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Daley SR, Kirby S, Sparling R. Adaptive evolution of Clostridium thermocellum ATCC 27405 on alternate carbon sources leads to altered fermentation profiles. Can J Microbiol 2024; 70:370-383. [PMID: 38832648 DOI: 10.1139/cjm-2024-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Consolidated bioprocessing candidate, Clostridium thermocellum, is a cellulose hydrolysis specialist, with the ability to ferment the released sugars to produce bioethanol. C. thermocellum is generally studied with model substrates Avicel and cellobiose to understand the metabolic pathway leading to ethanol. In the present study, adaptive laboratory evolution, allowing C. thermocellum DSM 1237 to adapt to growth on glucose, fructose, and sorbitol, with the prospect that some strains will adapt their metabolism to yield more ethanol. Adaptive growth on glucose and sorbitol resulted in an approximately 1 mM and 2 mM increase in ethanol yield per millimolar glucose equivalent, respectively, accompanied by a shift in the production of the other expected fermentation end products. The increase in ethanol yield observed for sorbitol adapted cells was due to the carbon source being more reduced compared to cellobiose. Glucose and cellobiose have similar oxidation states thus the increase in ethanol yield is due to the rerouting of electrons from other reduced metabolic products excluding H2 which did not decrease in yield. There was no increase in ethanol yield observed for fructose adapted cells, but there was an unanticipated elimination of formate production, also observed in sorbitol adapted cells suggesting that fructose has regulatory implications on formate production either at the transcription or protein level.
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Affiliation(s)
- Steve R Daley
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Samantha Kirby
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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2
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Vaz LP, Sears HB, Miranda EA, Holwerda EK, Lynd LR. Solubilization of sugarcane bagasse by mono and cocultures of thermophilic anaerobes with and without cotreatment. BIORESOURCE TECHNOLOGY 2024; 406:130982. [PMID: 38879055 DOI: 10.1016/j.biortech.2024.130982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
Cotreatment, mechanical disruption of lignocellulosic biomass during microbial fermentation, is a potential alternative to thermochemical pretreatment as a means of increasing the accessibility of lignocellulose to biological attack. Successful implementation of cotreatment requires microbes that can withstand milling, while solubilizing and utilizing carbohydrates from lignocellulose. In this context, cotreatment with thermophilic, lignocellulose-fermenting bacteria has been successfully evaluated for a number of lignocellulosic feedstocks. Here, cotreatment was applied to sugarcane bagasse using monocultures of the cellulose-fermenting Clostridium thermocellum and cocultures with the hemicellulose-fermenting Thermoanaerobacterium thermosaccharolyticum. This resulted in 76 % carbohydrate solubilization (a 1.8-fold increase over non-cotreated controls) on 10 g/L solids loading, having greater effect on the hemicellulose fraction. With cotreatment, fermentation by wild-type cultures at low substrate concentrations increased cumulative product formation by 45 % for the monoculture and 32 % for the coculture. These findings highlight the potential of cotreatment for enhancing deconstruction of sugarcane bagasse using thermophilic bacteria.
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Affiliation(s)
- Luisa P Vaz
- Universidade Estadual de Campinas, School of Chemical Engineering, Department of Materials and Bioprocess Engineering, Av. Albert Einstein 500, Campinas, SP 13083-852, Brazil
| | - Helen B Sears
- Thayer School of Engineering, Dartmouth College, 15 Thayer Drive, Hanover, NH 03755, USA
| | - Everson A Miranda
- Universidade Estadual de Campinas, School of Chemical Engineering, Department of Materials and Bioprocess Engineering, Av. Albert Einstein 500, Campinas, SP 13083-852, Brazil
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, 15 Thayer Drive, Hanover, NH 03755, USA.
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, 15 Thayer Drive, Hanover, NH 03755, USA
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3
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Dasgupta P, Vinil K, Kanaujia SP. Evolutionary trends indicate a coherent organization of sap operons. Res Microbiol 2024:104228. [PMID: 38972435 DOI: 10.1016/j.resmic.2024.104228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024]
Abstract
Human hosts possess a complex network of immune responses against microbial pathogens. The production of antimicrobial peptides (AMPs), which target the pathogen cell membranes and inhibit them from inhabiting the hosts, is one such mechanism. However, pathogens have evolved systems that encounter these host-produced AMPs. The Sap (sensitivity to antimicrobial peptides) transporter uptakes AMPs inside the microbial cell and proteolytically degrades them. The Sap transporters comprise five subunits encoded by genes in an operon. Despite its ubiquitous nature, its subunits are not found to be in tandem with many organisms. In this study, a total of 421 Sap transporters were analyzed for their operonic arrangement. Out of 421, a total of 352 operons were found to be in consensus arrangement, while the remaining 69 show a varying arrangement of genes. The analysis of the intergenic distance between the subunits of the sap operon suggests a signature pattern with sapAB (-4), sapBC (-14), sapCD (-1), and sapDF (-4 to 1). An evolutionary analysis of these operons favors the consensus arrangement of the Sap transporter systems, substantiating its prevalence in most of the Gram-negative pathogens. Overall, this study provides insight into bacterial evolution, favoring the maintenance of the genetic organization of essential pathogenicity factors.
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Affiliation(s)
- Pratik Dasgupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Kavya Vinil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India.
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4
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Tjo H, Conway JM. Sugar transport in thermophiles: Bridging lignocellulose deconstruction and bioconversion. J Ind Microbiol Biotechnol 2024; 51:kuae020. [PMID: 38866721 PMCID: PMC11212667 DOI: 10.1093/jimb/kuae020] [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: 03/14/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024]
Abstract
Biomass degrading thermophiles play an indispensable role in building lignocellulose-based supply chains. They operate at high temperatures to improve process efficiencies and minimize mesophilic contamination, can overcome lignocellulose recalcitrance through their native carbohydrate-active enzyme (CAZyme) inventory, and can utilize a wide range of sugar substrates. However, sugar transport in thermophiles is poorly understood and investigated, as compared to enzymatic lignocellulose deconstruction and metabolic conversion of sugars to value-added chemicals. Here, we review the general modes of sugar transport in thermophilic bacteria and archaea, covering the structural, molecular, and biophysical basis of their high-affinity sugar uptake. We also discuss recent genetic studies on sugar transporter function. With this understanding of sugar transport, we discuss strategies for how sugar transport can be engineered in thermophiles, with the potential to enhance the conversion of lignocellulosic biomass into renewable products. ONE-SENTENCE SUMMARY Sugar transport is the understudied link between extracellular biomass deconstruction and intracellular sugar metabolism in thermophilic lignocellulose bioprocessing.
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Affiliation(s)
- Hansen Tjo
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan M Conway
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA
- High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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5
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Xiao Y, Dong S, Liu YJ, You C, Feng Y, Cui Q. Key roles of β-glucosidase BglA for the catabolism of both laminaribiose and cellobiose in the lignocellulolytic bacterium Clostridium thermocellum. Int J Biol Macromol 2023; 250:126226. [PMID: 37558019 DOI: 10.1016/j.ijbiomac.2023.126226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
The thermophilic bacterium Clostridium thermocellum efficiently degrades polysaccharides into oligosaccharides. The metabolism of β-1,4-linked cello-oligosaccharides is initiated by three enzymes, i.e., the cellodextrin phosphorylase (Cdp), the cellobiose phosphorylase (Cbp), and the β-glucosidase A (BglA), in C. thermocellum. In comparison, how the oligosaccharides containing other kinds of linkage are utilized is rarely understood. In this study, we found that BglA could hydrolyze the β-1,3-disaccharide laminaribiose with much higher activity than that against the β-1,4-disaccharide cellobiose. The structural basis of the substrate specificity was analyzed by crystal structure determination and molecular docking. Genetic deletions of BglA and Cbp, respectively, and enzymatic analysis of cell extracts demonstrated that BglA is the key enzyme responsible for laminaribiose metabolism. Furthermore, the deletion of BglA can suppress the expression of Cbp and the deletion of Cbp can up-regulate the expression of BglA, indicating that BglA and Cbp have cross-regulation and BglA is also critical for cellobiose metabolism. These insights pave the way for both a fundamental understanding of metabolism and regulation in C. thermocellum and emphasize the importance of the degradation and utilization of polysaccharides containing β-1,3-linked glycosidic bonds in lignocellulose biorefinery.
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Affiliation(s)
- Yan Xiao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
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6
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Fosses A, Franche N, Parsiegla G, Denis Y, Maté M, de Philip P, Fierobe HP, Perret S. Role of the Solute-Binding Protein CuaD in the Signaling and Regulating Pathway of Cellobiose and Cellulose Utilization in Ruminiclostridium cellulolyticum. Microorganisms 2023; 11:1732. [PMID: 37512904 PMCID: PMC10384115 DOI: 10.3390/microorganisms11071732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
In Ruminiclostridium cellulolyticum, cellobiose is imported by the CuaABC ATP-binding cassette transporter containing the solute-binding protein (SBP) CuaA and is further degraded in the cytosol by the cellobiose phosphorylase CbpA. The genes encoding these proteins have been shown to be essential for cellobiose and cellulose utilization. Here, we show that a second SBP (CuaD), whose gene is adjacent to two genes encoding a putative two-component regulation system (CuaSR), forms a three-component system with CuaS and CuaR. Studies of mutant and recombinant strains of R. cellulolyticum have indicated that cuaD is important for the growth of strains on cellobiose and cellulose. Furthermore, the results of our RT-qPCR experiments suggest that both the three (CuaDSR)- and the two (CuaSR)-component systems are able to perceive the cellobiose signal. However, the strain producing the three-component system is more efficient in its cellobiose and cellulose utilization. As CuaD binds to CuaS, we propose an in-silico model of the complex made up of two extracellular domains of CuaS and two of CuaD. CuaD allows microorganisms to detect very low concentrations of cellobiose due to its high affinity and specificity for this disaccharide, and together with CuaSR, it triggers the expression of the cuaABC-cbpA genes involved in cellodextrins uptake.
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Affiliation(s)
| | | | | | - Yann Denis
- Aix Marseille Univ, CNRS, Plateforme Transcriptome, Marseille, France
| | - Maria Maté
- CNRS, Aix Marseille Univ, UMR7257 AFMB, Marseille, France
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7
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Qiu Y, Qiu Z, Xia J, Liu X, Zhang H, Yang Y, Hou W, Li X, He J. Co-expression of Xylose Transporter and Fructose-Bisphosphate Aldolase Enhances the Utilization of Xylose by Lactococcus lactis IO-1. Appl Biochem Biotechnol 2023; 195:816-831. [PMID: 36205844 DOI: 10.1007/s12010-022-04168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
The raw material cost of lactic acid fermentation accounts for the main part of the production cost, and this necessitates the exploration of the efficient use of cheap raw materials in lactic acid production. We compared the outcomes of the homologous expressions of xylose transporters (xylFGH, xylE, araE, and xylT), 6-phosphofructokinase (pfkA), fructose-bisphosphate aldolase (fbaA), and their co-expression in Lactococcus lactis IO-1 on lactic acid production using xylose as the raw material. We found that the production rate of lactic acid on xylose fermentation by L. lactis IO-1 overexpressing fbaA was the highest (14.42%). Among the xylose transporters investigated, XylT had the strongest xylose transport capacity in L. lactis IO-1, with an increase in the lactic acid production rate by 10.38%. The genes near the overexpression of fbaA or xylT in the metabolic pathway were more upregulated than the distant genes. The co-expression of fbaA and xylT increased the production rate of lactic acid by 27.84% on xylose fermentation by L. lactis IO-1. This work presents a novel strategy for the simultaneous enhancement of the expression of important genes at the beginning and midway of the xylose metabolic pathway of L. lactis IO-1, which could greatly improve the target production.
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Affiliation(s)
- Yejuan Qiu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Zhongyang Qiu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Jun Xia
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Xiaoyan Liu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Hanwen Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Yuxiang Yang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Wenyi Hou
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Xiangqian Li
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China.
| | - Jianlong He
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China.
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8
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Tao S, Qingbin M, Zhiling L, Caiyu S, Lixin L, Lilai L. Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium. Front Microbiol 2023; 13:1079279. [PMID: 36687593 PMCID: PMC9852859 DOI: 10.3389/fmicb.2022.1079279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/07/2022] [Indexed: 01/08/2023] Open
Abstract
The cellulosome of Ruminiclostridium thermocellum was one of the most efficient cellulase systems in nature. However, the product of cellulose degradation by R. thermocellum is cellobiose, which leads to the feedback inhibition of cellulosome, and it limits the R. thermocellum application in the field of cellulosic biomass consolidated bioprocessing (CBP) industry. In a previous study, R. thermocellum M3, which can hydrolyze cellulosic feedstocks into monosaccharides, was isolated from horse manure. In this study, the complete genome of R. thermocellum M3 was sequenced and assembled. The genome of R. thermocellum M3 was compared with the other R. thermocellum to reveal the mechanism of cellulosic saccharification by R. thermocellum M3. In addition, we predicted the key genes for the elimination of feedback inhibition of cellobiose in R. thermocellum. The results indicated that the whole genome sequence of R. thermocellum M3 consisted of 3.6 Mb of chromosomes with a 38.9% of GC%. To be specific, eight gene islands and 271 carbohydrate-active enzyme-encoded proteins were detected. Moreover, the results of gene function annotation showed that 2,071, 2,120, and 1,246 genes were annotated into the Clusters of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively, and most of the genes were involved in carbohydrate metabolism and enzymatic catalysis. Different from other R. thermocellum, strain M3 has three proteins related to β-glucosidase, and the cellobiose hydrolysis was enhanced by the synergy of gene BglA and BglX. Meanwhile, the GH42 family, CBM36 family, and AA8 family might participate in cellobiose degradation.
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Affiliation(s)
- Sheng Tao
- College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, China,*Correspondence: Sheng Tao,
| | - Meng Qingbin
- College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, China
| | - Li Zhiling
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China,Li Zhiling,
| | - Sun Caiyu
- College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, China
| | - Li Lixin
- College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, China
| | - Liu Lilai
- College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, China
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9
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Deciphering Cellodextrin and Glucose Uptake in Clostridium thermocellum. mBio 2022; 13:e0147622. [PMID: 36069444 PMCID: PMC9601137 DOI: 10.1128/mbio.01476-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Sugar uptake is of great significance in industrially relevant microorganisms. Clostridium thermocellum has extensive potential in lignocellulose biorefineries as an environmentally prominent, thermophilic, cellulolytic bacterium. The bacterium employs five putative ATP-binding cassette transporters which purportedly take up cellulose hydrolysates. Here, we first applied combined genetic manipulations and biophysical titration experiments to decipher the key glucose and cellodextrin transporters. In vivo gene inactivation of each transporter and in vitro calorimetric and nuclear magnetic resonance (NMR) titration of each putative sugar-binding protein with various saccharides supported the conclusion that only transporters A and B play the roles of glucose and cellodextrin transport, respectively. To gain insight into the structural mechanism of the transporter specificities, 11 crystal structures, both alone and in complex with appropriate saccharides, were solved for all 5 putative sugar-binding proteins, thus providing detailed specific interactions between the proteins and the corresponding saccharides. Considering the importance of transporter B as the major cellodextrin transporter, we further identified its cryptic, hitherto unknown ATPase-encoding gene as clo1313_2554, which is located outside the transporter B gene cluster. The crystal structure of the ATPase was solved, showing that it represents a typical nucleotide-binding domain of the ATP-binding cassette (ABC) transporter. Moreover, we determined that the inducing effect of cellobiose (G2) and cellulose on cellulosome production could be eliminated by deletion of transporter B genes, suggesting the coupling of sugar transport and regulation of cellulosome components. This study provides key basic information on the sugar uptake mechanism of C. thermocellum and will promote rational engineering of the bacterium for industrial application.
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10
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Internal Transcription Terminators Control Stoichiometry of ABC Transporters in Cellulolytic Clostridia. Microbiol Spectr 2022; 10:e0165621. [PMID: 35286151 PMCID: PMC9045158 DOI: 10.1128/spectrum.01656-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extracellular substrate-binding proteins (SBPs) of ATP-binding cassette (ABC) importers tend to be expressed in excess relative to their cognate translocators, but how the stoichiometry of ABC transporters is controlled remains unclear. Here, we elucidated a mechanism contributing to differential gene expression in operons encoding ABC importers by employing cellulolytic Clostridia species, specifically Ruminiclostridium cellulolyticum. We found that there were usually stem-loop structures downstream of SBP genes, which could prematurely terminate the transcription of ABC importers and were putative internal intrinsic terminators, resulting in high transcript levels of upstream SBP genes and low transcript levels of downstream cognate translocator genes. This was determined by their termination efficiencies. Internal terminators had a lower U content in their 3′ U-rich tracts and longer GC-rich stems, which distinguishes them from canonical terminators and potentially endows them with special termination efficiencies. The pairing of U-rich tracts and the formation of unpaired regions in these internal terminators contributed to their folding energies, affecting the stability of their upstream SBP transcripts. Our findings revealed a strategy of internal transcriptional terminators controlling in vivo stoichiometry of their flanking transcripts. IMPORTANCE Operons encoding protein complexes or metabolic pathways usually require fine-tuned gene expression ratios to create and maintain the appropriate stoichiometry for biological functions. In this study, a strategy for controlling differential expression of genes in an operon was proposed by utilizing ABC importers from Ruminiclostridium cellulolyticum. We found that a stem-loop structure is introduced into the intergenic regions of operons encoding ABC importers as the putative internal terminator, which results in the premature termination of transcription. Consequently, the stoichiometric ratio of genes flanking terminators is precisely determined by their termination efficiencies and folding energies at the transcriptional level. Thus, it can be utilized as a promising synthetic biology tool to control the differential expression of genes in an operon.
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11
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Nhim S, Waeonukul R, Uke A, Baramee S, Ratanakhanokchai K, Tachaapaikoon C, Pason P, Liu YJ, Kosugi A. Biological cellulose saccharification using a coculture of Clostridium thermocellum and Thermobrachium celere strain A9. Appl Microbiol Biotechnol 2022; 106:2133-2145. [PMID: 35157106 PMCID: PMC8930880 DOI: 10.1007/s00253-022-11818-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/30/2021] [Accepted: 01/30/2022] [Indexed: 11/29/2022]
Abstract
Abstract An anaerobic thermophilic bacterial strain, A9 (NITE P-03545), that secretes β-glucosidase was newly isolated from wastewater sediments by screening using esculin. The 16S rRNA gene sequence of strain A9 had 100% identity with that of Thermobrachium celere type strain JW/YL-NZ35. The complete genome sequence of strain A9 showed 98.4% average nucleotide identity with strain JW/YL-NZ35. However, strain A9 had different physiological properties from strain JW/YL-NZ35, which cannot secrete β-glucosidases or grow on cellobiose as the sole carbon source. The key β-glucosidase gene (TcBG1) of strain A9, which belongs to glycoside hydrolase family 1, was characterized. Recombinant β-glucosidase (rTcBG1) hydrolyzed cellooligosaccharides to glucose effectively. Furthermore, rTcBG1 showed high thermostability (at 60°C for 2 days) and high glucose tolerance (IC50 = 0.75 M glucose), suggesting that rTcBG1 could be used for biological cellulose saccharification in cocultures with Clostridium thermocellum. High cellulose degradation was observed when strain A9 was cocultured with C. thermocellum in a medium containing 50 g/l crystalline cellulose, and glucose accumulation in the culture supernatant reached 35.2 g/l. In contrast, neither a monoculture of C. thermocellum nor coculture of C. thermocellum with strain JW/YL-NZ35 realized efficient cellulose degradation or high glucose accumulation. These results show that the β-glucosidase secreted by strain A9 degrades cellulose effectively in combination with C. thermocellum cellulosomes and has the potential to be used in a new biological cellulose saccharification process that does not require supplementation with β-glucosidases. Key points • Strain A9 can secrete a thermostable β-glucosidase that has high glucose tolerance • A coculture of strain A9 and C. thermocellum showed high cellulose degradation • Strain A9 achieves biological saccharification without addition of β-glucosidase Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11818-0.
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Affiliation(s)
- Sreyneang Nhim
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Sirilak Baramee
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.,Shandong Energy Institute, Qingdao, 266101, People's Republic of China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, People's Republic of China
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
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12
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Handling Several Sugars at a Time: a Case Study of Xyloglucan Utilization by Ruminiclostridium cellulolyticum. mBio 2021; 12:e0220621. [PMID: 34749527 PMCID: PMC8576529 DOI: 10.1128/mbio.02206-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xyloglucan utilization by Ruminiclostridium cellulolyticum was formerly shown to imply the uptake of large xylogluco-oligosaccharides, followed by cytosolic depolymerization into glucose, galactose, xylose, and cellobiose. This raises the question of how the anaerobic bacterium manages the simultaneous presence of multiple sugars. Using genetic and biochemical approaches targeting the corresponding metabolic pathways, we observed that, surprisingly, all sugars are catabolized, collectively, but glucose consumption is prioritized. Most selected enzymes display unusual features, especially the GTP-dependent hexokinase of glycolysis, which appeared reversible and crucial for xyloglucan utilization. In contrast, mutant strains lacking either galactokinase, cellobiose-phosphorylase, or xylulokinase still catabolize xyloglucan but display variably altered growth. Furthermore, the xylogluco-oligosaccharide depolymerization process appeared connected to the downstream pathways through an intricate network of competitive and noncompetitive inhibitions. Altogether, our data indicate that xyloglucan utilization by R. cellulolyticum relies on an energy-saving central carbon metabolism deviating from current bacterial models, which efficiently prevents carbon overflow. IMPORTANCE The study of the decomposition of recalcitrant plant biomass is of great interest as the limiting step of terrestrial carbon cycle and to produce plant-derived valuable chemicals and energy. While extracellular cellulose degradation and catabolism have been studied in detail, few publications describe the complete metabolism of hemicelluloses and, to date, the published models are limited to the extracellular degradation and sequential entry of simple sugars. Here, we describe how the model anaerobic bacterium Ruminiclostridium cellulolyticum deals with the synchronous intracellular release of glucose, galactose, xylose, and cellobiose upon cytosolic depolymerization of imported xyloglucan oligosaccharides. The described novel metabolic strategy involves the simultaneous activity of different metabolic pathways coupled to a network of inhibitions controlling the carbon flux and is distinct from the ubiquitously observed sequential uptake and metabolism of carbohydrates known as the diauxic shift. Our results highlight the diversity of cellular responses related to a complex environment.
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13
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Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution. Microorganisms 2021; 9:microorganisms9071445. [PMID: 34361881 PMCID: PMC8303734 DOI: 10.3390/microorganisms9071445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022] Open
Abstract
Hungateiclostridium thermocellum ATCC 27405 is a promising bacterium for consolidated bioprocessing with a robust ability to degrade lignocellulosic biomass through a multienzyme cellulosomal complex. The bacterium uses the released cellodextrins, glucose polymers of different lengths, as its primary carbon source and energy. In contrast, the bacterium exhibits poor growth on monosaccharides such as fructose and glucose. This phenomenon raises many important questions concerning its glycolytic pathways and sugar transport systems. Until now, the detailed mechanisms of H. thermocellum adaptation to growth on hexose sugars have been relatively poorly explored. In this study, adaptive laboratory evolution was applied to train the bacterium in hexose sugars-based media, and genome resequencing was used to detect the genes that got mutated during adaptation period. RNA-seq data of the first culture growing on either fructose or glucose revealed that several glycolytic genes in the Embden–Mayerhof–Parnas pathway were expressed at lower levels in these cells than in cellobiose-grown cells. After seven consecutive transfer events on fructose and glucose (~42 generations for fructose-adapted cells and ~40 generations for glucose-adapted cells), several genes in the EMP glycolysis of the evolved strains increased the levels of mRNA expression, accompanied by a faster growth, a greater biomass yield, a higher ethanol titer than those in their parent strains. Genomic screening also revealed several mutation events in the genomes of the evolved strains, especially in those responsible for sugar transport and central carbon metabolism. Consequently, these genes could be applied as potential targets for further metabolic engineering to improve this bacterium for bio-industrial usage.
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14
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Yayo J, Kuil T, Olson DG, Lynd LR, Holwerda EK, van Maris AJA. Laboratory Evolution and Reverse Engineering of Clostridium thermocellum for Growth on Glucose and Fructose. Appl Environ Microbiol 2021; 87:e03017-20. [PMID: 33608285 PMCID: PMC8091016 DOI: 10.1128/aem.03017-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/10/2021] [Indexed: 02/04/2023] Open
Abstract
The native ability of Clostridium thermocellum to efficiently solubilize cellulose makes it an interesting platform for sustainable biofuel production through consolidated bioprocessing. Together with other improvements, industrial implementation of C. thermocellum, as well as fundamental studies into its metabolism, would benefit from improved and reproducible consumption of hexose sugars. To investigate growth of C. thermocellum on glucose or fructose, as well as the underlying molecular mechanisms, laboratory evolution was performed in carbon-limited chemostats with increasing concentrations of glucose or fructose and decreasing cellobiose concentrations. Growth on both glucose and fructose was achieved with biomass yields of 0.09 ± 0.00 and 0.18 ± 0.00 gbiomass gsubstrate-1, respectively, compared to 0.15 ± 0.01 gbiomass gsubstrate-1 for wild type on cellobiose. Single-colony isolates had no or short lag times on the monosaccharides, while wild type showed 42 ± 4 h on glucose and >80 h on fructose. With good growth on glucose, fructose, and cellobiose, the fructose isolates were chosen for genome sequence-based reverse metabolic engineering. Deletion of a putative transcriptional regulator (Clo1313_1831), which upregulated fructokinase activity, reduced lag time on fructose to 12 h with a growth rate of 0.11 ± 0.01 h-1 and resulted in immediate growth on glucose at 0.24 ± 0.01 h-1 Additional introduction of a G-to-V mutation at position 148 in cbpA resulted in immediate growth on fructose at 0.32 ± 0.03 h-1 These insights can guide engineering of strains for fundamental studies into transport and the upper glycolysis, as well as maximizing product yields in industrial settings.IMPORTANCEC. thermocellum is an important candidate for sustainable and cost-effective production of bioethanol through consolidated bioprocessing. In addition to unsurpassed cellulose deconstruction, industrial application and fundamental studies would benefit from improvement of glucose and fructose consumption. This study demonstrated that C. thermocellum can be evolved for reproducible constitutive growth on glucose or fructose. Subsequent genome sequencing, gene editing, and physiological characterization identified two underlying mutations with a role in (regulation of) transport or metabolism of the hexose sugars. In light of these findings, such mutations have likely (and unknowingly) also occurred in previous studies with C. thermocellum using hexose-based media with possible broad regulatory consequences. By targeted modification of these genes, industrial and research strains of C. thermocellum can be engineered to (i) reduce glucose accumulation, (ii) study cellodextrin transport systems in vivo, (iii) allow experiments at >120 g liter-1 soluble substrate concentration, or (iv) reduce costs for labeling studies.
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Affiliation(s)
- Johannes Yayo
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Teun Kuil
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
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15
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Ichikawa S, Tsuge Y, Karita S. Metabolome Analysis of Constituents in Membrane Vesicles for Clostridium thermocellum Growth Stimulation. Microorganisms 2021; 9:microorganisms9030593. [PMID: 33805707 PMCID: PMC8002186 DOI: 10.3390/microorganisms9030593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 11/24/2022] Open
Abstract
The cultivation of the cellulolytic bacterium, Clostridium thermocellum, can have cost-effective cellulosic biomass utilizations, such as consolidated bioprocessing, simultaneous biological enzyme production and saccharification. However, these processes require a longer cultivation term of approximately 1 week. We demonstrate that constituents of the C. thermocellum membrane vesicle fraction significantly promoted the growth rate of C. thermocellum. Similarly, cell-free Bacillus subtilis broth was able to increase C. thermocellum growth rate, while several B. subtilis single-gene deletion mutants, e.g., yxeJ, yxeH, ahpC, yxdK, iolF, decreased the growth stimulation ability. Metabolome analysis revealed signal compounds for cell–cell communication in the C. thermocellum membrane vesicle fraction (ethyl 2-decenoate, ethyl 4-decenoate, and 2-dodecenoic acid) and B. subtilis broth (nicotinamide, indole-3-carboxaldehyde, urocanic acid, nopaline, and 6-paradol). These findings suggest that the constituents in membrane vesicles from C. thermocellum and B. subtilis could promote C. thermocellum growth, leading to improved efficiency of cellulosic biomass utilization.
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Affiliation(s)
- Shunsuke Ichikawa
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
- Correspondence: ; Tel.: +89-59-231-9254; Fax: +89-59-231-9352
| | - Yoichiro Tsuge
- Faculty of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan;
| | - Shuichi Karita
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan;
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16
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Qu C, Zhang Y, Dai K, Fu H, Wang J. Metabolic engineering of Thermoanaerobacterium aotearoense SCUT27 for glucose and cellobiose co-utilization by identification and overexpression of the endogenous cellobiose operon. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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17
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Nidetzky B, Zhong C. Phosphorylase-catalyzed bottom-up synthesis of short-chain soluble cello-oligosaccharides and property-tunable cellulosic materials. Biotechnol Adv 2020; 51:107633. [PMID: 32966861 DOI: 10.1016/j.biotechadv.2020.107633] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/23/2020] [Accepted: 09/06/2020] [Indexed: 12/13/2022]
Abstract
Cellulose-based materials are produced industrially in countless varieties via top-down processing of natural lignocellulose substrates. By contrast, cellulosic materials are only rarely prepared via bottom up synthesis and oligomerization-induced self-assembly of cellulose chains. Building up a cellulose chain via precision polymerization is promising, however, for it offers tunability and control of the final chemical structure. Synthetic cellulose derivatives with programmable material properties might thus be obtained. Cellodextrin phosphorylase (CdP; EC 2.4.1.49) catalyzes iterative β-1,4-glycosylation from α-d-glucose 1-phosphate, with the ability to elongate a diversity of acceptor substrates, including cellobiose, d-glucose and a range of synthetic glycosides having non-sugar aglycons. Depending on the reaction conditions leading to different degrees of polymerization (DP), short-chain soluble cello-oligosaccharides (COS) or insoluble cellulosic materials are formed. Here, we review the characteristics of CdP as bio-catalyst for synthetic applications and show advances in the enzymatic production of COS and reducing end-modified, tailored cellulose materials. Recent studies reveal COS as interesting dietary fibers that could provide a selective prebiotic effect. The bottom-up synthesized celluloses involve chains of DP ≥ 9, as precipitated in solution, and they form ~5 nm thick sheet-like crystalline structures of cellulose allomorph II. Solvent conditions and aglycon structures can direct the cellulose chain self-assembly towards a range of material architectures, including hierarchically organized networks of nanoribbons, or nanorods as well as distorted nanosheets. Composite materials are also formed. The resulting materials can be useful as property-tunable hydrogels and feature site-specific introduction of functional and chemically reactive groups. Therefore, COS and cellulose obtained via bottom-up synthesis can expand cellulose applications towards product classes that are difficult to access via top-down processing of natural materials.
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Affiliation(s)
- Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz 8010, Austria; Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, Graz 8010, Austria.
| | - Chao Zhong
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz 8010, Austria
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18
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Chandravanshi M, Samanta R, Kanaujia SP. Conformational Trapping of a β-Glucosides-Binding Protein Unveils the Selective Two-Step Ligand-Binding Mechanism of ABC Importers. J Mol Biol 2020; 432:5711-5734. [PMID: 32866452 DOI: 10.1016/j.jmb.2020.08.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 12/26/2022]
Abstract
Substrate-binding proteins (SBPs), selectively capture ligand(s) and ensure their translocation via its cognate ATP-binding cassette (ABC) import system. SBPs bind their cognate ligand(s) via an induced-fit mechanism known as the "Venus Fly-trap"; however, this mechanism lacks the atomic details of all conformational landscape as the confirmatory evidence(s) in its support. In this study, we delineate the atomic details of an SBP, β-glucosides-binding protein (βGlyBP) from Thermus thermophilus HB8. The protein βGlyBP is multi-specific and binds to different types of β-glucosides varying in their glycosidic linkages viz. β-1,2; β-1,3; β-1,4 and β-1,6 with a degree of polymerization of 2-5 glucosyl units. Structurally, the protein βGlyBP possesses four subdomains (N1, N2, C1 and C2). The unliganded protein βGlyBP remains in an open state, which closes upon binding to sophorose (SOP2), laminari-oligosaccharides (LAMn), cello-oligosaccharides (CELn), and gentiobiose (GEN2). This study reports, for the first time, four different structural states (open-unliganded, partial-open-unliganded, open-liganded and closed-liganded) of the protein βGlyBP, revealing its conformational changes upon ligand binding and suggesting a two-step induced-fit mechanism. Further, results suggest that the conformational changes of N1 and C1 subdomains drive the ligand binding, unlike that of the whole N- and C-terminal domains (NTD and CTD) as known in the "Venus Fly-trap" mechanism. Additionally, profiling of stereo-selection mechanism for α- and β-glucosides reveals that in the ligand-binding site four secondary structural elements (L1, H1, H2 and H3) drive the ligand selection. In summary, results demonstrate that the details of conformational changes and ligand selection are pre-encoded in the SBPs.
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Affiliation(s)
- Monika Chandravanshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Reshama Samanta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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19
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Transcriptomic analysis of a Clostridium thermocellum strain engineered to utilize xylose: responses to xylose versus cellobiose feeding. Sci Rep 2020; 10:14517. [PMID: 32884054 PMCID: PMC7471329 DOI: 10.1038/s41598-020-71428-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
Clostridium (Ruminiclostridium) thermocellum is recognized for its ability to ferment cellulosic biomass directly, but it cannot naturally grow on xylose. Recently, C. thermocellum (KJC335) was engineered to utilize xylose through expressing a heterologous xylose catabolizing pathway. Here, we compared KJC335′s transcriptomic responses to xylose versus cellobiose as the primary carbon source and assessed how the bacteria adapted to utilize xylose. Our analyses revealed 417 differentially expressed genes (DEGs) with log2 fold change (FC) >|1| and 106 highly DEGs (log2 FC >|2|). Among the DEGs, two putative sugar transporters, cbpC and cbpD, were up-regulated, suggesting their contribution to xylose transport and assimilation. Moreover, the up-regulation of specific transketolase genes (tktAB) suggests the importance of this enzyme for xylose metabolism. Results also showed remarkable up-regulation of chemotaxis and motility associated genes responding to xylose feeding, as well as widely varying gene expression in those encoding cellulosomal enzymes. For the down-regulated genes, several were categorized in gene ontology terms oxidation–reduction processes, ATP binding and ATPase activity, and integral components of the membrane. This study informs potentially critical, enabling mechanisms to realize the conceptually attractive Next-Generation Consolidated BioProcessing approach where a single species is sufficient for the co-fermentation of cellulose and hemicellulose.
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20
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Zhong C, Ukowitz C, Domig KJ, Nidetzky B. Short-Chain Cello-oligosaccharides: Intensification and Scale-up of Their Enzymatic Production and Selective Growth Promotion among Probiotic Bacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8557-8567. [PMID: 32687709 PMCID: PMC7458430 DOI: 10.1021/acs.jafc.0c02660] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Short-chain cello-oligosaccharides (COS; degree of polymerization, DP ≤ 6) are promising water-soluble dietary fibers. An efficient approach to their bottom-up synthesis is from sucrose and glucose using glycoside phosphorylases. Here, we show the intensification and scale up (20 mL; gram scale) of COS production to 93 g/L product and in 82 mol % yield from sucrose (0.5 M). The COS were comprised of DP 3 (33 wt %), DP 4 (34 wt %), DP 5 (24 wt %), and DP 6 (9 wt %) and involved minimal loss (≤10 mol %) to insoluble fractions. After isolation (≥95% purity; ≥90% yield), the COS were examined for growth promotion of probiotic strains. Benchmarked against inulin, trans-galacto-oligosaccharides, and cellobiose, COS showed up to 4.1-fold stimulation of cell density for Clostridium butyricum, Lactococcus lactis subsp. lactis, Lactobacillus paracasei subsp. paracasei, and Lactobacillus rhamnosus but were less efficient with Bifidobacterium sp. This study shows the COS as selectively functional carbohydrates with prebiotic potential and demonstrates their efficient enzymatic production.
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Affiliation(s)
- Chao Zhong
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Graz 8010, Austria
| | - Christina Ukowitz
- Institute
of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences
(BOKU), Vienna 1190, Austria
| | - Konrad J. Domig
- Institute
of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences
(BOKU), Vienna 1190, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Graz 8010, Austria
- Austrian
Centre of Industrial Biotechnology (acib), Graz 8010, Austria
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21
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Miyake M, Terada T, Shimokawa M, Sugimoto N, Arakawa T, Shimizu K, Igarashi K, Fujita K, Fushinobu S. Structural analysis of β-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum. FEBS J 2020; 287:5114-5129. [PMID: 32246585 DOI: 10.1111/febs.15315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/09/2020] [Accepted: 03/26/2020] [Indexed: 12/29/2022]
Abstract
Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for β-arabinooligosaccharides, which are present in the hydroxyproline-rich glycoproteins of edible plants. Whereas microbial degradation systems for α-linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting β-linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate-binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the β-arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf-β1,2-Araf (β-Ara2 ) with a Kd of 0.150 μm, but did not bind L-arabinose or methyl-β-Ara2 . Therefore, the SBP was termed β-arabinobiose-binding protein (BABP). Crystal structures of BABP complexed with β-Ara2 were determined at resolutions of up to 1.78 Å. The findings showed that β-Ara2 was bound to BABP within a short tunnel between two lobes as an α-anomeric form at its reducing end. BABP forms extensive interactions with β-Ara2 , and its binding mode was unique among SBPs. A molecular dynamics simulation revealed that the closed conformation of substrate-bound BABP is stable, whereas substrate-free form can adopt a fully open and two distinct semi-open states. The importer system specific for β-Ara2 may contribute to microbial survival in biological niches with limited amounts of digestible carbohydrates. DATABASE: Atomic coordinates and structure factors (codes 6LCE and 6LCF) have been deposited in the Protein Data Bank (http://wwpdb.org/).
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Affiliation(s)
| | - Tohru Terada
- The Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | | | - Naohisa Sugimoto
- Department of Biomaterial Sciences, The University of Tokyo, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | | | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, The University of Tokyo, Japan.,VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
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22
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Raut MP, Couto N, Karunakaran E, Biggs CA, Wright PC. Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85. Sci Rep 2019; 9:16542. [PMID: 31719545 PMCID: PMC6851124 DOI: 10.1038/s41598-019-52675-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 10/22/2019] [Indexed: 02/04/2023] Open
Abstract
Fibrobacter succinogenes S85, isolated from the rumen of herbivores, is capable of robust lignocellulose degradation. However, the mechanism by which it achieves this is not fully elucidated. In this study, we have undertaken the most comprehensive quantitative proteomic analysis, to date, of the changes in the cell envelope protein profile of F. succinogenes S85 in response to growth on cellulose. Our results indicate that the cell envelope proteome undergoes extensive rearrangements to accommodate the cellulolytic degradation machinery, as well as associated proteins involved in adhesion to cellulose and transport and metabolism of cellulolytic products. Molecular features of the lignocellulolytic enzymes suggest that the Type IX secretion system is involved in the translocation of these enzymes to the cell envelope. Finally, we demonstrate, for the first time, that cyclic-di-GMP may play a role in mediating catabolite repression, thereby facilitating the expression of proteins involved in the adhesion to lignocellulose and subsequent lignocellulose degradation and utilisation. Understanding the fundamental aspects of lignocellulose degradation in F. succinogenes will aid the development of advanced lignocellulosic biofuels.
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Affiliation(s)
- Mahendra P Raut
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Narciso Couto
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK.,Centre for Applied Pharmacokinetic Research, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK
| | - Esther Karunakaran
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Catherine A Biggs
- School of Engineering, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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23
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Yoav S, Stern J, Salama-Alber O, Frolow F, Anbar M, Karpol A, Hadar Y, Morag E, Bayer EA. Directed Evolution of Clostridium thermocellum β-Glucosidase A Towards Enhanced Thermostability. Int J Mol Sci 2019; 20:E4701. [PMID: 31547488 PMCID: PMC6801902 DOI: 10.3390/ijms20194701] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 12/27/2022] Open
Abstract
β-Glucosidases are key enzymes in the process of cellulose utilization. It is the last enzyme in the cellulose hydrolysis chain, which converts cellobiose to glucose. Since cellobiose is known to have a feedback inhibitory effect on a variety of cellulases, β-glucosidase can prevent this inhibition by hydrolyzing cellobiose to non-inhibitory glucose. While the optimal temperature of the Clostridium thermocellum cellulosome is 70 °C, C. thermocellum β-glucosidase A is almost inactive at such high temperatures. Thus, in the current study, a random mutagenesis directed evolutionary approach was conducted to produce a thermostable mutant with Kcat and Km, similar to those of the wild-type enzyme. The resultant mutant contained two mutations, A17S and K268N, but only the former was found to affect thermostability, whereby the inflection temperature (Ti) was increased by 6.4 °C. A17 is located near the central cavity of the native enzyme. Interestingly, multiple alignments revealed that position 17 is relatively conserved, whereby alanine is replaced only by serine. Upon the addition of the thermostable mutant to the C. thermocellum secretome for subsequent hydrolysis of microcrystalline cellulose at 70 °C, a higher soluble glucose yield (243%) was obtained compared to the activity of the secretome supplemented with the wild-type enzyme.
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Affiliation(s)
- Shahar Yoav
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, the Advanced School for Environmental Studies, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Orly Salama-Alber
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Michael Anbar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Alon Karpol
- CelDezyner, 2 Bergman St, Tamar Science Park, Rehovot 7670504, Israel.
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, the Advanced School for Environmental Studies, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
| | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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Wang F, Wang M, Zhao Q, Niu K, Liu S, He D, Liu Y, Xu S, Fang X. Exploring the Relationship Between Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17. Front Microbiol 2019; 10:2035. [PMID: 31551972 PMCID: PMC6746925 DOI: 10.3389/fmicb.2019.02035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/19/2019] [Indexed: 11/13/2022] Open
Abstract
Characterizing and engineering microbial communities for lignocellulosic biofuel production has received widespread attention. Previous research has established that Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17 coculture significantly improves overall cellulosic biofuel production efficiency. Here, we investigated this interaction and revealed the mechanism underlying the improved efficiency observed. In contrast to the previously reported mutualistic relationship, a harmful effect toward C. thermocellum JN4 was observed in these microbial consortia. Although T. thermosaccharolyticum GD17 relieves the carbon catabolite repression of C. thermocellum JN4 regarding obtaining more cellobiose or glucose released from lignocellulose, T. thermosaccharolyticum GD17 significantly hampers the growth of C. thermocellum JN4 in coculture. The increased formation of end products is due to the strong competitive metabolic advantage of T. thermosaccharolyticum GD17 over C. thermocellum JN4 in the conversion of glucose or cellobiose into final products. The possibility of controlling and rebalancing these microbial consortia to modulate cellulose degradation was achieved by adding T. thermosaccharolyticum GD17 stimulants into the system. As cellulolytic bacteria are usually at a metabolic disadvantage, these discoveries may apply to a large proportion of cellulosic biofuel-producing microbial consortia. These findings provide a reference for engineering efficient and modular microbial consortia for modulating cellulosic conversion.
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Affiliation(s)
- Fangzhong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shasha Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Didi He
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yan Liu
- College of Life Science, Qufu Normal University, Qufu, China
| | - Shiping Xu
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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25
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ABC Transporters Required for Hexose Uptake by Clostridium phytofermentans. J Bacteriol 2019; 201:JB.00241-19. [PMID: 31109990 DOI: 10.1128/jb.00241-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/13/2019] [Indexed: 01/02/2023] Open
Abstract
The mechanisms by which bacteria uptake solutes across the cell membrane broadly impact their cellular energetics. Here, we use functional genomic, genetic, and biophysical approaches to reveal how Clostridium (Lachnoclostridium) phytofermentans, a model bacterium that ferments lignocellulosic biomass, uptakes plant hexoses using highly specific, nonredundant ATP-binding cassette (ABC) transporters. We analyze the transcription patterns of its 173 annotated sugar transporter genes to find those upregulated on specific carbon sources. Inactivation of these genes reveals that individual ABC transporters are required for uptake of hexoses and hexo-oligosaccharides and that distinct ABC transporters are used for oligosaccharides versus their constituent monomers. The thermodynamics of sugar binding shows that substrate specificity of these transporters is encoded by the extracellular solute-binding subunit. As sugars are not phosphorylated during ABC transport, we identify intracellular hexokinases based on in vitro activities. These mechanisms used by Clostridia to uptake plant hexoses are key to understanding soil and intestinal microbiomes and to engineer strains for industrial transformation of lignocellulose.IMPORTANCE Plant-fermenting Clostridia are anaerobic bacteria that recycle plant matter in soil and promote human health by fermenting dietary fiber in the intestine. Clostridia degrade plant biomass using extracellular enzymes and then uptake the liberated sugars for fermentation. The main sugars in plant biomass are hexoses, and here, we identify how hexoses are taken in to the cell by the model organism Clostridium phytofermentans We show that this bacterium uptakes hexoses using a set of highly specific, nonredundant ABC transporters. Once in the cell, the hexoses are phosphorylated by intracellular hexokinases. This study provides insight into the functioning of abundant members of soil and intestinal microbiomes and identifies gene targets to engineer strains for industrial lignocellulosic fermentation.
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26
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Glucose production from cellulose through biological simultaneous enzyme production and saccharification using recombinant bacteria expressing the β-glucosidase gene. J Biosci Bioeng 2019; 127:340-344. [DOI: 10.1016/j.jbiosc.2018.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 12/18/2022]
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27
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Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose. Metab Eng 2018; 48:94-108. [DOI: 10.1016/j.ymben.2018.05.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/15/2018] [Accepted: 05/31/2018] [Indexed: 01/02/2023]
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28
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Xiong W, Reyes LH, Michener WE, Maness P, Chou KJ. Engineering cellulolytic bacterium
Clostridium thermocellum
to co‐ferment cellulose‐ and hemicellulose‐derived sugars simultaneously. Biotechnol Bioeng 2018. [DOI: 10.1002/bit.26590] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Wei Xiong
- National Renewable Energy Laboratory BioSciences Center GoldenColorado
| | - Luis H. Reyes
- National Renewable Energy Laboratory BioSciences Center GoldenColorado
- Product and Process Design Group, Department of Chemical Engineering Universidad de los Andes Bogotá D.C. Colombia
| | - William E. Michener
- National Renewable Energy Laboratory National Bioenergy Center GoldenColorado
| | - Pin‐Ching Maness
- National Renewable Energy Laboratory BioSciences Center GoldenColorado
| | - Katherine J. Chou
- National Renewable Energy Laboratory BioSciences Center GoldenColorado
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29
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Gandini C, Tarraran L, Kalemasi D, Pessione E, Mazzoli R. RecombinantLactococcus lactisfor efficient conversion of cellodextrins into L-lactic acid. Biotechnol Bioeng 2017; 114:2807-2817. [DOI: 10.1002/bit.26400] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/01/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Chiara Gandini
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Loredana Tarraran
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Denis Kalemasi
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Enrica Pessione
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Roberto Mazzoli
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
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30
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Parisutham V, Chandran SP, Mukhopadhyay A, Lee SK, Keasling JD. Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries. BIORESOURCE TECHNOLOGY 2017; 239:496-506. [PMID: 28535986 DOI: 10.1016/j.biortech.2017.05.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 05/28/2023]
Abstract
Complete hydrolysis of cellulose has been a key characteristic of biomass technology because of the limitation of industrial production hosts to use cellodextrin, the partial hydrolysis product of cellulose. Cellobiose, a β-1,4-linked glucose dimer, is a major cellodextrin of the enzymatic hydrolysis (via endoglucanase and exoglucanase) of cellulose. Conversion of cellobiose to glucose is executed by β-glucosidase. The complete extracellular hydrolysis of celluloses has several critical barriers in biomass technology. An alternative bioengineering strategy to make the bioprocessing less challenging is to engineer microbes with the abilities to hydrolyze and assimilate the cellulosic-hydrolysate cellodextrin. Microorganisms engineered to metabolize cellobiose rather than the monomeric glucose can provide several advantages for lignocellulose-based biorefineries. This review describes the recent advances and challenges in engineering efficient intracellular cellobiose metabolism in industrial hosts. This review also describes the limitations of and future prospectives in engineering intracellular cellobiose metabolism.
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Affiliation(s)
- Vinuselvi Parisutham
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sathesh-Prabu Chandran
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sung Kuk Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering & Department of Bioengineering, UC Berkeley, Berkeley, CA 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, KogleAllé, DK2970 Hørsholm, Denmark; Synthetic Biology Engineering Research Center (Synberc), Berkeley, CA 94720, USA
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31
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Choi J, Klingeman DM, Brown SD, Cox CD. The LacI family protein GlyR3 co-regulates the celC operon and manB in Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:163. [PMID: 28652864 PMCID: PMC5483248 DOI: 10.1186/s13068-017-0849-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/16/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum utilizes a wide variety of free and cellulosomal cellulases and accessory enzymes to hydrolyze polysaccharides present in complex substrates. To date only a few studies have unveiled the details by which the expression of these cellulases are regulated. Recent studies have described the auto regulation of the celC operon and determined that the celC-glyR3-licA gene cluster and nearby manB-celT gene cluster are co-transcribed as polycistronic mRNA. RESULTS In this paper, we demonstrate that the GlyR3 protein mediates the regulation of manB. We first identify putative GlyR3 binding sites within or just upstream of the coding regions of manB and celT. Using an electrophoretic mobility shift assay (EMSA), we determined that a higher concentration of GlyR3 is required to effectively bind to the putative manB site in comparison to the celC site. Neither the putative celT site nor random DNA significantly binds GlyR3. While laminaribiose interfered with GlyR3 binding to the celC binding site, binding to the manB site was unaffected. In the presence of laminaribiose, in vivo transcription of the celC-glyR3-licA gene cluster increases, while manB expression is repressed, compared to in the absence of laminaribiose, consistent with the results from the EMSA. An in vitro transcription assay demonstrated that GlyR3 and laminaribiose interactions were responsible for the observed patters of in vivo transcription. CONCLUSIONS Together these results reveal a mechanism by which manB is expressed at low concentrations of GlyR3 but repressed at high concentrations. In this way, C. thermocellum is able to co-regulate both the celC and manB gene clusters in response to the availability of β-1,3-polysaccharides in its environment.
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Affiliation(s)
- Jinlyung Choi
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Dawn M. Klingeman
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Steven D. Brown
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chris D. Cox
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
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32
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Dumitrache A, Klingeman DM, Natzke J, Rodriguez M, Giannone RJ, Hettich RL, Davison BH, Brown SD. Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells. Sci Rep 2017; 7:43583. [PMID: 28240279 PMCID: PMC5327387 DOI: 10.1038/srep43583] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/25/2017] [Indexed: 01/01/2023] Open
Abstract
Clostridium (Ruminiclostridium) thermocellum is a model organism for its ability to deconstruct plant biomass and convert the cellulose into ethanol. The bacterium forms biofilms adherent to lignocellulosic feedstocks in a continuous cell-monolayer in order to efficiently break down and uptake cellulose hydrolysates. We developed a novel bioreactor design to generate separate sessile and planktonic cell populations for omics studies. Sessile cells had significantly greater expression of genes involved in catabolism of carbohydrates by glycolysis and pyruvate fermentation, ATP generation by proton gradient, the anabolism of proteins and lipids and cellular functions critical for cell division consistent with substrate replete conditions. Planktonic cells had notably higher gene expression for flagellar motility and chemotaxis, cellulosomal cellulases and anchoring scaffoldins, and a range of stress induced homeostasis mechanisms such as oxidative stress protection by antioxidants and flavoprotein co-factors, methionine repair, Fe-S cluster assembly and repair in redox proteins, cell growth control through tRNA thiolation, recovery of damaged DNA by nucleotide excision repair and removal of terminal proteins by proteases. This study demonstrates that microbial attachment to cellulose substrate produces widespread gene expression changes for critical functions of this organism and provides physiological insights for two cells populations relevant for engineering of industrially-ready phenotypes.
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Affiliation(s)
- Alexandru Dumitrache
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Dawn M Klingeman
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Jace Natzke
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Miguel Rodriguez
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Richard J Giannone
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Robert L Hettich
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Brian H Davison
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Steven D Brown
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
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33
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Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG. Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum. Sci Rep 2017; 7:43355. [PMID: 28230109 PMCID: PMC5322536 DOI: 10.1038/srep43355] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022] Open
Abstract
Clostridium thermocellum could potentially be used as a microbial biocatalyst to produce renewable fuels directly from lignocellulosic biomass due to its ability to rapidly solubilize plant cell walls. While the organism readily ferments sugars derived from cellulose, pentose sugars from xylan are not metabolized. Here, we show that non-fermentable pentoses inhibit growth and end-product formation during fermentation of cellulose-derived sugars. Metabolomic experiments confirmed that xylose is transported intracellularly and reduced to the dead-end metabolite xylitol. Comparative RNA-seq analysis of xylose-inhibited cultures revealed several up-regulated genes potentially involved in pentose transport and metabolism, which were targeted for disruption. Deletion of the ATP-dependent transporter, CbpD partially alleviated xylose inhibition. A putative xylitol dehydrogenase, encoded by Clo1313_0076, was also deleted resulting in decreased total xylitol production and yield by 41% and 46%, respectively. Finally, xylose-induced inhibition corresponds with the up-regulation and biogenesis of a cyclical AgrD-type, pentapeptide. Medium supplementation with the mature cyclical pentapeptide also inhibits bacterial growth. Together, these findings provide new foundational insights needed for engineering improved pentose utilizing strains of C. thermocellum and reveal the first functional Agr-type cyclic peptide to be produced by a thermophilic member of the Firmicutes.
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Affiliation(s)
- Tobin J Verbeke
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Richard J Giannone
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dawn M Klingeman
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nancy L Engle
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Thomas Rydzak
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Adam M Guss
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Timothy J Tschaplinski
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Steven D Brown
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Robert L Hettich
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James G Elkins
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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34
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LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313. Appl Environ Microbiol 2017; 83:AEM.02751-16. [PMID: 28003194 DOI: 10.1128/aem.02751-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/14/2016] [Indexed: 12/30/2022] Open
Abstract
Organisms regulate gene expression in response to the environment to coordinate metabolic reactions. Clostridium thermocellum expresses enzymes for both lignocellulose solubilization and its fermentation to produce ethanol. One LacI regulator termed GlyR3 in C. thermocellum ATCC 27405 was previously identified as a repressor of neighboring genes with repression relieved by laminaribiose (a β-1,3 disaccharide). To better understand the three C. thermocellum LacI regulons, deletion mutants were constructed using the genetically tractable DSM1313 strain. DSM1313 lacI genes Clo1313_2023, Clo1313_0089, and Clo1313_0396 encode homologs of GlyR1, GlyR2, and GlyR3 from strain ATCC 27405, respectively. Growth on cellobiose or pretreated switchgrass was unaffected by any of the gene deletions under controlled-pH fermentations. Global gene expression patterns from time course analyses identified glycoside hydrolase genes encoding hemicellulases, including cellulosomal enzymes, that were highly upregulated (5- to 100-fold) in the absence of each LacI regulator, suggesting that these were repressed under wild-type conditions and that relatively few genes were controlled by each regulator under the conditions tested. Clo1313_2022, encoding lichenase enzyme LicB, was derepressed in a ΔglyR1 strain. Higher expression of Clo1313_1398, which encodes the Man5A mannanase, was observed in a ΔglyR2 strain, and α-mannobiose was identified as a probable inducer for GlyR2-regulated genes. For the ΔglyR3 strain, upregulation of the two genes adjacent to glyR3 in the celC-glyR3-licA operon was consistent with earlier studies. Electrophoretic mobility shift assays have confirmed LacI transcription factor binding to specific regions of gene promoters.IMPORTANCE Understanding C. thermocellum gene regulation is of importance for improved fundamental knowledge of this industrially relevant bacterium. Most LacI transcription factors regulate local genomic regions; however, a small number of those genes encode global regulatory proteins with extensive regulons. This study indicates that there are small specific C. thermocellum LacI regulons. The identification of LacI repressor activity for hemicellulase gene expression is a key result of this work and will add to the small body of existing literature on the area of gene regulation in C. thermocellum.
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35
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Bai X, Wang X, Wang S, Ji X, Guan Z, Zhang W, Lu X. Functional Studies of β-Glucosidases of Cytophaga hutchinsonii and Their Effects on Cellulose Degradation. Front Microbiol 2017; 8:140. [PMID: 28210251 PMCID: PMC5288383 DOI: 10.3389/fmicb.2017.00140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/19/2017] [Indexed: 11/17/2022] Open
Abstract
Cytophaga hutchinsonii can rapidly digest crystalline cellulose without free cellulases or cellulosomes. Its cell-contact cellulose degradation mechanism is unknown. In this study, the four β-glucosidase (bgl) genes in C. hutchinsonii were singly and multiply deleted, and the functions of these β-glucosidases in cellobiose and cellulose degradation were investigated. We found that the constitutively expressed BglB played a key role in cellobiose utilization, while BglA which was induced by cellobiose could partially make up for the deletion of bglB. The double deletion mutant ΔbglA/bglB lost the ability to digest cellobiose and could not thrive in cellulose medium, indicating that β-glucosidases were important for cellulose degradation. When cultured in cellulose medium, a small amount of glucose accumulated in the medium in the initial stage of growth for the wild type, while almost no glucose accumulated for ΔbglA/bglB. When supplemented with a small amount of glucose, ΔbglA/bglB started to degrade cellulose and grew in cellulose medium. We inferred that glucose might be essential for initiating cellulose degradation, and with additional glucose, C. hutchinsonii could partially utilize cellulose without β-glucosidases. We also found that there were both cellulose binding cells and free cells when cultured in cellulose. Since direct contact between C. hutchinsonii cells and cellulose is necessary for cellulose degradation, we deduced that the free cells which were convenient to explore new territory in the environment might be fed by the adherent cells which could produce cello-oligosaccharide and glucose into the environment. This study enriched our knowledge of the cellulolytic pathway of C. hutchinsonii.
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Affiliation(s)
- Xinfeng Bai
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Xifeng Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Sen Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Xiaofei Ji
- Department of Pathogenic Biology, Binzhou Medical University Yantai, China
| | - Zhiwei Guan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
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Fosses A, Maté M, Franche N, Liu N, Denis Y, Borne R, de Philip P, Fierobe HP, Perret S. A seven-gene cluster in Ruminiclostridium cellulolyticum is essential for signalization, uptake and catabolism of the degradation products of cellulose hydrolysis. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:250. [PMID: 29093754 PMCID: PMC5663094 DOI: 10.1186/s13068-017-0933-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/19/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Like a number of anaerobic and cellulolytic Gram-positive bacteria, the model microorganism Ruminiclostridium cellulolyticum produces extracellular multi-enzymatic complexes called cellulosomes, which efficiently degrade the crystalline cellulose. Action of the complexes on cellulose releases cellobiose and longer cellodextrins but to date, little is known about the transport and utilization of the produced cellodextrins in the bacterium. A better understanding of the uptake systems and fermentation of sugars derived from cellulose could have a major impact in the field of biofuels production. RESULTS We characterized a putative ABC transporter devoted to cellodextrins uptake, and a cellobiose phosphorylase (CbpA) in R. cellulolyticum. The genes encoding the components of the ABC transporter (a binding protein CuaA and two integral membrane proteins) and CbpA are expressed as a polycistronic transcriptional unit induced in the presence of cellobiose. Upstream, another polycistronic transcriptional unit encodes a two-component system (sensor and regulator), and a second binding protein CuaD, and is constitutively expressed. The products might form a three-component system inducing the expression of cuaABC and cbpA since we showed that CuaR is able to recognize the region upstream of cuaA. Biochemical analysis showed that CbpA is a strict cellobiose phosphorylase inactive on longer cellodextrins; CuaA binds to all cellodextrins (G2-G5) tested, whereas CuaD is specific to cellobiose and presents a higher affinity to this sugar. This results are in agreement with their function in transport and signalization, respectively. Characterization of a cuaD mutant, and its derivatives, indicated that the ABC transporter and CbpA are essential for growth on cellobiose and cellulose. CONCLUSIONS For the first time in a Gram-positive strain, we identified a three-component system and a conjugated ABC transporter/cellobiose phosphorylase system which was shown to be essential for the growth of the model cellulolytic bacterium R. cellulolyticum on cellobiose and cellulose. This efficient and energy-saving system of transport and phosphorolysis appears to be the major cellobiose utilization pathway in R. cellulolyticum, and seems well adapted to cellulolytic life-style strain. It represents a new way to enable engineered strains to utilize cellodextrins for the production of biofuels or chemicals of interest from cellulose.
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Affiliation(s)
| | - Maria Maté
- Aix Marseille Univ, CNRS, AFMB, Marseille, France
| | | | - Nian Liu
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Yann Denis
- Aix Marseille Univ, CNRS, Plateforme Transcriptome, Marseille, France
| | - Romain Borne
- Aix Marseille Univ, CNRS, LCB, Marseille, France
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Advances in Consolidated Bioprocessing Using Clostridium thermocellumand Thermoanaerobacter saccharolyticum. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch10] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Thompson RA, Dahal S, Garcia S, Nookaew I, Trinh CT. Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:194. [PMID: 27602057 PMCID: PMC5012057 DOI: 10.1186/s13068-016-0607-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/26/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Clostridium thermocellum is a gram-positive thermophile that can directly convert lignocellulosic material into biofuels. The metabolism of C. thermocellum contains many branches and redundancies which limit biofuel production, and typical genetic techniques are time-consuming. Further, the genome sequence of a genetically tractable strain C. thermocellum DSM 1313 has been recently sequenced and annotated. Therefore, developing a comprehensive, predictive, genome-scale metabolic model of DSM 1313 is desired for elucidating its complex phenotypes and facilitating model-guided metabolic engineering. RESULTS We constructed a genome-scale metabolic model iAT601 for DSM 1313 using the KEGG database as a scaffold and an extensive literature review and bioinformatic analysis for model refinement. Next, we used several sets of experimental data to train the model, e.g., estimation of the ATP requirement for growth-associated maintenance (13.5 mmol ATP/g DCW/h) and cellulosome synthesis (57 mmol ATP/g cellulosome/h). Using our tuned model, we investigated the effect of cellodextrin lengths on cell yields, and could predict in silico experimentally observed differences in cell yield based on which cellodextrin species is assimilated. We further employed our tuned model to analyze the experimentally observed differences in fermentation profiles (i.e., the ethanol to acetate ratio) between cellobiose- and cellulose-grown cultures and infer regulatory mechanisms to explain the phenotypic differences. Finally, we used the model to design over 250 genetic modification strategies with the potential to optimize ethanol production, 6155 for hydrogen production, and 28 for isobutanol production. CONCLUSIONS Our developed genome-scale model iAT601 is capable of accurately predicting complex cellular phenotypes under a variety of conditions and serves as a high-quality platform for model-guided strain design and metabolic engineering to produce industrial biofuels and chemicals of interest.
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Affiliation(s)
- R. Adam Thompson
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sanjeev Dahal
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sergio Garcia
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr., DO#432, Knoxville, TN 37996 USA
| | - Intawat Nookaew
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Cong T. Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr., DO#432, Knoxville, TN 37996 USA
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A Novel Manno-Oligosaccharide Binding Protein Identified in Alkaliphilic Bacillus sp. N16-5 Is Involved in Mannan Utilization. PLoS One 2016; 11:e0150059. [PMID: 26978267 PMCID: PMC4792470 DOI: 10.1371/journal.pone.0150059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/09/2016] [Indexed: 11/19/2022] Open
Abstract
ManH, a novel substrate-binding protein of an ABC transporter, was identified from the mannan utilization gene cluster of Bacillus sp. N16-5. We cloned, overexpressed, and purified ManH and measured its binding affinity to different substrates by isothermal titration calorimetry. ManH binds to mannotriose, mannotetraose, mannopentose, and galactosyl-mannotriose with dissociation constants in the micromolar range. Deletion of manH led to decreased growth ability of the strain when cultivated in medium with manno-oligosaccharides or mannan as the carbon source. ManH belongs to a manno-oligosaccharide transporter and plays an important role in mannan utilization by Bacillus sp. N16-5.
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Mechanisms involved in xyloglucan catabolism by the cellulosome-producing bacterium Ruminiclostridium cellulolyticum. Sci Rep 2016; 6:22770. [PMID: 26946939 PMCID: PMC4780118 DOI: 10.1038/srep22770] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/23/2016] [Indexed: 12/23/2022] Open
Abstract
Xyloglucan, a ubiquitous highly branched plant polysaccharide, was found to be rapidly degraded and metabolized by the cellulosome-producing bacterium Ruminiclostridium cellulolyticum. Our study shows that at least four cellulosomal enzymes displaying either endo- or exoxyloglucanase activities, achieve the extracellular degradation of xyloglucan into 4-glucosyl backbone xyloglucan oligosaccharides. The released oligosaccharides (composed of up to 9 monosaccharides) are subsequently imported by a highly specific ATP-binding cassette transporter (ABC-transporter), the expression of the corresponding genes being strongly induced by xyloglucan. This polysaccharide also triggers the synthesis of cytoplasmic β-galactosidase, α-xylosidase, and β-glucosidase that act sequentially to convert the imported oligosaccharides into galactose, xylose, glucose and unexpectedly cellobiose. Thus R. cellulolyticum has developed an energy-saving strategy to metabolize this hemicellulosic polysaccharide that relies on the action of the extracellular cellulosomes, a highly specialized ABC-transporter, and cytoplasmic enzymes acting in a specific order. This strategy appears to be widespread among cellulosome-producing mesophilic bacteria which display highly similar gene clusters encoding the cytosolic enzymes and the ABC-transporter.
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Xu Q, Resch MG, Podkaminer K, Yang S, Baker JO, Donohoe BS, Wilson C, Klingeman DM, Olson DG, Decker SR, Giannone RJ, Hettich RL, Brown SD, Lynd LR, Bayer EA, Himmel ME, Bomble YJ. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities. SCIENCE ADVANCES 2016; 2:e1501254. [PMID: 26989779 PMCID: PMC4788478 DOI: 10.1126/sciadv.1501254] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/30/2015] [Indexed: 05/18/2023]
Abstract
Clostridium thermocellum is the most efficient microorganism for solubilizing lignocellulosic biomass known to date. Its high cellulose digestion capability is attributed to efficient cellulases consisting of both a free-enzyme system and a tethered cellulosomal system wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins to generate large protein complexes attached to the bacterial cell wall. This study demonstrates that C. thermocellum also uses a type of cellulosomal system not bound to the bacterial cell wall, called the "cell-free" cellulosomal system. The cell-free cellulosome complex can be seen as a "long range cellulosome" because it can diffuse away from the cell and degrade polysaccharide substrates remotely from the bacterial cell. The contribution of these two types of cellulosomal systems in C. thermocellum was elucidated by characterization of mutants with different combinations of scaffoldin gene deletions. The primary scaffoldin, CipA, was found to play the most important role in cellulose degradation by C. thermocellum, whereas the secondary scaffoldins have less important roles. Additionally, the distinct and efficient mode of action of the C. thermocellum exoproteome, wherein the cellulosomes splay or divide biomass particles, changes when either the primary or secondary scaffolds are removed, showing that the intact wild-type cellulosomal system is necessary for this essential mode of action. This new transcriptional and proteomic evidence shows that a functional primary scaffoldin plays a more important role compared to secondary scaffoldins in the proper regulation of CAZyme genes, cellodextrin transport, and other cellular functions.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Michael G. Resch
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Kara Podkaminer
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - John O. Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Charlotte Wilson
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dawn M. Klingeman
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Daniel G. Olson
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Stephen R. Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Richard J. Giannone
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Robert L. Hettich
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven D. Brown
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lee R. Lynd
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | | | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Corresponding author. E-mail:
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Falter C, Zwikowics C, Eggert D, Blümke A, Naumann M, Wolff K, Ellinger D, Reimer R, Voigt CA. Glucanocellulosic ethanol: the undiscovered biofuel potential in energy crops and marine biomass. Sci Rep 2015; 5:13722. [PMID: 26324382 PMCID: PMC4555182 DOI: 10.1038/srep13722] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/27/2015] [Indexed: 12/17/2022] Open
Abstract
Converting biomass to biofuels is a key strategy in substituting fossil fuels to mitigate climate change. Conventional strategies to convert lignocellulosic biomass to ethanol address the fermentation of cellulose-derived glucose. Here we used super-resolution fluorescence microscopy to uncover the nanoscale structure of cell walls in the energy crops maize and Miscanthus where the typical polymer cellulose forms an unconventional layered architecture with the atypical (1, 3)-β-glucan polymer callose. This raised the question about an unused potential of (1, 3)-β-glucan in the fermentation of lignocellulosic biomass. Engineering biomass conversion for optimized (1, 3)-β-glucan utilization, we increased the ethanol yield from both energy crops. The generation of transgenic Miscanthus lines with an elevated (1, 3)-β-glucan content further increased ethanol yield providing a new strategy in energy crop breeding. Applying the (1, 3)-β-glucan-optimized conversion method on marine biomass from brown macroalgae with a naturally high (1, 3)-β-glucan content, we not only substantially increased ethanol yield but also demonstrated an effective co-fermentation of plant and marine biomass. This opens new perspectives in combining different kinds of feedstock for sustainable and efficient biofuel production, especially in coastal regions.
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Affiliation(s)
- Christian Falter
- Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Claudia Zwikowics
- Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Dennis Eggert
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Antje Blümke
- Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Marcel Naumann
- Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Kerstin Wolff
- Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Dorothea Ellinger
- Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Rudolph Reimer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Christian A Voigt
- Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
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Sand A, Holwerda EK, Ruppertsberger NM, Maloney M, Olson DG, Nataf Y, Borovok I, Sonenshein AL, Bayer EA, Lamed R, Lynd LR, Shoham Y. Three cellulosomal xylanase genes inClostridium thermocellumare regulated by both vegetative SigA (σA) and alternative SigI6 (σI6) factors. FEBS Lett 2015; 589:3133-40. [DOI: 10.1016/j.febslet.2015.08.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/10/2015] [Accepted: 08/14/2015] [Indexed: 11/29/2022]
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Development of a regulatable plasmid-based gene expression system for Clostridium thermocellum. Appl Microbiol Biotechnol 2015; 99:7589-99. [DOI: 10.1007/s00253-015-6610-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/07/2015] [Accepted: 04/15/2015] [Indexed: 01/31/2023]
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Akinosho H, Yee K, Close D, Ragauskas A. The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications. Front Chem 2014; 2:66. [PMID: 25207268 PMCID: PMC4143619 DOI: 10.3389/fchem.2014.00066] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/28/2014] [Indexed: 01/25/2023] Open
Abstract
First isolated in 1926, Clostridium thermocellum has recently received increased attention as a high utility candidate for use in consolidated bioprocessing (CBP) applications. These applications, which seek to process lignocellulosic biomass directly into useful products such as ethanol, are gaining traction as economically feasible routes toward the production of fuel and other high value chemical compounds as the shortcomings of fossil fuels become evident. This review evaluates C. thermocellum's role in this transitory process by highlighting recent discoveries relating to its genomic, transcriptomic, proteomic, and metabolomic responses to varying biomass sources, with a special emphasis placed on providing an overview of its unique, multivariate enzyme cellulosome complex and the role that this structure performs during biomass degradation. Both naturally evolved and genetically engineered strains are examined in light of their unique attributes and responses to various biomass treatment conditions, and the genetic tools that have been employed for their creation are presented. Several future routes for potential industrial usage are presented, and it is concluded that, although there have been many advances to significantly improve C. thermocellum's amenability to industrial use, several hurdles still remain to be overcome as this unique organism enjoys increased attention within the scientific community.
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Affiliation(s)
- Hannah Akinosho
- School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology Atlanta, GA, USA ; Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA
| | - Kelsey Yee
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dan Close
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Arthur Ragauskas
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Department of Chemical and Biomolecular Engineering and Department of Forestry, Wildlife, and Fisheries, University of Tennessee Knoxville, TN, USA
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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47
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Wei H, Fu Y, Magnusson L, Baker JO, Maness PC, Xu Q, Yang S, Bowersox A, Bogorad I, Wang W, Tucker MP, Himmel ME, Ding SY. Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq. Front Microbiol 2014; 5:142. [PMID: 24782837 PMCID: PMC3990059 DOI: 10.3389/fmicb.2014.00142] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/19/2014] [Indexed: 01/01/2023] Open
Abstract
The anaerobic, thermophilic bacterium, Clostridium thermocellum, secretes multi-protein enzyme complexes, termed cellulosomes, which synergistically interact with the microbial cell surface and efficiently disassemble plant cell wall biomass. C. thermocellum has also been considered a potential consolidated bioprocessing (CBP) organism due to its ability to produce the biofuel products, hydrogen, and ethanol. We found that C. thermocellum fermentation of pretreated yellow poplar (PYP) produced 30 and 39% of ethanol and hydrogen product concentrations, respectively, compared to fermentation of cellobiose. RNA-seq was used to analyze the transcriptional profiles of these cells. The PYP-grown cells taken for analysis at the late stationary phase showed 1211 genes up-regulated and 314 down-regulated by more than two-fold compared to the cellobiose-grown cells. These affected genes cover a broad spectrum of specific functional categories. The transcriptional analysis was further validated by sub-proteomics data taken from the literature; as well as by quantitative reverse transcription-PCR (qRT-PCR) analyses of selected genes. Specifically, 47 cellulosomal protein-encoding genes, genes for 4 pairs of SigI-RsgI for polysaccharide sensing, 7 cellodextrin ABC transporter genes, and a set of NAD(P)H hydogenase and alcohol dehydrogenase genes were up-regulated for cells growing on PYP compared to cellobiose. These genes could be potential candidates for future studies aimed at gaining insight into the regulatory mechanism of this organism as well as for improvement of C. thermocellum in its role as a CBP organism.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Yan Fu
- Center for Plant Genomics, Iowa State University Ames, IA, USA
| | - Lauren Magnusson
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Andrew Bowersox
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA ; National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Igor Bogorad
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Melvin P Tucker
- National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
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Wilson CM, Rodriguez M, Johnson CM, Martin SL, Chu TM, Wolfinger RD, Hauser LJ, Land ML, Klingeman DM, Syed MH, Ragauskas AJ, Tschaplinski TJ, Mielenz JR, Brown SD. Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:179. [PMID: 24295562 PMCID: PMC3880215 DOI: 10.1186/1754-6834-6-179] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/19/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. The aim of this study was to investigate C. thermocellum genes required to ferment biomass substrates and to conduct a robust comparison of DNA microarray and RNA sequencing (RNA-seq) analytical platforms. RESULTS C. thermocellum ATCC 27405 fermentations were conducted with a 5 g/L solid substrate loading of either pretreated switchgrass or Populus. Quantitative saccharification and inductively coupled plasma emission spectroscopy (ICP-ES) for elemental analysis revealed composition differences between biomass substrates, which may have influenced growth and transcriptomic profiles. High quality RNA was prepared for C. thermocellum grown on solid substrates and transcriptome profiles were obtained for two time points during active growth (12 hours and 37 hours postinoculation). A comparison of two transcriptomic analytical techniques, microarray and RNA-seq, was performed and the data analyzed for statistical significance. Large expression differences for cellulosomal genes were not observed. We updated gene predictions for the strain and a small novel gene, Cthe_3383, with a putative AgrD peptide quorum sensing function was among the most highly expressed genes. RNA-seq data also supported different small regulatory RNA predictions over others. The DNA microarray gave a greater number (2,351) of significant genes relative to RNA-seq (280 genes when normalized by the kernel density mean of M component (KDMM) method) in an analysis of variance (ANOVA) testing method with a 5% false discovery rate (FDR). When a 2-fold difference in expression threshold was applied, 73 genes were significantly differentially expressed in common between the two techniques. Sulfate and phosphate uptake/utilization genes, along with genes for a putative efflux pump system were some of the most differentially regulated transcripts when profiles for C. thermocellum grown on either pretreated switchgrass or Populus were compared. CONCLUSIONS Our results suggest that a high degree of agreement in differential gene expression measurements between transcriptomic platforms is possible, but choosing an appropriate normalization regime is essential.
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Affiliation(s)
- Charlotte M Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Courtney M Johnson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | | | | | - Loren J Hauser
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Miriam L Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dawn M Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mustafa H Syed
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Arthur J Ragauskas
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jonathan R Mielenz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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49
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Sandoval-Espinola WJ, Makwana ST, Chinn MS, Thon MR, Azcárate-Peril MA, Bruno-Bárcena JM. Comparative phenotypic analysis and genome sequence of Clostridium beijerinckii SA-1, an offspring of NCIMB 8052. MICROBIOLOGY (READING, ENGLAND) 2013; 159:2558-2570. [PMID: 24068240 PMCID: PMC7336276 DOI: 10.1099/mic.0.069534-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 09/24/2013] [Indexed: 01/07/2023]
Abstract
Production of butanol by solventogenic clostridia is controlled through metabolic regulation of the carbon flow and limited by its toxic effects. To overcome cell sensitivity to solvents, stress-directed evolution methodology was used three decades ago on Clostridium beijerinckii NCIMB 8052 that spawned the SA-1 strain. Here, we evaluated SA-1 solventogenic capabilities when growing on a previously validated medium containing, as carbon- and energy-limiting substrates, sucrose and the products of its hydrolysis d-glucose and d-fructose and only d-fructose. Comparative small-scale batch fermentations with controlled pH (pH 6.5) showed that SA-1 is a solvent hyper-producing strain capable of generating up to 16.1 g l(-1) of butanol and 26.3 g l(-1) of total solvents, 62.3 % and 63 % more than NCIMB 8052, respectively. This corresponds to butanol and solvent yields of 0.3 and 0.49 g g(-1), respectively (63 % and 65 % increase compared with NCIMB 8052). SA-1 showed a deficiency in d-fructose transport as suggested by its 7 h generation time compared with 1 h for NCIMB 8052. To potentially correlate physiological behaviour with genetic mutations, the whole genome of SA-1 was sequenced using the Illumina GA IIx platform. PCR and Sanger sequencing were performed to analyse the putative variations. As a result, four errors were confirmed and validated in the reference genome of NCIMB 8052 and a total of 10 genetic polymorphisms in SA-1. The genetic polymorphisms included eight single nucleotide variants, one small deletion and one large insertion that it is an additional copy of the insertion sequence ISCb1. Two of the genetic polymorphisms, the serine threonine phosphatase cbs_4400 and the solute binding protein cbs_0769, may possibly explain some of the observed physiological behaviour, such as rerouting of the metabolic carbon flow, deregulation of the d-fructose phosphotransferase transport system and delayed sporulation.
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Affiliation(s)
| | - Satya T. Makwana
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695-7615, USA
| | - Mari S. Chinn
- Department of Biological and Agricultural Engineering, North Carolina State University, Raleigh, NC 27695-7615, USA
| | - Michael R. Thon
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Calle Del Duero 12, Villamayor 37185, Spain
| | - M. Andrea Azcárate-Peril
- Department of Cell Biology and Physiology, School of Medicine and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC 27599-7545, USA
| | - José M. Bruno-Bárcena
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695-7615, USA
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50
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Wilson CM, Yang S, Rodriguez M, Ma Q, Johnson CM, Dice L, Xu Y, Brown SD. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:131. [PMID: 24028713 PMCID: PMC3848806 DOI: 10.1186/1754-6834-6-131] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 09/04/2013] [Indexed: 05/23/2023]
Abstract
BACKGROUND The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. A previous C. thermocellum ethanol stress study showed that the largest transcriptomic response was in genes and proteins related to nitrogen uptake and metabolism. RESULTS In this study, C. thermocellum was grown to mid-exponential phase and treated with furfural or heat to a final concentration of 3 g.L-1 or 68°C respectively to investigate general and specific physiological and regulatory stress responses. Samples were taken at 10, 30, 60 and 120 min post-shock, and from untreated control fermentations, for transcriptomic analyses and fermentation product determinations and compared to a published dataset from an ethanol stress study. Urea uptake genes were induced following furfural stress, but not to the same extent as ethanol stress and transcription from these genes was largely unaffected by heat stress. The largest transcriptomic response to furfural stress was genes for sulfate transporter subunits and enzymes in the sulfate assimilatory pathway, although these genes were also affected late in the heat and ethanol stress responses. Lactate production was higher in furfural treated culture, although the lactate dehydrogenase gene was not differentially expressed under this condition. Other redox related genes such as a copy of the rex gene, a bifunctional acetaldehyde-CoA/alcohol dehydrogenase and adjacent genes did show lower expression after furfural stress compared to the control, heat and ethanol fermentation profiles. Heat stress induced expression from chaperone related genes and overlap was observed with the responses to the other stresses. This study suggests the involvement of C. thermocellum genes with functions in oxidative stress protection, electron transfer, detoxification, sulfur and nitrogen acquisition, and DNA repair mechanisms in its stress responses and the use of different regulatory networks to coordinate and control adaptation. CONCLUSIONS This study has identified C. thermocellum gene regulatory motifs and aspects of physiology and gene regulation for further study. The nexus between future systems biology studies and recently developed genetic tools for C. thermocellum offers the potential for more rapid strain development and for broader insights into this organism's physiology and regulation.
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Affiliation(s)
- Charlotte M Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Shihui Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Present address: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Qin Ma
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Courtney M Johnson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lezlee Dice
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Ying Xu
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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