecting its activity on the substrate. The amount of binding was found to be dependent on the Avicel concentration and optimal binding occurred when the ligand concentration was 15 mg ml(-1). Optimal CBD binding occurred at pH 7.0 and at an incubation temperature of 28 degrees C. The effects of dithiothreitol (DTT), 2-mercaptoethanol, acetone, butanol, ethanol and butyric acid were also investigated. CONCLUSIONS Temperature, pH, DTT, 2-mercaptoethanol and solvents were shown to affect the binding of C. cellulovorans CBD to Avicel. SIGNIFICANCE AND IMPACT OF THE STUDY Clostridium cellulovorans CBD binding to Avicel is affected by physical conditions and chemicals.
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Affiliation(s)
- L M Lavan
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown, South Africa
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Doi RH. Cellulases of mesophilic microorganisms: cellulosome and noncellulosome producers. Ann N Y Acad Sci 2007; 1125:267-79. [PMID: 18096849 DOI: 10.1196/annals.1419.002] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The cellulolytic activity of mesophilic bacteria and fungi is described, with special emphasis on the large extracellular enzyme complex called the cellulosome. The cellulosome is composed of a scaffolding protein, which is attached to various cellulolytic and hemicellulolytic enzymes, and this complex allows the organisms to degrade plant cell walls very efficently. The enzymes include a variety of cellulases, hemicellulases, and pectinases that work synergistically to degrade complex cell-wall molecules.
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Affiliation(s)
- Roy H Doi
- Section of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA.
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Blouzard JC, Bourgeois C, de Philip P, Valette O, Bélaïch A, Tardif C, Bélaïch JP, Pagès S. Enzyme diversity of the cellulolytic system produced by Clostridium cellulolyticum explored by two-dimensional analysis: identification of seven genes encoding new dockerin-containing proteins. J Bacteriol 2007; 189:2300-9. [PMID: 17209020 PMCID: PMC1899368 DOI: 10.1128/jb.00917-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enzyme diversity of the cellulolytic system produced by Clostridium cellulolyticum grown on crystalline cellulose as a sole carbon and energy source was explored by two-dimensional electrophoresis. The cellulolytic system of C. cellulolyticum is composed of at least 30 dockerin-containing proteins (designated cellulosomal proteins) and 30 noncellulosomal components. Most of the known cellulosomal proteins, including CipC, Cel48F, Cel8C, Cel9G, Cel9E, Man5K, Cel9M, and Cel5A, were identified by using two-dimensional Western blot analysis with specific antibodies, whereas Cel5N, Cel9J, and Cel44O were identified by using N-terminal sequencing. Unknown enzymes having carboxymethyl cellulase or xylanase activities were detected by zymogram analysis of two-dimensional gels. Some of these enzymes were identified by N-terminal sequencing as homologs of proteins listed in the NCBI database. Using Trap-Dock PCR and DNA walking, seven genes encoding new dockerin-containing proteins were cloned and sequenced. Some of these genes are clustered. Enzymes encoded by these genes belong to glycoside hydrolase families GH2, GH9, GH10, GH26, GH27, and GH59. Except for members of family GH9, which contains only cellulases, the new modular glycoside hydrolases discovered in this work could be involved in the degradation of different hemicellulosic substrates, such as xylan or galactomannan.
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Affiliation(s)
- Jean-Charles Blouzard
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM, Centre National de la Recherche Scientifique and Université de Provence, Marseille, France
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Percival Zhang YH, Himmel ME, Mielenz JR. Outlook for cellulase improvement: screening and selection strategies. Biotechnol Adv 2006; 24:452-81. [PMID: 16690241 DOI: 10.1016/j.biotechadv.2006.03.003] [Citation(s) in RCA: 663] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Revised: 03/06/2006] [Accepted: 03/11/2006] [Indexed: 10/24/2022]
Abstract
Cellulose is the most abundant renewable natural biological resource, and the production of biobased products and bioenergy from less costly renewable lignocellulosic materials is important for the sustainable development of human beings. A reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for each cellulase component enzyme, as well as on the reconstitution of cellulase components. Here, we review quantitative cellulase activity assays using soluble and insoluble substrates, and focus on their advantages and limitations. Because there are no clear relationships between cellulase activities on soluble substrates and those on insoluble substrates, soluble substrates should not be used to screen or select improved cellulases for processing relevant solid substrates, such as plant cell walls. Cellulase improvement strategies based on directed evolution using screening on soluble substrates have been only moderately successful, and have primarily targeted improvement in thermal tolerance. Heterogeneity of insoluble cellulose, unclear dynamic interactions between insoluble substrate and cellulase components, and the complex competitive and/or synergic relationship among cellulase components limit rational design and/or strategies, depending on activity screening approaches. Herein, we hypothesize that continuous culture using insoluble cellulosic substrates could be a powerful selection tool for enriching beneficial cellulase mutants from the large library displayed on the cell surface.
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Affiliation(s)
- Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Barak Y, Handelsman T, Nakar D, Mechaly A, Lamed R, Shoham Y, Bayer EA. Matching fusion protein systems for affinity analysis of two interacting families of proteins: the cohesin-dockerin interaction. J Mol Recognit 2005; 18:491-501. [PMID: 16167300 DOI: 10.1002/jmr.749] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Cellulosomes are multi-enzyme complexes that orchestrate the efficient degradation of cellulose and related plant cell wall polysaccharides. The complex is maintained by the high-affinity protein-protein interaction between two complementary modules: the cohesin and the dockerin. In order to characterize the interaction between different cohesins and dockerins, we have developed matching fusion-protein systems, which harbor either the cohesin or the dockerin component. For this purpose, corresponding plasmid cassettes were designed, which encoded for the following carrier proteins: (i) a thermostable xylanase with an appended His-tag; and (ii) a highly stable cellulose-binding module (CBM). The resultant xylanase-dockerin and CBM-cohesin fusion products exhibited high expression levels of soluble protein. The expressed, affinity-purified proteins were extremely stable, and the functionality of the cohesin or dockerin component was retained. The fusion protein system was used to establish a sensitive and reliable, semi-quantitative enzyme-linked affinity assay for determining multiple samples of cohesin-dockerin interactions in microtiter plates. A variety of cohesin-dockerin systems, which had been examined previously using other methodologies, were revisited applying the affinity-based enzyme assay, the results of which served to verify the validity of the approach.
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Affiliation(s)
- Yoav Barak
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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Han SO, Yukawa H, Inui M, Doi RH. Molecular cloning and transcriptional and expression analysis of engO, encoding a new noncellulosomal family 9 enzyme, from Clostridium cellulovorans. J Bacteriol 2005; 187:4884-9. [PMID: 15995203 PMCID: PMC1169505 DOI: 10.1128/jb.187.14.4884-4889.2005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium cellulovorans produces a major noncellulosomal family 9 endoglucanase EngO. A genomic DNA fragment (40 kb) containing engO and neighboring genes was cloned. The nucleotide sequence contained reading frames for endoglucanase EngO, a putative response regulator, and a putative sensor histidine kinase protein. The engO gene consists of 2,172 bp and encodes a protein of 724 amino acids with a molecular weight of 79,474. Northern hybridizations revealed that the engO gene is transcribed as a monocistronic 2.6-kb mRNA. 5' RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) PCR analysis indicated that the single transcriptional start site of engO was located 264 bp upstream from the first nucleotide of the translation initiation codon. Alignment of the engO promoter region provided evidence for highly conserved sequences that exhibited strong similarity to the sigma(A) consensus promoter sequences of gram-positive bacteria. EngO contains a typical N-terminal signal peptide of 28 amino acid residues, followed by a 149-amino-acid sequence which is homologous to the family 4-9 carbohydrate-binding domain. Downstream of this domain was an immunoglobulin-like domain of 89 amino acids. The C terminus contains a family 9 catalytic domain of glycosyl hydrolase. Mass spectrometry analysis of EngO was in agreement with that deduced from the nucleotide sequence. Expression of engO mRNA increased from early to middle exponential phase and decreased during the early stationary phase. EngO was highly active toward carboxymethyl cellulose but showed no activity towards xylan. It was optimally active at 40 to 50 degrees C and pH 5 to 6. The analysis of the products from the cellulose hydrolysis through thin-layer chromatography indicated its endoglucanase activity.
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Affiliation(s)
- Sung Ok Han
- Section of Molecular and Cellular Biology, University of California, Davis, 95616, USA
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Polizeli MLTM, Rizzatti ACS, Monti R, Terenzi HF, Jorge JA, Amorim DS. Xylanases from fungi: properties and industrial applications. Appl Microbiol Biotechnol 2005; 67:577-91. [PMID: 15944805 DOI: 10.1007/s00253-005-1904-7] [Citation(s) in RCA: 664] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Revised: 12/29/2004] [Accepted: 12/31/2004] [Indexed: 10/25/2022]
Abstract
Xylan is the principal type of hemicellulose. It is a linear polymer of beta-D-xylopyranosyl units linked by (1-4) glycosidic bonds. In nature, the polysaccharide backbone may be added to 4-O-methyl-alpha-D-glucuronopyranosyl units, acetyl groups, alpha-L-arabinofuranosyl, etc., in variable proportions. An enzymatic complex is responsible for the hydrolysis of xylan, but the main enzymes involved are endo-1,4-beta-xylanase and beta-xylosidase. These enzymes are produced by fungi, bacteria, yeast, marine algae, protozoans, snails, crustaceans, insect, seeds, etc., but the principal commercial source is filamentous fungi. Recently, there has been much industrial interest in xylan and its hydrolytic enzymatic complex, as a supplement in animal feed, for the manufacture of bread, food and drinks, textiles, bleaching of cellulose pulp, ethanol and xylitol production. This review describes some properties of xylan and its metabolism, as well as the biochemical properties of xylanases and their commercial applications.
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Affiliation(s)
- M L T M Polizeli
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto-Universidade de São Paulo, Av. Bandeirantes, 3900, Bairro Monte Alegre , 14040-901 Ribeirão Preto, São Paulo, Brazil.
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Han SO, Yukawa H, Inui M, Doi RH. Isolation and expression of the xynB gene and its product, XynB, a consistent component of the Clostridium cellulovorans cellulosome. J Bacteriol 2005; 186:8347-55. [PMID: 15576784 PMCID: PMC532426 DOI: 10.1128/jb.186.24.8347-8355.2004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleotide sequence of the Clostridium cellulovorans xynB gene, which encodes the XynB xylanase, consists of 1,821 bp and encodes a protein of 607 amino acids with a molecular weight of 65,976. XynB contains a typical N-terminal signal peptide of 29 amino acid residues, followed by a 147-amino-acid sequence that is homologous to the family 4-9 (subfamily 9 in family 4) carbohydrate-binding domain. Downstream of this domain is a family 10 catalytic domain of glycosyl hydrolase. The C terminus separated from the catalytic domain by a short linker sequence contains a dockerin domain responsible for cellulosome assembly. The XynB sequence from mass spectrometry and N-terminal amino acid sequence analyses agreed with that deduced from the nucleotide sequence. XynB was highly active toward xylan, but not active toward carboxymethyl cellulose. The enzyme was optimally active at 40 degrees C and pH 5.0. Northern hybridizations revealed that xynB is transcribed as a monocistronic 1.9-kb mRNA. RNA ligase-mediated rapid amplification of 5' cDNA ends by PCR (RLM-5'RACE PCR) analysis of C. cellulovorans RNA identified a single transcriptional start site of xynB located 47 bp upstream from the first nucleotide of the translation initiation codon. Alignment of the xynB promoter region provided evidence for highly conserved sequences that exhibited strong similarity to the sigmaA consensus promoter sequences of gram-positive bacteria. Expression of xynB mRNA increased from early to middle exponential phase and decreased during the early stationary phase when the cells were grown on cellobiose. No alternative promoter was observed by RLM-5'RACE PCR and reverse transcriptase PCR analyses during expression. The analysis of the products from xylan hydrolysis by thin-layer chromatography indicated its endoxylanase activity. The results suggest that XynB is a consistent and major cellulosomal enzyme during growth on cellulose or xylan.
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Affiliation(s)
- Sung Ok Han
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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Davey MR, Anthony P, Power JB, Lowe KC. Plant protoplasts: status and biotechnological perspectives. Biotechnol Adv 2004; 23:131-71. [PMID: 15694124 DOI: 10.1016/j.biotechadv.2004.09.008] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2004] [Revised: 09/13/2004] [Accepted: 09/23/2004] [Indexed: 11/27/2022]
Abstract
Plant protoplasts ("naked" cells) provide a unique single cell system to underpin several aspects of modern biotechnology. Major advances in genomics, proteomics, and metabolomics have stimulated renewed interest in these osmotically fragile wall-less cells. Reliable procedures are available to isolate and culture protoplasts from a range of plants, including both monocotyledonous and dicotyledonous crops. Several parameters, particularly the source tissue, culture medium, and environmental factors, influence the ability of protoplasts and protoplast-derived cells to express their totipotency and to develop into fertile plants. Importantly, novel approaches to maximise the efficiency of protoplast-to-plant systems include techniques already well established for animal and microbial cells, such as electrostimulation and exposure of protoplasts to surfactants and respiratory gas carriers, especially perfluorochemicals and hemoglobin. However, despite at least four decades of concerted effort and technology transfer between laboratories worldwide, many species still remain recalcitrant in culture. Nevertheless, isolated protoplasts are unique to a range of experimental procedures. In the context of plant genetic manipulation, somatic hybridisation by protoplast fusion enables nuclear and cytoplasmic genomes to be combined, fully or partially, at the interspecific and intergeneric levels to circumvent naturally occurring sexual incompatibility barriers. Uptake of isolated DNA into protoplasts provides the basis for transient and stable nuclear transformation, and also organelle transformation to generate transplastomic plants. Isolated protoplasts are also exploited in numerous miscellaneous studies involving membrane function, cell structure, synthesis of pharmaceutical products, and toxicological assessments. This review focuses upon the most recent developments in protoplast-based technologies.
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Affiliation(s)
- Michael R Davey
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
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Cho HY, Yukawa H, Inui M, Doi RH, Wong SL. Production of minicellulosomes from Clostridium cellulovorans in Bacillus subtilis WB800. Appl Environ Microbiol 2004; 70:5704-7. [PMID: 15345466 PMCID: PMC520898 DOI: 10.1128/aem.70.9.5704-5707.2004] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two genes encoding EngB endoglucanase and mini-CbpA1 scaffolding protein of Clostridium cellulovorans were constructed and coexpressed in Bacillus subtilis WB800. The resulting minicellulosomes were isolated by gel filtration chromatography and characterized. Biochemical and immunological evidence indicated that fraction II contained minicellulosomes consisting of mini-CbpA1 and EngB. The in vivo synthesis of minicellulosomes suggests that it will be possible in the future to insert into B. subtilis cellulosomal genes that will allow growth on cellulosic materials and the production of various designer cellulosomes with specific functions.
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Affiliation(s)
- Hee-Yeon Cho
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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Xu Q, Barak Y, Kenig R, Shoham Y, Bayer EA, Lamed R. A novel Acetivibrio cellulolyticus anchoring scaffoldin that bears divergent cohesins. J Bacteriol 2004; 186:5782-9. [PMID: 15317783 PMCID: PMC516847 DOI: 10.1128/jb.186.17.5782-5789.2004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Accepted: 06/02/2004] [Indexed: 11/20/2022] Open
Abstract
Sequencing of a cellulosome-integrating gene cluster in Acetivibrio cellulolyticus was completed. The cluster contains four tandem scaffoldin genes (scaA, scaB, scaC, and scaD) bounded upstream and downstream, respectively, by a presumed cellobiose phosphorylase and a nucleotide methylase. The sequences and properties of scaA, scaB, and scaC were reported previously, and those of scaD are reported here. The scaD gene encodes an 852-residue polypeptide that includes a signal peptide, three cohesins, and a C-terminal S-layer homology (SLH) module. The calculated molecular weight of the mature ScaD is 88,960; a 67-residue linker segment separates cohesins 1 and 2, and two approximately 30-residue linkers separate cohesin 2 from 3 and cohesin 3 from the SLH module. The presence of an SLH module in ScaD indicates its role as an anchoring protein. The first two ScaD cohesins can be classified as type II, similar to the four cohesins of ScaB. Surprisingly, the third ScaD cohesin belongs to the type I cohesins, like the seven ScaA cohesins. ScaD is the first scaffoldin to be described that contains divergent types of cohesins as integral parts of the polypeptide chain. The recognition properties among selected recombinant cohesins and dockerins from the different scaffoldins of the gene cluster were investigated by affinity blotting. The results indicated that the divergent types of ScaD cohesins also differ in their preference of dockerins. ScaD thus plays a dual role, both as a primary scaffoldin, capable of direct incorporation of a single dockerin-borne enzyme, and as a secondary scaffoldin that anchors the major primary scaffoldin, ScaA and its complement of enzymes to the cell surface.
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Affiliation(s)
- Qi Xu
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Ramat Aviv, Israel
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