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Novak JK, Gardner JG. Current models in bacterial hemicellulase-encoding gene regulation. Appl Microbiol Biotechnol 2024; 108:39. [PMID: 38175245 PMCID: PMC10766802 DOI: 10.1007/s00253-023-12977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The discovery and characterization of bacterial carbohydrate-active enzymes is a fundamental component of biotechnology innovation, particularly for renewable fuels and chemicals; however, these studies have increasingly transitioned to exploring the complex regulation required for recalcitrant polysaccharide utilization. This pivot is largely due to the current need to engineer and optimize enzymes for maximal degradation in industrial or biomedical applications. Given the structural simplicity of a single cellulose polymer, and the relatively few enzyme classes required for complete bioconversion, the regulation of cellulases in bacteria has been thoroughly discussed in the literature. However, the diversity of hemicelluloses found in plant biomass and the multitude of carbohydrate-active enzymes required for their deconstruction has resulted in a less comprehensive understanding of bacterial hemicellulase-encoding gene regulation. Here we review the mechanisms of this process and common themes found in the transcriptomic response during plant biomass utilization. By comparing regulatory systems from both Gram-negative and Gram-positive bacteria, as well as drawing parallels to cellulase regulation, our goals are to highlight the shared and distinct features of bacterial hemicellulase-encoding gene regulation and provide a set of guiding questions to improve our understanding of bacterial lignocellulose utilization. KEY POINTS: • Canonical regulatory mechanisms for bacterial hemicellulase-encoding gene expression include hybrid two-component systems (HTCS), extracytoplasmic function (ECF)-σ/anti-σ systems, and carbon catabolite repression (CCR). • Current transcriptomic approaches are increasingly being used to identify hemicellulase-encoding gene regulatory patterns coupled with computational predictions for transcriptional regulators. • Future work should emphasize genetic approaches to improve systems biology tools available for model bacterial systems and emerging microbes with biotechnology potential. Specifically, optimization of Gram-positive systems will require integration of degradative and fermentative capabilities, while optimization of Gram-negative systems will require bolstering the potency of lignocellulolytic capabilities.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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2
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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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3
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Laemthong T, Bing RG, Crosby JR, Manesh MJH, Adams MWW, Kelly RM. Role of cell-substrate association during plant biomass solubilization by the extreme thermophile Caldicellulosiruptor bescii. Extremophiles 2023; 27:6. [PMID: 36802247 PMCID: PMC10514702 DOI: 10.1007/s00792-023-01290-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023]
Abstract
Caldicellulosiruptor species are proficient at solubilizing carbohydrates in lignocellulosic biomass through surface (S)-layer bound and secretomic glycoside hydrolases. Tāpirins, surface-associated, non-catalytic binding proteins in Caldicellulosiruptor species, bind tightly to microcrystalline cellulose, and likely play a key role in natural environments for scavenging scarce carbohydrates in hot springs. However, the question arises: If tāpirin concentration on Caldicellulosiruptor cell walls increased above native levels, would this offer any benefit to lignocellulose carbohydrate hydrolysis and, hence, biomass solubilization? This question was addressed by engineering the genes for tight-binding, non-native tāpirins into C. bescii. The engineered C. bescii strains bound more tightly to microcrystalline cellulose (Avicel) and biomass compared to the parent. However, tāpirin overexpression did not significantly improve solubilization or conversion for wheat straw or sugarcane bagasse. When incubated with poplar, the tāpirin-engineered strains increased solubilization by 10% compared to the parent, and corresponding acetate production, a measure of carbohydrate fermentation intensity, was 28% higher for the Calkr_0826 expression strain and 18.5% higher for the Calhy_0908 expression strain. These results show that enhanced binding to the substrate, beyond the native capability, did not improve C. bescii solubilization of plant biomass, but in some cases may improve conversion of released lignocellulose carbohydrates to fermentation products.
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Affiliation(s)
- Tunyaboon Laemthong
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
- Department of Chemical Engineering, Thammasat University, Pathum Thani, 12120, Thailand
| | - Ryan G Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - James R Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Mohamad J H Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA.
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4
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Swinnen S, Zurek C, Krämer M, Heger RM, Domeyer JE, Ziegler J, Svetlitchnyi VA, Läufer A. A novel SfaNI-like restriction-modification system in Caldicellulosiruptor extents the genetic engineering toolbox for this genus. PLoS One 2022; 17:e0279562. [PMID: 36580476 PMCID: PMC9799307 DOI: 10.1371/journal.pone.0279562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/11/2022] [Indexed: 12/30/2022] Open
Abstract
Caldicellulosiruptor is a genus of thermophilic to hyper-thermophilic microorganisms that express and secrete an arsenal of enzymes degrading lignocellulosic biomasses into fermentable sugars. Because of this distinguished feature, strains of Caldicellulosiruptor have been considered as promising candidates for consolidated bioprocessing. Although a few Caldicellulosiruptor strains with industrially relevant characteristics have been isolated to date, it is apparent that further improvement of the strains is essential for industrial application. The earlier identification of the HaeIII-like restriction-modification system in C. bescii strain DSM 6725 has formed the basis for genetic methods with the aim to improve the strain's lignocellulolytic activity and ethanol production. In this study, a novel SfaNI-like restriction-modification system was identified in Caldicellulosiruptor sp. strain BluCon085, consisting of an endonuclease and two methyltransferases that recognize the reverse-complement sequences 5'-GATGC-3' and 5'-GCATC-3'. Methylation of the adenine in both sequences leads to an asymmetric methylation pattern in the genomic DNA of strain BluCon085. Proteins with high percentage of identity to the endonuclease and two methyltransferases were identified in the genomes of C. saccharolyticus strain DSM 8903, C. naganoensis strain DSM 8991, C. changbaiensis strain DSM 26941 and Caldicellulosiruptor sp. strain F32, suggesting that a similar restriction-modification system may be active also in these strains and respective species. We show that methylation of plasmid and linear DNA by the identified methyltransferases, obtained by heterologous expression in Escherichia coli, is sufficient for successful transformation of Caldicellulosiruptor sp. strain DIB 104C. The genetic engineering toolbox developed in this study forms the basis for rational strain improvement of strain BluCon085, a derivative from strain DIB 104C with exceptionally high L-lactic acid production. The toolbox may also work for other species of the genus Caldicellulosiruptor that have so far not been genetically tractable.
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5
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Liang J, van Kranenburg R, Bolhuis A, Leak DJ. Removing carbon catabolite repression in Parageobacillus thermoglucosidasius DSM 2542. Front Microbiol 2022; 13:985465. [PMID: 36338101 PMCID: PMC9631020 DOI: 10.3389/fmicb.2022.985465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Parageobacillus thermoglucosidasius is a thermophilic bacterium of interest for lignocellulosic biomass fermentation. However, carbon catabolite repression (CCR) hinders co-utilization of pentoses and hexoses in the biomass substrate. Hence, to optimize the fermentation process, it is critical to remove CCR in the fermentation strains with minimal fitness cost. In this study, we investigated whether CCR could be removed from P. thermoglucosidasius DSM 2542 by mutating the Ser46 regulatory sites on HPr and Crh to a non-reactive alanine residue. It was found that neither the ptsH1 (HPr-S46A) nor the crh1 (Crh-S46A) mutation individually eliminated CCR in P. thermoglucosidasius DSM 2542. However, it was not possible to generate a ptsH1 crh1 double mutant. While the Crh-S46A mutation had no obvious fitness effect in DSM 2542, the ptsH1 mutation had a negative impact on cell growth and sugar utilization under fermentative conditions. Under these conditions, the ptsH1 mutation was associated with the production of a brown pigment, believed to arise from methylglyoxal production, which is harmful to cells. Subsequently, a less directed adaptive evolution approach was employed, in which DSM 2542 was grown in a mixture of 2-deoxy-D-glucose(2-DG) and xylose. This successfully removed CCR from P. thermoglucosidasius DSM 2542. Two selection strategies were applied to optimize the phenotypes of evolved strains. Genome sequencing identified key mutations affecting the PTS components PtsI and PtsG, the ribose operon repressor RbsR and adenine phosphoribosyltransferase APRT. Genetic complementation and bioinformatics analysis revealed that the presence of wild type rbsR and apt inhibited xylose uptake or utilization, while ptsI and ptsG might play a role in the regulation of CCR in P. thermoglucosidasius DSM 2542.
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Affiliation(s)
- Jinghui Liang
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Centre for Sustainable and Circular Technologies (CSCT), University of Bath, Bath, United Kingdom
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
- Corbion, Gorinchem, Netherlands
| | - Albert Bolhuis
- Department of Pharmacy and Pharmacology, Centre for Therapeutic Innovation, University of Bath, Bath, United Kingdom
| | - David J. Leak
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Centre for Sustainable and Circular Technologies (CSCT), University of Bath, Bath, United Kingdom
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6
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Bing RG, Straub CT, Sulis DB, Wang JP, Adams MWW, Kelly RM. Plant biomass fermentation by the extreme thermophile Caldicellulosiruptor bescii for co-production of green hydrogen and acetone: Technoeconomic analysis. BIORESOURCE TECHNOLOGY 2022; 348:126780. [PMID: 35093526 PMCID: PMC10560548 DOI: 10.1016/j.biortech.2022.126780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/18/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
A variety of chemical and biological processes have been proposed for conversion of sustainable low-cost feedstocks into industrial products. Here, a biorefinery concept is formulated, modeled, and analyzed in which a naturally (hemi)cellulolytic and extremely thermophilic bacterium, Caldicellulosiruptor bescii, is metabolically engineered to convert the carbohydrate content of lignocellulosic biomasses (i.e., soybean hulls, transgenic poplar) into green hydrogen and acetone. Experimental validation of C. bescii fermentative performance demonstrated 82% carbohydrate solubilization of soybean hulls and 55% for transgenic poplar. A detailed technical design, including equipment specifications, provides the basis for an economic analysis that establishes metabolic engineering targets. This robust industrial process leveraging metabolically engineered C. bescii yields 206 kg acetone and 25 kg H2 per metric ton of soybean hull, or 174 kg acetone and 21 kg H2 per metric ton transgenic poplar. Beyond this specific case, the model demonstrates industrial feasibility and economic advantages of thermophilic fermentation.
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Affiliation(s)
- Ryan G Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Daniel B Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Jack P Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States.
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7
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Liang J, Roberts A, van Kranenburg R, Bolhuis A, Leak DJ. Relaxed control of sugar utilization in Parageobacillus thermoglucosidasius DSM 2542. Microbiol Res 2021; 256:126957. [PMID: 35032723 DOI: 10.1016/j.micres.2021.126957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/22/2021] [Accepted: 12/27/2021] [Indexed: 01/08/2023]
Abstract
Though carbon catabolite repression (CCR) has been intensively studied in some more characterised organisms, there is a lack of information of CCR in thermophiles. In this work, CCR in the thermophile, Parageobacillus thermoglucosidasius DSM 2542 has been studied during growth on pentose sugars in the presence of glucose. Physiological studies under fermentative conditions revealed a loosely controlled CCR when DSM 2542 was grown in minimal medium supplemented with a mixture of glucose and xylose. This atypical CCR pattern was also confirmed by studying xylose isomerase expression level by qRT-PCR. Fortuitously, the pheB gene, which encodes catechol 2, 3-dioxygenase was found to have a cre site highly similar to the consensus catabolite-responsive element (cre) at its 3' end and was used to confirm that expression of pheB from a plasmid was under stringent CCR control. Bioinformatic analysis suggested that the CCR regulation of xylose metabolism in P. thermoglucosidasius DSM 2542 might occur primarily via control of expression of pentose transporter operons. Relaxed control of sugar utilization might reflect a lower affinity of the CcpA-HPr (Ser46-P) or CcpA-Crh (Ser46-P) complexes to the cre(s) in these operons.
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Affiliation(s)
- Jinghui Liang
- Department of Biology and Biochemistry, University of Bath, UK.
| | - Adam Roberts
- Department of Biology and Biochemistry, University of Bath, UK
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, The Netherlands; Corbion, Arkelsedijk 46, 4206 AC, Gorinchem, The Netherlands
| | - Albert Bolhuis
- Department of Pharmacy and Pharmacology, University of Bath, UK
| | - David J Leak
- Department of Biology and Biochemistry, University of Bath, UK
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8
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Byrne E, Björkmalm J, Bostick JP, Sreenivas K, Willquist K, van Niel EWJ. Characterization and adaptation of Caldicellulosiruptor strains to higher sugar concentrations, targeting enhanced hydrogen production from lignocellulosic hydrolysates. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:210. [PMID: 34717729 PMCID: PMC8557575 DOI: 10.1186/s13068-021-02058-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The members of the genus Caldicellulosiruptor have the potential for future integration into a biorefinery system due to their capacity to generate hydrogen close to the theoretical limit of 4 mol H2/mol hexose, use a wide range of sugars and can grow on numerous lignocellulose hydrolysates. However, members of this genus are unable to survive in high sugar concentrations, limiting their ability to grow on more concentrated hydrolysates, thus impeding their industrial applicability. In this study five members of this genus, C. owensensis, C. kronotskyensis, C. bescii, C. acetigenus and C. kristjanssonii, were developed to tolerate higher sugar concentrations through an adaptive laboratory evolution (ALE) process. The developed mixed population C. owensensis CO80 was further studied and accompanied by the development of a kinetic model based on Monod kinetics to quantitatively compare it with the parental strain. RESULTS Mixed populations of Caldicellulosiruptor tolerant to higher glucose concentrations were obtained with C. owensensis adapted to grow up to 80 g/L glucose; other strains in particular C. kristjanssonii demonstrated a greater restriction to adaptation. The C. owensensis CO80 mixed population was further studied and demonstrated the ability to grow in glucose concentrations up to 80 g/L glucose, but with reduced volumetric hydrogen productivities ([Formula: see text]) and incomplete sugar conversion at elevated glucose concentrations. In addition, the carbon yield decreased with elevated concentrations of glucose. The ability of the mixed population C. owensensis CO80 to grow in high glucose concentrations was further described with a kinetic growth model, which revealed that the critical sugar concentration of the cells increased fourfold when cultivated at higher concentrations. When co-cultured with the adapted C. saccharolyticus G5 mixed culture at a hydraulic retention time (HRT) of 20 h, C. owensensis constituted only 0.09-1.58% of the population in suspension. CONCLUSIONS The adaptation of members of the Caldicellulosiruptor genus to higher sugar concentrations established that the ability to develop improved strains via ALE is species dependent, with C. owensensis adapted to grow on 80 g/L, whereas C. kristjanssonii could only be adapted to 30 g/L glucose. Although C. owensensis CO80 was adapted to a higher sugar concentration, this mixed population demonstrated reduced [Formula: see text] with elevated glucose concentrations. This would indicate that while ALE permits adaptation to elevated sugar concentrations, this approach does not result in improved fermentation performances at these higher sugar concentrations. Moreover, the observation that planktonic mixed culture of CO80 was outcompeted by an adapted C. saccharolyticus, when co-cultivated in continuous mode, indicates that the robustness of CO80 mixed culture should be improved for industrial application.
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Affiliation(s)
- Eoin Byrne
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00, Lund, Sweden
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland
| | - Johanna Björkmalm
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00, Lund, Sweden
- RISE, Ideon Science Park, Building Beta 2 3v Scheelevägen 17, 22370, Lund, Sweden
| | - James P Bostick
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00, Lund, Sweden
- Coriolis Pharma Research GmbH, Fraunhoferstrasse 18B, 82152, Planegg, Germany
| | - Krishnan Sreenivas
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00, Lund, Sweden
| | - Karin Willquist
- RISE, Ideon Science Park, Building Beta 2 3v Scheelevägen 17, 22370, Lund, Sweden
| | - Ed W J van Niel
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00, Lund, Sweden.
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Rodionov DA, Rodionova IA, Rodionov VA, Arzamasov AA, Zhang K, Rubinstein GM, Tanwee TNN, Bing RG, Crosby JR, Nookaew I, Basen M, Brown SD, Wilson CM, Klingeman DM, Poole FL, Zhang Y, Kelly RM, Adams MWW. Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii. mSystems 2021; 6:e0134520. [PMID: 34060910 PMCID: PMC8579813 DOI: 10.1128/msystems.01345-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/04/2021] [Indexed: 11/20/2022] Open
Abstract
Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade polysaccharide components of plant cell walls and subsequently utilize the constituting mono- and oligosaccharides. Through metabolic engineering, ethanol and other industrially important end products can be produced. Previous experimental studies identified a variety of carbohydrate-active enzymes in model species Caldicellulosiruptor saccharolyticus and Caldicellulosiruptor bescii, while prior transcriptomic experiments identified their putative carbohydrate uptake transporters. We investigated the mechanisms of transcriptional regulation of carbohydrate utilization genes using a comparative genomics approach applied to 14 Caldicellulosiruptor species. The reconstruction of carbohydrate utilization regulatory network includes the predicted binding sites for 34 mostly local regulators and point to the regulatory mechanisms controlling expression of genes involved in degradation of plant biomass. The Rex and CggR regulons control the central glycolytic and primary redox reactions. The identified transcription factor binding sites and regulons were validated with transcriptomic and transcription start site experimental data for C. bescii grown on cellulose, cellobiose, glucose, xylan, and xylose. The XylR and XynR regulons control xylan-induced transcriptional response of genes involved in degradation of xylan and xylose utilization. The reconstructed regulons informed the carbohydrate utilization reconstruction analysis and improved functional annotations of 51 transporters and 11 catabolic enzymes. Using gene deletion, we confirmed that the shared ATPase component MsmK is essential for growth on oligo- and polysaccharides but not for the utilization of monosaccharides. By elucidating the carbohydrate utilization framework in C. bescii, strategies for metabolic engineering can be pursued to optimize yields of bio-based fuels and chemicals from lignocellulose. IMPORTANCE To develop functional metabolic engineering platforms for nonmodel microorganisms, a comprehensive understanding of the physiological and metabolic characteristics is critical. Caldicellulosiruptor bescii and other species in this genus have untapped potential for conversion of unpretreated plant biomass into industrial fuels and chemicals. The highly interactive and complex machinery used by C. bescii to acquire and process complex carbohydrates contained in lignocellulose was elucidated here to complement related efforts to develop a metabolic engineering platform with this bacterium. Guided by the findings here, a clearer picture of how C. bescii natively drives carbohydrate utilization is provided and strategies to engineer this bacterium for optimal conversion of lignocellulose to commercial products emerge.
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Affiliation(s)
- Dmitry A. Rodionov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Irina A. Rodionova
- Department of Bioengineering, University of California—San Diego, La Jolla, California, USA
| | - Vladimir A. Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandr A. Arzamasov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Ke Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Gabriel M. Rubinstein
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Tania N. N. Tanwee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - James R. Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mirko Basen
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Biowissenschaften, Mikrobiologie, Universität Rostock, Rostock, Germany
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Charlotte M. Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- University of Otago, Dunedin, New Zealand
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Farris L. Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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10
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Costantini PE, Firrincieli A, Fedi S, Parolin C, Viti C, Cappelletti M, Vitali B. Insight into phenotypic and genotypic differences between vaginal Lactobacillus crispatus BC5 and Lactobacillus gasseri BC12 to unravel nutritional and stress factors influencing their metabolic activity. Microb Genom 2021; 7. [PMID: 34096840 PMCID: PMC8461478 DOI: 10.1099/mgen.0.000575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The vaginal microbiota, normally characterized by lactobacilli presence, is crucial for vaginal health. Members belonging to L. crispatus and L. gasseri species exert crucial protective functions against pathogens, although a total comprehension of factors that influence their dominance in healthy women is still lacking. Here we investigated the complete genome sequence and comprehensive phenotypic profile of L. crispatus strain BC5 and L. gasseri strain BC12, two vaginal strains featured by anti-bacterial and anti-viral activities. Phenotype microarray (PM) results revealed an improved capacity of BC5 to utilize different carbon sources as compared to BC12, although some specific carbon sources that can be associated to the human diet were only metabolized by BC12, i.e. uridine, amygdalin, tagatose. Additionally, the two strains were mostly distinct in the capacity to utilize the nitrogen sources under analysis. On the other hand, BC12 showed tolerance/resistance towards twice the number of stressors (i.e. antibiotics, toxic metals etc.) with respect to BC5. The divergent phenotypes observed in PM were supported by the identification in either BC5 or BC12 of specific genetic determinants that were found to be part of the core genome of each species. The PM results in combination with comparative genome data provide insights into the possible environmental factors and genetic traits supporting the predominance of either L. crispatus BC5 or L. gasseri BC12 in the vaginal niche, giving also indications for metabolic predictions at the species level.
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Affiliation(s)
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Carlo Viti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Beatrice Vitali
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
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Vongkampang T, Sreenivas K, Engvall J, Grey C, van Niel EWJ. Characterization of simultaneous uptake of xylose and glucose in Caldicellulosiruptor kronotskyensis for optimal hydrogen production. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:91. [PMID: 33832529 PMCID: PMC8034154 DOI: 10.1186/s13068-021-01938-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Caldicellulosiruptor kronotskyensis has gained interest for its ability to grow on various lignocellulosic biomass. The aim of this study was to investigate the growth profiles of C. kronotskyensis in the presence of mixtures of glucose-xylose. Recently, we characterized a diauxic-like pattern for C. saccharolyticus on lignocellulosic sugar mixtures. In this study, we aimed to investigate further whether C. kronotskyensis has adapted to uptake glucose in the disaccharide form (cellobiose) rather than the monosaccharide (glucose). RESULTS Interestingly, growth of C. kronotskyensis on glucose and xylose mixtures did not display diauxic-like growth patterns. Closer investigation revealed that, in contrast to C. saccharolyticus, C. kronotskyensis does not possess a second uptake system for glucose. Both C. saccharolyticus and C. kronotskyensis share the characteristics of preferring xylose over glucose. Growth on xylose was twice as fast (μmax = 0.57 h-1) as on glucose (μmax = 0.28 h-1). A study of the sugar uptake was made with different glucose-xylose ratios to find a kinetic relationship between the two sugars for transport into the cell. High concentrations of glucose inhibited xylose uptake and vice versa. The inhibition constants were estimated to be KI,glu = 0.01 cmol L-1 and KI,xyl = 0.001 cmol L-1, hence glucose uptake was more severely inhibited by xylose uptake. Bioinformatics analysis could not exclude that C. kronotskyensis possesses more than one transporter for glucose. As a next step it was investigated whether glucose uptake by C. kronotskyensis improved in the form of cellobiose. Indeed, cellobiose is taken up faster than glucose; nevertheless, the growth rate on each sugar remained similar. CONCLUSIONS C. kronotskyensis possesses a xylose transporter that might take up glucose at an inferior rate even in the absence of xylose. Alternatively, glucose can be taken up in the form of cellobiose, but growth performance is still inferior to growth on xylose. Therefore, we propose that the catabolism of C. kronotskyensis has adapted more strongly to pentose rather than hexose, thereby having obtained a specific survival edge in thermophilic lignocellulosic degradation communities.
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Affiliation(s)
- Thitiwut Vongkampang
- Division of Applied Microbiology, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
| | - Krishnan Sreenivas
- Division of Applied Microbiology, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Jonathan Engvall
- Division of Applied Microbiology, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Carl Grey
- Division of Biotechnology, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Ed W J van Niel
- Division of Applied Microbiology, Lund University, P.O. Box 124, 221 00, Lund, Sweden
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Yun JH, Cho DH, Lee B, Lee YJ, Choi DY, Kim HS, Chang YK. Utilization of the acid hydrolysate of defatted Chlorella biomass as a sole fermentation substrate for the production of biosurfactant from Bacillus subtilis C9. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101868] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Sander KB, Chung D, Klingeman DM, Giannone RJ, Rodriguez M, Whitham J, Hettich RL, Davison BH, Westpheling J, Brown SD. Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:50. [PMID: 32190115 PMCID: PMC7071700 DOI: 10.1186/s13068-020-01690-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/27/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Caldicellulosiruptor bescii, a promising biocatalyst being developed for use in consolidated bioprocessing of lignocellulosic materials to ethanol, grows poorly and has reduced conversion at elevated medium osmolarities. Increasing tolerance to elevated fermentation osmolarities is desired to enable performance necessary of a consolidated bioprocessing (CBP) biocatalyst. RESULTS Two strains of C. bescii showing growth phenotypes in elevated osmolarity conditions were identified. The first strain, ORCB001, carried a deletion of the FapR fatty acid biosynthesis and malonyl-CoA metabolism repressor and had a severe growth defect when grown in high-osmolarity conditions-introduced as the addition of either ethanol, NaCl, glycerol, or glucose to growth media. The second strain, ORCB002, displayed a growth rate over three times higher than its genetic parent when grown in high-osmolarity medium. Unexpectedly, a genetic complement ORCB002 exhibited improved growth, failing to revert the observed phenotype, and suggesting that mutations other than the deleted transcription factor (the fruR/cra gene) are responsible for the growth phenotype observed in ORCB002. Genome resequencing identified several other genomic alterations (three deleted regions, three substitution mutations, one silent mutation, and one frameshift mutation), which may be responsible for the observed increase in osmolarity tolerance in the fruR/cra-deficient strain, including a substitution mutation in dnaK, a gene previously implicated in osmoresistance in bacteria. Differential expression analysis and transcription factor binding site inference indicates that FapR negatively regulates malonyl-CoA and fatty acid biosynthesis, as it does in many other bacteria. FruR/Cra regulates neighboring fructose metabolism genes, as well as other genes in global manner. CONCLUSIONS Two systems able to effect tolerance to elevated osmolarities in C. bescii are identified. The first is fatty acid biosynthesis. The other is likely the result of one or more unintended, secondary mutations present in another transcription factor deletion strain. Though the locus/loci and mechanism(s) responsible remain unknown, candidate mutations are identified, including a mutation in the dnaK chaperone coding sequence. These results illustrate both the promise of targeted regulatory manipulation for osmotolerance (in the case of fapR) and the challenges (in the case of fruR/cra).
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Affiliation(s)
- Kyle B. Sander
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN USA
- Present Address: Department of Bioengineering, University of California, Berkeley, Berkeley, CA USA
| | - Daehwan Chung
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Department of Genetics, University of Georgia, Athens, GA USA
- Present Address: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Dawn M. Klingeman
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Richard J. Giannone
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Miguel Rodriguez
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jason Whitham
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Present Address: Becton Dickinson Diagnostics, Sparks Glencoe, MD USA
| | - Robert L. Hettich
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Brian H. Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Janet Westpheling
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Department of Genetics, University of Georgia, Athens, GA USA
| | - Steven D. Brown
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Present Address: LanzaTech, Skokie, IL USA
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Blumer-Schuette SE. Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology. Microorganisms 2020; 8:E385. [PMID: 32164310 PMCID: PMC7142884 DOI: 10.3390/microorganisms8030385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 11/16/2022] Open
Abstract
Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place.
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Okonkwo O, Escudie R, Bernet N, Mangayil R, Lakaniemi AM, Trably E. Bioaugmentation enhances dark fermentative hydrogen production in cultures exposed to short-term temperature fluctuations. Appl Microbiol Biotechnol 2019; 104:439-449. [PMID: 31754763 PMCID: PMC6942602 DOI: 10.1007/s00253-019-10203-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/27/2019] [Accepted: 10/19/2019] [Indexed: 01/20/2023]
Abstract
Hydrogen-producing mixed cultures were subjected to a 48-h downward or upward temperature fluctuation from 55 to 35 or 75 °C. Hydrogen production was monitored during the fluctuations and for three consecutive batch cultivations at 55 °C to evaluate the impact of temperature fluctuations and bioaugmentation with synthetic mixed culture of known H2 producers either during or after the fluctuation. Without augmentation, H2 production was significantly reduced during the downward temperature fluctuation and no H2 was produced during the upward fluctuation. H2 production improved significantly during temperature fluctuation when bioaugmentation was applied to cultures exposed to downward or upward temperatures. However, when bioaugmentation was applied after the fluctuation, i.e., when the cultures were returned to 55 °C, the H2 yields obtained were between 1.6 and 5% higher than when bioaugmentation was applied during the fluctuation. Thus, the results indicate the usefulness of bioaugmentation in process recovery, especially if bioaugmentation time is optimised.
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Affiliation(s)
| | | | | | - Rahul Mangayil
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Aino-Maija Lakaniemi
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Eric Trably
- LBE, Univ Montpellier, INRA, Narbonne, France
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Mekonnen E, Kebede A, Tafesse T, Tafesse M. Investigation of carbon substrate utilization patterns of three ureolytic bacteria. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Watanabe S, Fukumori F, Nishiwaki H, Sakurai Y, Tajima K, Watanabe Y. Novel non-phosphorylative pathway of pentose metabolism from bacteria. Sci Rep 2019; 9:155. [PMID: 30655589 PMCID: PMC6336799 DOI: 10.1038/s41598-018-36774-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/30/2018] [Indexed: 11/09/2022] Open
Abstract
Pentoses, including D-xylose, L-arabinose, and D-arabinose, are generally phosphorylated to D-xylulose 5-phosphate in bacteria and fungi. However, in non-phosphorylative pathways analogous to the Entner-Dodoroff pathway in bacteria and archaea, such pentoses can be converted to pyruvate and glycolaldehyde (Route I) or α-ketoglutarate (Route II) via a 2-keto-3-deoxypentonate (KDP) intermediate. Putative gene clusters related to these metabolic pathways were identified on the genome of Herbaspirillum huttiense IAM 15032 using a bioinformatic analysis. The biochemical characterization of C785_RS13685, one of the components encoded to D-arabinonate dehydratase, differed from the known acid-sugar dehydratases. The biochemical characterization of the remaining components and a genetic expression analysis revealed that D- and L-KDP were converted not only to α-ketoglutarate, but also pyruvate and glycolate through the participation of dehydrogenase and hydrolase (Route III). Further analyses revealed that the Route II pathway of D-arabinose metabolism was not evolutionally related to the analogous pathway from archaea.
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Affiliation(s)
- Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan. .,Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan. .,Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
| | - Fumiyasu Fukumori
- Faculty of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan
| | - Hisashi Nishiwaki
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.,Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Yasuhiro Sakurai
- Department of Bio-molecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Kunihiko Tajima
- Department of Bio-molecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Yasuo Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.,Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
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Uncoupling Fermentative Synthesis of Molecular Hydrogen from Biomass Formation in Thermotoga maritima. Appl Environ Microbiol 2018; 84:AEM.00998-18. [PMID: 29959252 DOI: 10.1128/aem.00998-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/24/2018] [Indexed: 01/08/2023] Open
Abstract
When carbohydrates are fermented by the hyperthermophilic anaerobe Thermotoga maritima, molecular hydrogen (H2) is formed in strict proportion to substrate availability. Excretion of the organic acids acetate and lactate provide an additional sink for removal of excess reductant. However, mechanisms controlling energy management of these metabolic pathways are largely unexplored. To investigate this topic, transient gene inactivation was used to block lactate production as a strategy to produce spontaneous mutant cell lines that overproduced H2 through mutation of unpredicted genetic targets. Single-crossover homologous chromosomal recombination was used to disrupt lactate dehydrogenase (encoded by ldh) with a truncated ldh fused to a kanamycin resistance cassette expressed from a native P groESL promoter. Passage of the unstable recombinant resulted in loss of the genetic marker and recovery of evolved cell lines, including strain Tma200. Relative to the wild type, and considering the mass balance of fermentation substrate and products, Tma200 grew more slowly, produced H2 at levels above the physiologic limit, and simultaneously consumed less maltose while oxidizing it more efficiently. Whole-genome resequencing indicated that the ABC maltose transporter subunit, encoded by malK3, had undergone repeated mutation, and high-temperature anaerobic [14C]maltose transport assays demonstrated that the rate of maltose transport was reduced. Transfer of the malK3 mutation into a clean genetic background also conferred increased H2 production, confirming that the mutant allele was sufficient for increased H2 synthesis. These data indicate that a reduced rate of maltose uptake was accompanied by an increase in H2 production, changing fermentation efficiency and shifting energy management.IMPORTANCE Biorenewable energy sources are of growing interest to mitigate climate change, but like other commodities with nominal value, require innovation to maximize yields. Energetic considerations constrain production of many biofuels, such as molecular hydrogen (H2) because of the competing needs for cell mass synthesis and metabolite formation. Here we describe cell lines of the extremophile Thermotoga maritima that exceed the physiologic limits for H2 formation arising from genetic changes in fermentative metabolism. These cell lines were produced using a novel method called transient gene inactivation combined with adaptive laboratory evolution. Genome resequencing revealed unexpected changes in a maltose transport protein. Reduced rates of sugar uptake were accompanied by lower rates of growth and enhanced productivity of H2.
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19
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Björkmalm J, Byrne E, van Niel EWJ, Willquist K. A non-linear model of hydrogen production by Caldicellulosiruptor saccharolyticus for diauxic-like consumption of lignocellulosic sugar mixtures. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:175. [PMID: 29977336 PMCID: PMC6013967 DOI: 10.1186/s13068-018-1171-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Caldicellulosiruptor saccharolyticus is an attractive hydrogen producer suitable for growth on various lignocellulosic substrates. The aim of this study was to quantify uptake of pentose and hexose monosaccharides in an industrial substrate and to present a kinetic growth model of C. saccharolyticus that includes sugar uptake on defined and industrial media. The model is based on Monod and Hill kinetics extended with gas-to-liquid mass transfer and a cybernetic approach to describe diauxic-like growth. RESULTS Mathematical expressions were developed to describe hydrogen production by C. saccharolyticus consuming glucose, xylose, and arabinose. The model parameters were calibrated against batch fermentation data. The experimental data included four different cases: glucose, xylose, sugar mixture, and wheat straw hydrolysate (WSH) fermentations. The fermentations were performed without yeast extract. The substrate uptake rate of C. saccharolyticus on single sugar-defined media was higher on glucose compared to xylose. In contrast, in the defined sugar mixture and WSH, the pentoses were consumed faster than glucose. Subsequently, the cultures entered a lag phase when all pentoses were consumed after which glucose uptake rate increased. This phenomenon suggested a diauxic-like behavior as was deduced from the successive appearance of two peaks in the hydrogen and carbon dioxide productivity. The observation could be described with a modified diauxic model including a second enzyme system with a higher affinity for glucose being expressed when pentose saccharides are consumed. This behavior was more pronounced when WSH was used as substrate. CONCLUSIONS The previously observed co-consumption of glucose and pentoses with a preference for the latter was herein confirmed. However, once all pentoses were consumed, C. saccharolyticus most probably expressed another uptake system to account for the observed increased glucose uptake rate. This phenomenon could be quantitatively captured in a kinetic model of the entire diauxic-like growth process. Moreover, the observation indicates a regulation system that has fundamental research relevance, since pentose and glucose uptake in C. saccharolyticus has only been described with ABC transporters, whereas previously reported diauxic growth phenomena have been correlated mainly to PTS systems for sugar uptake.
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Affiliation(s)
- Johanna Björkmalm
- Department of Energy and Circular Economy, RISE Research Institutes of Sweden, PO Box 857, 501 15 Borås, Sweden
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - Eoin Byrne
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - Ed W. J. van Niel
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - Karin Willquist
- Department of Energy and Circular Economy, RISE Research Institutes of Sweden, PO Box 857, 501 15 Borås, Sweden
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20
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Native xylose-inducible promoter expands the genetic tools for the biomass-degrading, extremely thermophilic bacterium Caldicellulosiruptor bescii. Extremophiles 2018; 22:629-638. [PMID: 29797090 DOI: 10.1007/s00792-018-1023-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/02/2018] [Indexed: 12/20/2022]
Abstract
Regulated control of both homologous and heterologous gene expression is essential for precise genetic manipulation and metabolic engineering of target microorganisms. However, there are often no options available for inducible promoters when working with non-model microorganisms. These include extremely thermophilic, cellulolytic bacteria that are of interest for renewable lignocellulosic conversion to biofuels and chemicals. In fact, improvements to the genetic systems in these organisms often cease once transformation is achieved. This present study expands the tools available for genetically engineering Caldicellulosiruptor bescii, the most thermophilic cellulose-degrader known growing up to 90 °C on unpretreated plant biomass. A native xylose-inducible (P xi ) promoter was utilized to control the expression of the reporter gene (ldh) encoding lactate dehydrogenase. The P xi -ldh construct resulted in a both increased ldh expression (20-fold higher) and lactate dehydrogenase activity (32-fold higher) in the presence of xylose compared to when glucose was used as a substrate. Finally, lactate production during growth of the recombinant C. bescii strain was proportional to the initial xylose concentration, showing that tunable expression of genes is now possible using this xylose-inducible system. This study represents a major step in the use of C. bescii as a potential platform microorganism for biotechnological applications using renewable biomass.
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21
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Lee BD, Apel WA, Sheridan PP, DeVeaux LC. Glycoside hydrolase gene transcription by Alicyclobacillus acidocaldarius during growth on wheat arabinoxylan and monosaccharides: a proposed xylan hydrolysis mechanism. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:110. [PMID: 29686728 PMCID: PMC5901876 DOI: 10.1186/s13068-018-1110-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 04/06/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Metabolism of carbon bound in wheat arabinoxylan (WAX) polysaccharides by bacteria requires a number of glycoside hydrolases active toward different bonds between sugars and other molecules. Alicyclobacillus acidocaldarius is a Gram-positive thermoacidophilic bacterium capable of growth on a variety of mono-, di-, oligo-, and polysaccharides. Nineteen proposed glycoside hydrolases have been annotated in the A. acidocaldarius Type Strain ATCC27009/DSM 446 genome. Experiments were performed to understand the effect of monosaccharides on gene expression during growth on the polysaccharide, WAX. RESULTS Molecular analysis using high-density oligonucleotide microarrays was performed on A. acidocaldarius strain ATCC27009 when growing on WAX. When a culture growing exponentially at the expense of arabinoxylan saccharides was challenged with glucose or xylose, most glycoside hydrolases were downregulated. Interestingly, regulation was more intense when xylose was added to the culture than when glucose was added, showing a clear departure from classical carbon catabolite repression demonstrated by many Gram-positive bacteria. In silico analyses of the regulated glycoside hydrolases, along with the results from the microarray analyses, yielded a potential mechanism for arabinoxylan metabolism by A. acidocaldarius. Glycoside hydrolases expressed by this strain may have broad substrate specificity, and initial hydrolysis is catalyzed by an extracellular xylanase, while subsequent steps are likely performed inside the growing cell. CONCLUSIONS Glycoside hydrolases, for the most part, appear to be found in clusters, throughout the A. acidocaldarius genome. Not all of the glycoside hydrolase genes found at loci within these clusters were regulated during the experiment, indicating that a specific subset of the 19 glycoside hydrolase genes found in A. acidocaldarius were used during metabolism of WAX. While specific functions of the glycoside hydrolases were not tested as part of the research discussed, many of the glycoside hydrolases found in the A. acidocaldarius Type Strain appear to have a broader substrate range than that represented by the glycoside hydrolase family in which the enzymes were categorized.
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Affiliation(s)
- Brady D. Lee
- Biological Systems Department, Idaho National Laboratory, P. O. Box 1625, Idaho Falls, ID 83415 USA
- Department of Biological Sciences, Idaho State University, Campus Box 8007, Pocatello, ID 83209 USA
- Present Address: Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA USA
| | - William A. Apel
- Biological Systems Department, Idaho National Laboratory, P. O. Box 1625, Idaho Falls, ID 83415 USA
| | - Peter P. Sheridan
- Department of Biological Sciences, Idaho State University, Campus Box 8007, Pocatello, ID 83209 USA
| | - Linda C. DeVeaux
- Department of Biology, New Mexico Institute of Mining and Technology, 801 Leroy Pl, Socorro, NM 87801 USA
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Characterization of a thermostable glycoside hydrolase family 36 α-galactosidase from Caldicellulosiruptor bescii. J Biosci Bioeng 2017; 124:289-295. [DOI: 10.1016/j.jbiosc.2017.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/16/2017] [Indexed: 01/25/2023]
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Identification of the ATPase Subunit of the Primary Maltose Transporter in the Hyperthermophilic Anaerobe Thermotoga maritima. Appl Environ Microbiol 2017; 83:AEM.00930-17. [PMID: 28687653 DOI: 10.1128/aem.00930-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/04/2017] [Indexed: 12/18/2022] Open
Abstract
Thermotoga maritima is a hyperthermophilic anaerobic bacterium that produces molecular hydrogen (H2) by fermentation. It catabolizes a broad range of carbohydrates through the action of diverse ABC transporters. However, in T. maritima and related species, highly similar genes with ambiguous annotation obscure a precise understanding of genome function. In T. maritima, three putative malK genes, all annotated as ATPase subunits, exhibited high identity to each other. To distinguish between these genes, malK disruption mutants were constructed by gene replacement, and the resulting mutant cell lines were characterized. Only a disruption of malK3 produced a defect in maltose catabolism. To verify that the mutant phenotype arose specifically from malK3 inactivation, the malK3 mutation was repaired by recombination, and maltose catabolism was restored. This study demonstrates the importance of a maltose ABC-type transporter and its relationship to sugar metabolism in T. maritimaIMPORTANCE The application and further development of a genetic system was used here to investigate gene paralogs in the hyperthermophile Thermotoga maritima The occurrence of three ABC transporter ATPase subunits all annotated as malK was evaluated using a combination of genetic and bioinformatic approaches. The results clarify the role of only one malK gene in maltose catabolism in a nonmodel organism noted for fermentative hydrogen production.
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Blumer-Schuette SE, Zurawski JV, Conway JM, Khatibi P, Lewis DL, Li Q, Chiang VL, Kelly RM. Caldicellulosiruptor saccharolyticus transcriptomes reveal consequences of chemical pretreatment and genetic modification of lignocellulose. Microb Biotechnol 2017; 10:1546-1557. [PMID: 28322023 PMCID: PMC5658599 DOI: 10.1111/1751-7915.12494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 11/28/2022] Open
Abstract
Recalcitrance of plant biomass is a major barrier for commercially feasible cellulosic biofuel production. Chemical and enzymatic assays have been developed to measure recalcitrance and carbohydrate composition; however, none of these assays can directly report which polysaccharides a candidate microbe will sense during growth on these substrates. Here, we propose using the transcriptomic response of the plant biomass‐deconstructing microbe, Caldicellulosiruptor saccharolyticus, as a direct measure of how suitable a sample of plant biomass may be for fermentation based on the bioavailability of polysaccharides. Key genes were identified using the global gene response of the microbe to model plant polysaccharides and various types of unpretreated, chemically pretreated and genetically modified plant biomass. While the majority of C. saccharolyticus genes responding were similar between plant biomasses; subtle differences were discernable, most importantly between chemically pretreated or genetically modified biomass that both exhibit similar levels of solubilization by the microbe. Furthermore, the results here present a new paradigm for assessing plant–microbe interactions that can be deployed as a biological assay to report on the complexity and recalcitrance of plant biomass.
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Affiliation(s)
- Sara E Blumer-Schuette
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jeffrey V Zurawski
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jonathan M Conway
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Piyum Khatibi
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Derrick L Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Quanzi Li
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Vincent L Chiang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
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Counts JA, Zeldes BM, Lee LL, Straub CT, Adams MWW, Kelly RM. Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28206708 DOI: 10.1002/wsbm.1377] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/12/2022]
Abstract
The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as 'extreme thermophiles' and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs-basically, anywhere there is hot water. Initial efforts to study extreme thermophiles faced challenges with their isolation from difficult to access locales, problems with their cultivation in laboratories, and lack of molecular tools. Fortunately, because of their relatively small genomes, many extreme thermophiles were among the first organisms to be sequenced, thereby opening up the application of systems biology-based methods to probe their unique physiological, metabolic and biotechnological features. The bacterial genera Caldicellulosiruptor, Thermotoga and Thermus, and the archaea belonging to the orders Thermococcales and Sulfolobales, are among the most studied extreme thermophiles to date. The recent emergence of genetic tools for many of these organisms provides the opportunity to move beyond basic discovery and manipulation to biotechnologically relevant applications of metabolic engineering. WIREs Syst Biol Med 2017, 9:e1377. doi: 10.1002/wsbm.1377 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Laura L Lee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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Peng T, Pan S, Christopher LP, Sparling R, Levin DB. Growth and metabolic profiling of the novel thermophilic bacterium Thermoanaerobacter sp. strain YS13. Can J Microbiol 2016; 62:762-71. [PMID: 27569998 DOI: 10.1139/cjm-2016-0040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A strictly anaerobic, thermophilic bacterium, designated strain YS13, was isolated from a geothermal hot spring. Phylogenetic analysis using the 16S rRNA genes and cpn60 UT genes suggested strain YS13 as a species of Thermoanaerobacter. Using cellobiose or xylose as carbon source, YS13 was able to grow over a wide range of temperatures (45-70 °C), and pHs (pH 5.0-9.0), with optimum growth at 65 °C and pH 7.0. Metabolic profiling on cellobiose, glucose, or xylose in 1191 medium showed that H2, CO2, ethanol, acetate, and lactate were the major metabolites. Lactate was the predominant end product from glucose or cellobiose fermentations, whereas H2 and acetate were the dominant end products from xylose fermentation. The metabolic balance shifted away from ethanol to H2, acetate, and lactate when YS13 was grown on cellobiose as temperatures increased from 45 to 70 °C. When YS13 was grown on xylose, a metabolic shift from lactate to H2, CO2, and acetate was observed in cultures as the temperature of incubation increased from 45 to 65 °C, whereas a shift from ethanol and CO2 to H2, acetate, and lactate was observed in cultures incubated at 70 °C.
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Affiliation(s)
- Tingting Peng
- a Department of Food Science, Huazhong Agricultural University, Wuhan, China.,d Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 3N3, Canada
| | - Siyi Pan
- a Department of Food Science, Huazhong Agricultural University, Wuhan, China
| | - Lew P Christopher
- b Biorefining Research Institute, Lakehead University, Thunder Bay, ON P7B 5Z5, Canada
| | - Richard Sparling
- c Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 3N3, Canada
| | - David B Levin
- d Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 3N3, Canada
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27
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Ghio S, Insani EM, Piccinni FE, Talia PM, Grasso DH, Campos E. GH10 XynA is the main xylanase identified in the crude enzymatic extract of Paenibacillus sp. A59 when grown on xylan or lignocellulosic biomass. Microbiol Res 2016; 186-187:16-26. [DOI: 10.1016/j.micres.2016.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/23/2016] [Accepted: 02/29/2016] [Indexed: 12/15/2022]
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28
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Conway JM, Pierce WS, Le JH, Harper GW, Wright JH, Tucker AL, Zurawski JV, Lee LL, Blumer-Schuette SE, Kelly RM. Multidomain, Surface Layer-associated Glycoside Hydrolases Contribute to Plant Polysaccharide Degradation by Caldicellulosiruptor Species. J Biol Chem 2016; 291:6732-47. [PMID: 26814128 DOI: 10.1074/jbc.m115.707810] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Indexed: 01/08/2023] Open
Abstract
The genome of the extremely thermophilic bacterium Caldicellulosiruptor kronotskyensisencodes 19 surface layer (S-layer) homology (SLH) domain-containing proteins, the most in any Caldicellulosiruptorspecies genome sequenced to date. These SLH proteins include five glycoside hydrolases (GHs) and one polysaccharide lyase, the genes for which were transcribed at high levels during growth on plant biomass. The largest GH identified so far in this genus, Calkro_0111 (2,435 amino acids), is completely unique toC. kronotskyensisand contains SLH domains. Calkro_0111 was produced recombinantly inEscherichia colias two pieces, containing the GH16 and GH55 domains, respectively, as well as putative binding and spacer domains. These displayed endo- and exoglucanase activity on the β-1,3-1,6-glucan laminarin. A series of additional truncation mutants of Calkro_0111 revealed the essential architectural features required for catalytic function. Calkro_0402, another of the SLH domain GHs inC. kronotskyensis, when produced inE. coli, was active on a variety of xylans and β-glucans. Unlike Calkro_0111, Calkro_0402 is highly conserved in the genus Caldicellulosiruptorand among other biomass-degrading Firmicutes but missing from Caldicellulosiruptor bescii As such, the gene encoding Calkro_0402 was inserted into the C. besciigenome, creating a mutant strain with its S-layer extensively decorated with Calkro_0402. This strain consequently degraded xylans more extensively than wild-typeC. bescii The results here provide new insights into the architecture and role of SLH domain GHs and demonstrate that hemicellulose degradation can be enhanced through non-native SLH domain GHs engineered into the genomes of Caldicellulosiruptorspecies.
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Affiliation(s)
- Jonathan M Conway
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - William S Pierce
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Jaycee H Le
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - George W Harper
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - John H Wright
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Allyson L Tucker
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Jeffrey V Zurawski
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Laura L Lee
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Sara E Blumer-Schuette
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Robert M Kelly
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
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29
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Sayed M, Dishisha T, Sayed WF, Salem WM, Temerk HA, Pyo SH. Selective oxidation of trimethylolpropane to 2,2-bis(hydroxymethyl)butyric acid using growing cells of Corynebacterium sp. ATCC 21245. J Biotechnol 2016; 221:62-9. [PMID: 26804932 DOI: 10.1016/j.jbiotec.2016.01.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 01/04/2016] [Accepted: 01/19/2016] [Indexed: 11/27/2022]
Abstract
Multifunctional chemicals including hydroxycarboxylic acids are gaining increasing interest due to their growing applications in the polymer industry. One approach for their production is a biological selective oxidation of polyols, which is difficult to achieve by conventional chemical catalysis. In the present study, trimethylolpropane (TMP), a trihydric alcohol, was subjected to selective oxidation using growing cells of Corynebacterium sp. ATCC 21245 as a biocatalyst and yielding the dihydroxy-monocarboxylic acid, 2,2-bis(hydroxymethyl)butyric acid (BHMB). The study revealed that co-substrates are crucial for this reaction. Among the different evaluated co-substrates, a mixture of glucose, xylose and acetate at a ratio of 5:5:2 was found optimum. The optimal conditions for biotransformation were pH 8, 1v/v/m airflow and 500rpm stirring speed. In batch mode of operation, 70.6% of 5g/l TMP was converted to BHMB in 10 days. For recovery of the product the adsorption pattern of BHMB to the anion exchange resin, Ambersep(®) 900 (OH(-)), was investigated in batch and column experiments giving maximum static and dynamic binding capacities of 135 and 144mg/g resin, respectively. BHMB was separated with 89.7% of recovery yield from the fermentation broth. The approach is applicable for selective oxidation of other highly branched polyols by biotransformation.
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Affiliation(s)
- Mahmoud Sayed
- Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden; Department of Botany, Faculty of Science, South Valley University, Qena, Egypt
| | - Tarek Dishisha
- Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden; Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Egypt
| | - Waiel F Sayed
- Department of Botany, Faculty of Science, South Valley University, Qena, Egypt
| | - Wesam M Salem
- Department of Botany, Faculty of Science, South Valley University, Qena, Egypt
| | - Hanan A Temerk
- Department of Botany, Faculty of Science, South Valley University, Qena, Egypt
| | - Sang-Hyun Pyo
- Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden; Department of Food Bioscience and Technology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea.
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30
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Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VGH, Koropatkin NM, McBride MJ, Pope PB. A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:260. [PMID: 27933102 PMCID: PMC5127042 DOI: 10.1186/s13068-016-0674-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/17/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Chitin is the second most abundant polysaccharide on earth and as such a great target for bioconversion applications. The phylum Bacteroidetes is one of nature's most ubiquitous bacterial lineages and is essential in the global carbon cycle with many members being highly efficient degraders of complex carbohydrates. However, despite their specialist reputation in carbohydrate conversion, mechanisms for degrading recalcitrant crystalline polysaccharides such as chitin and cellulose are hitherto unknown. RESULTS Here we describe a complete functional analysis of a novel polysaccharide utilization locus (PUL) in the soil Bacteroidete Flavobacterium johnsoniae, tailored for conversion of chitin. The F. johnsoniae chitin utilization locus (ChiUL) consists of eleven contiguous genes encoding carbohydrate capture and transport proteins, enzymes, and a two-component sensor-regulator system. The key chitinase (ChiA) encoded by ChiUL is atypical in terms of known Bacteroidetes-affiliated PUL mechanisms as it is not anchored to the outer cell membrane and consists of multiple catalytic domains. We demonstrate how the extraordinary hydrolytic efficiency of ChiA derives from synergy between its multiple chitinolytic (endo- and exo-acting) and previously unidentified chitin-binding domains. Reverse genetics show that ChiA and PUL-encoded proteins involved in sugar binding, import, and chitin sensing are essential for efficient chitin utilization. Surprisingly, the ChiUL encodes two pairs of SusC/D-like outer membrane proteins. Ligand-binding and structural studies revealed functional differences between the two SusD-like proteins that enhance scavenging of chitin from the environment. The combined results from this study provide insight into the mechanisms employed by Bacteroidetes to degrade recalcitrant polysaccharides and reveal important novel aspects of the PUL paradigm. CONCLUSIONS By combining reverse genetics to map essential PUL genes, structural studies on outer membrane chitin-binding proteins, and enzymology, we provide insight into the mechanisms employed by Bacteroidetes to degrade recalcitrant polysaccharides and introduce a new saccharolytic mechanism used by the phylum Bacteroidetes. The presented discovery and analysis of the ChiUL will greatly benefit future enzyme discovery efforts as well as studies regarding enzymatic intramolecular synergism.
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Affiliation(s)
- Johan Larsbrink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Yongtao Zhu
- Department of Biological Sciences, University of Wisconsin—Milwaukee, Milwaukee, WI 53201 USA
| | - Sampada S. Kharade
- Department of Biological Sciences, University of Wisconsin—Milwaukee, Milwaukee, WI 53201 USA
| | - Kurt J. Kwiatkowski
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Nicole M. Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Mark J. McBride
- Department of Biological Sciences, University of Wisconsin—Milwaukee, Milwaukee, WI 53201 USA
| | - Phillip B. Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
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Sharma R, Lamsal BP, Colonna WJ. Pretreatment of fibrous biomass and growth of biosurfactant-producing Bacillus subtilis on biomass-derived fermentable sugars. Bioprocess Biosyst Eng 2015; 39:105-13. [DOI: 10.1007/s00449-015-1494-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
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32
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Comparative Analysis of Extremely Thermophilic Caldicellulosiruptor Species Reveals Common and Unique Cellular Strategies for Plant Biomass Utilization. Appl Environ Microbiol 2015; 81:7159-70. [PMID: 26253670 DOI: 10.1128/aem.01622-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/26/2015] [Indexed: 11/20/2022] Open
Abstract
Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70°C to simple sugars, acetate, lactate, CO2, and H2. Caldicellulosiruptor bescii, C. kronotskyensis, and C. saccharolyticus solubilized 38%, 36%, and 29% (by weight) of unpretreated switchgrass (Panicum virgatum) (5 g/liter), respectively, which was about half of the amount of crystalline cellulose (Avicel; 5 g/liter) that was solubilized under the same conditions. The lower yields with C. saccharolyticus, not appreciably greater than the thermal control for switchgrass, were unexpected, given that its genome encodes the same glycoside hydrolase 9 (GH9)-GH48 multidomain cellulase (CelA) found in the other two species. However, the genome of C. saccharolyticus lacks two other cellulases with GH48 domains, which could be responsible for its lower levels of solubilization. Transcriptomes for growth of each species comparing cellulose to switchgrass showed that many carbohydrate ABC transporters and multidomain extracellular glycoside hydrolases were differentially regulated, reflecting the heterogeneity of lignocellulose. However, significant differences in transcription levels for conserved genes among the three species were noted, indicating unexpectedly diverse regulatory strategies for deconstruction for these closely related bacteria. Genes encoding the Che-type chemotaxis system and flagellum biosynthesis were upregulated in C. kronotskyensis and C. bescii during growth on cellulose, implicating motility in substrate utilization. The results here show that capacity for plant biomass deconstruction varies across Caldicellulosiruptor species and depends in a complex way on GH genome inventory, substrate composition, and gene regulation.
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33
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Petit E, Coppi MV, Hayes JC, Tolonen AC, Warnick T, Latouf WG, Amisano D, Biddle A, Mukherjee S, Ivanova N, Lykidis A, Land M, Hauser L, Kyrpides N, Henrissat B, Lau J, Schnell DJ, Church GM, Leschine SB, Blanchard JL. Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PLoS One 2015; 10:e0118285. [PMID: 26035711 PMCID: PMC4452783 DOI: 10.1371/journal.pone.0118285] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.
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Affiliation(s)
- Elsa Petit
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Maddalena V. Coppi
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - James C. Hayes
- Graduate Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Andrew C. Tolonen
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)-Genoscope, Unité Mixte de Recherche (UMR)-8030, National Center for Scientific Research (CNRS), Evry, France
| | - Thomas Warnick
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - William G. Latouf
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Danielle Amisano
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Amy Biddle
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Supratim Mukherjee
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Natalia Ivanova
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Athanassios Lykidis
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Miriam Land
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Loren Hauser
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Nikos Kyrpides
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Unité mixte de recherche (UMR)-6098, National Center for Scientific Research (CNRS), and Universités d’Aix-Marseille I and II, Marseille, France
| | - Joanne Lau
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Danny J. Schnell
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susan B. Leschine
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Jeffrey L. Blanchard
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Graduate Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
- Graduate Program in Organismal and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- * E-mail:
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Blumer-Schuette SE, Alahuhta M, Conway JM, Lee LL, Zurawski JV, Giannone RJ, Hettich RL, Lunin VV, Himmel ME, Kelly RM. Discrete and structurally unique proteins (tāpirins) mediate attachment of extremely thermophilic Caldicellulosiruptor species to cellulose. J Biol Chem 2015; 290:10645-56. [PMID: 25720489 DOI: 10.1074/jbc.m115.641480] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Indexed: 11/06/2022] Open
Abstract
A variety of catalytic and noncatalytic protein domains are deployed by select microorganisms to deconstruct lignocellulose. These extracellular proteins are used to attach to, modify, and hydrolyze the complex polysaccharides present in plant cell walls. Cellulolytic enzymes, often containing carbohydrate-binding modules, are key to this process; however, these enzymes are not solely responsible for attachment. Few mechanisms of attachment have been discovered among bacteria that do not form large polypeptide structures, called cellulosomes, to deconstruct biomass. In this study, bioinformatics and proteomics analyses identified unique, discrete, hypothetical proteins ("tāpirins," origin from Māori: to join), not directly associated with cellulases, that mediate attachment to cellulose by species in the noncellulosomal, extremely thermophilic bacterial genus Caldicellulosiruptor. Two tāpirin genes are located directly downstream of a type IV pilus operon in strongly cellulolytic members of the genus, whereas homologs are absent from the weakly cellulolytic Caldicellulosiruptor species. Based on their amino acid sequence, tāpirins are specific to these extreme thermophiles. Tāpirins are also unusual in that they share no detectable protein domain signatures with known polysaccharide-binding proteins. Adsorption isotherm and trans vivo analyses demonstrated the carbohydrate-binding module-like affinity of the tāpirins for cellulose. Crystallization of a cellulose-binding truncation from one tāpirin indicated that these proteins form a long β-helix core with a shielded hydrophobic face. Furthermore, they are structurally unique and define a new class of polysaccharide adhesins. Strongly cellulolytic Caldicellulosiruptor species employ tāpirins to complement substrate-binding proteins from the ATP-binding cassette transporters and multidomain extracellular and S-layer-associated glycoside hydrolases to process the carbohydrate content of lignocellulose.
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Affiliation(s)
- Sara E Blumer-Schuette
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Markus Alahuhta
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Jonathan M Conway
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Laura L Lee
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Jeffrey V Zurawski
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Richard J Giannone
- the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Robert L Hettich
- the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Vladimir V Lunin
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Michael E Himmel
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Robert M Kelly
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905,
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35
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Vishnivetskaya TA, Hamilton-Brehm SD, Podar M, Mosher JJ, Palumbo AV, Phelps TJ, Keller M, Elkins JG. Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park. MICROBIAL ECOLOGY 2015; 69:333-345. [PMID: 25319238 DOI: 10.1007/s00248-014-0500-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 09/16/2014] [Indexed: 06/04/2023]
Abstract
The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this study, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversity in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55-85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures.
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Affiliation(s)
- Tatiana A Vishnivetskaya
- BioEnergy Science Center, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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Distinct roles for carbohydrate-binding modules of glycoside hydrolase 10 (GH10) and GH11 xylanases from Caldicellulosiruptor sp. strain F32 in thermostability and catalytic efficiency. Appl Environ Microbiol 2015; 81:2006-14. [PMID: 25576604 DOI: 10.1128/aem.03677-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylanases are crucial for lignocellulosic biomass deconstruction and generally contain noncatalytic carbohydrate-binding modules (CBMs) accessing recalcitrant polymers. Understanding how multimodular enzymes assemble can benefit protein engineering by aiming at accommodating various environmental conditions. Two multimodular xylanases, XynA and XynB, which belong to glycoside hydrolase families 11 (GH11) and GH10, respectively, have been identified from Caldicellulosiruptor sp. strain F32. In this study, both xylanases and their truncated mutants were overexpressed in Escherichia coli, purified, and characterized. GH11 XynATM1 lacking CBM exhibited a considerable improvement in specific activity (215.8 U nmol(-1) versus 94.7 U nmol(-1)) and thermal stability (half-life of 48 h versus 5.5 h at 75°C) compared with those of XynA. However, GH10 XynB showed higher enzyme activity and thermostability than its truncated mutant without CBM. Site-directed mutagenesis of N-terminal amino acids resulted in a mutant, XynATM1-M, with 50% residual activity improvement at 75°C for 48 h, revealing that the disordered region influenced protein thermostability negatively. The thermal stability of both xylanases and their truncated mutants were consistent with their melting temperature (Tm), which was determined by using differential scanning calorimetry. Through homology modeling and cross-linking analysis, we demonstrated that for XynB, the resistance against thermoinactivation generally was enhanced through improving both domain properties and interdomain interactions, whereas for XynA, no interdomain interactions were observed. Optimized intramolecular interactions can accelerate thermostability, which provided microbes a powerful evolutionary strategy to assemble catalysts that are adapted to various ecological conditions.
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Meng DD, Ying Y, Zhang KD, Lu M, Li FL. Depiction of carbohydrate-active enzyme diversity in Caldicellulosiruptor sp. F32 at the genome level reveals insights into distinct polysaccharide degradation features. MOLECULAR BIOSYSTEMS 2015; 11:3164-73. [DOI: 10.1039/c5mb00409h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Diverse and distinctive encoding sequences of CAZyme in the genome of Caldicellulosiruptor sp. F32 enable the deconstruction of unpretreated lignocellulose.
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Affiliation(s)
- Dong-Dong Meng
- Key Laboratory of Biofuels
- Shandong Provincial Key Laboratory of Energy Genetics
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
| | - Yu Ying
- Key Laboratory of Biofuels
- Shandong Provincial Key Laboratory of Energy Genetics
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
| | - Kun-Di Zhang
- Key Laboratory of Biofuels
- Shandong Provincial Key Laboratory of Energy Genetics
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
| | - Ming Lu
- Key Laboratory of Biofuels
- Shandong Provincial Key Laboratory of Energy Genetics
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
| | - Fu-Li Li
- Key Laboratory of Biofuels
- Shandong Provincial Key Laboratory of Energy Genetics
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
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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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Basen M, Rhaesa AM, Kataeva I, Prybol CJ, Scott IM, Poole FL, Adams MWW. Degradation of high loads of crystalline cellulose and of unpretreated plant biomass by the thermophilic bacterium Caldicellulosiruptor bescii. BIORESOURCE TECHNOLOGY 2014; 152:384-92. [PMID: 24316482 DOI: 10.1016/j.biortech.2013.11.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/06/2013] [Accepted: 11/10/2013] [Indexed: 05/04/2023]
Abstract
The thermophilic bacterium Caldicellulosiruptor bescii grows at 78 °C on high concentrations (200 g L(-1)) of both crystalline cellulose and unpretreated switchgrass, while low concentrations (<20 g L(-1)) of acid-pretreated switchgrass inhibit growth. Degradation of crystalline cellulose, but not that of unpretreated switchgrass, was limited by nitrogen and vitamin (folate) availability. Under optimal conditions, C. bescii solubilized approximately 60% of the crystalline cellulose and 30% of the unpretreated switchgrass using initial substrate concentrations of 50 g L(-1). Further fermentation of crystalline cellulose and of switchgrass was inhibited by organic acid end-products and by a specific inhibitor of C. bescii growth that did not affect other thermophilic bacteria, respectively. Soluble mono- and oligosaccharides, organic acids, carbon dioxide, and microbial biomass, quantitatively accounted for the crystalline cellulose and plant biomass carbon utilized. C. bescii therefore degrades industrially-relevant concentrations of lignocellulosic biomass that have not undergone pretreatment thereby demonstrating its potential utility in biomass conversion.
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Affiliation(s)
- Mirko Basen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Amanda M Rhaesa
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Irina Kataeva
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Cameron J Prybol
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Israel M Scott
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
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Groom J, Chung D, Young J, Westpheling J. Heterologous complementation of a pyrF deletion in Caldicellulosiruptor hydrothermalis generates a new host for the analysis of biomass deconstruction. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:132. [PMID: 25254074 PMCID: PMC4172971 DOI: 10.1186/s13068-014-0132-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/28/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Members of the thermophilic, anaerobic Gram-positive bacterial genus Caldicellulosiruptor grow optimally at 65 to 78°C and degrade lignocellulosic biomass without conventional pretreatment. Decomposition of complex cell wall polysaccharides is a major bottleneck in the conversion of plant biomass to biofuels and chemicals, and conventional biomass pretreatment includes exposure to high temperatures, acids, or bases as well as enzymatic digestion. Members of this genus contain a variety of glycosyl hydrolases, pectinases, and xylanases, but the contribution of these individual enzymes to biomass deconstruction is largely unknown. C. hydrothermalis is of special interest because it is the least cellulolytic of all the Caldicellulosiruptor species so far characterized, making it an ideal naïve system to study key cellulolytic enzymes from these bacteria. RESULTS To develop methods for genetic manipulation of C. hydrothermalis, we selected a spontaneous deletion of pyrF, a gene in the pyrimidine biosynthetic pathway, resulting in a strain that was a uracil auxotroph resistant to 5-fluoroorotic acid (5-FOA). This strain allowed the selection of prototrophic transformants with either replicating or non-replicating plasmids containing the wild-type pyrF gene. Counter-selection of the pyrF wild-type allele on non-replicating vectors allowed the construction of chromosomal deletions. To eliminate integration of the non-replicating plasmid at the pyrF locus in the C. hydrothermalis chromosome, we used the non-homologous Clostridium thermocellum wild-type pyrF allele to complement the C. hydrothermalis pyrF deletion. The autonomously replicating shuttle vector was maintained at 25 to 115 copies per chromosome. Deletion of the ChyI restriction enzyme in C. hydrothermalis increased the transformation efficiency by an order of magnitude and demonstrated the ability to construct deletions and insertions in the genome of this new host. CONCLUSIONS The use of C. hydrothermalis as a host for homologous and heterologous expression of enzymes important for biomass deconstruction will enable the identification of enzymes that contribute to the special ability of these bacteria to degrade complex lignocellulosic substrates as well as facilitate the construction of strains to improve and extend their substrate utilization capabilities.
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Affiliation(s)
- Joseph Groom
- />Department of Genetics, University of Georgia, Athens, GA 30602 USA
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Daehwan Chung
- />Department of Genetics, University of Georgia, Athens, GA 30602 USA
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jenna Young
- />Department of Genetics, University of Georgia, Athens, GA 30602 USA
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Janet Westpheling
- />Department of Genetics, University of Georgia, Athens, GA 30602 USA
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
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Lin L, Xu J. Dissecting and engineering metabolic and regulatory networks of thermophilic bacteria for biofuel production. Biotechnol Adv 2013; 31:827-37. [DOI: 10.1016/j.biotechadv.2013.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/06/2013] [Accepted: 03/10/2013] [Indexed: 01/08/2023]
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Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity. ISME JOURNAL 2013; 8:88-102. [PMID: 23949661 DOI: 10.1038/ismej.2013.120] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/30/2013] [Accepted: 06/07/2013] [Indexed: 11/08/2022]
Abstract
Cellulose is the most abundant biopolymer on Earth. Optimising energy recovery from this renewable but recalcitrant material is a key issue. The metaproteome expressed by thermophilic communities during cellulose anaerobic digestion was investigated in microcosms. By multiplying the analytical replicates (65 protein fractions analysed by MS/MS) and relying solely on public protein databases, more than 500 non-redundant protein functions were identified. The taxonomic community structure as inferred from the metaproteomic data set was in good overall agreement with 16S rRNA gene tag pyrosequencing and fluorescent in situ hybridisation analyses. Numerous functions related to cellulose and hemicellulose hydrolysis and fermentation catalysed by bacteria related to Caldicellulosiruptor spp. and Clostridium thermocellum were retrieved, indicating their key role in the cellulose-degradation process and also suggesting their complementary action. Despite the abundance of acetate as a major fermentation product, key methanogenesis enzymes from the acetoclastic pathway were not detected. In contrast, enzymes from the hydrogenotrophic pathway affiliated to Methanothermobacter were almost exclusively identified for methanogenesis, suggesting a syntrophic acetate oxidation process coupled to hydrogenotrophic methanogenesis. Isotopic analyses confirmed the high dominance of the hydrogenotrophic methanogenesis. Very surprising was the identification of an abundant proteolytic activity from Coprothermobacter proteolyticus strains, probably acting as scavenger and/or predator performing proteolysis and fermentation. Metaproteomics thus appeared as an efficient tool to unravel and characterise metabolic networks as well as ecological interactions during methanisation bioprocesses. More generally, metaproteomics provides direct functional insights at a limited cost, and its attractiveness should increase in the future as sequence databases are growing exponentially.
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Talluri S, Raj SM, Christopher LP. Consolidated bioprocessing of untreated switchgrass to hydrogen by the extreme thermophile Caldicellulosiruptor saccharolyticus DSM 8903. BIORESOURCE TECHNOLOGY 2013; 139:272-9. [PMID: 23665687 DOI: 10.1016/j.biortech.2013.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 05/10/2023]
Abstract
The abilities of the extreme thermophilic bacterium Caldicellulosiruptor saccharolyticus DSM 8903 to ferment switchgrass (SWG), microcrystalline cellulose (MCC) and glucose to hydrogen (H2) in one-step were examined. Hydrogen production from glucose reached the theoretical maximum for dark fermentation of 4 mol H2/mol glucose. The H2 yield on MCC and SWG after 6 days of fermentation was 23.2 mmol H2/L or 9.4 mmol H2/g MCC and 14.3 mmol H2/L or 11.2 mmol H2/g SWG, respectively. The rate of H2 formation however was higher on MCC (0.7 mmol/Lh) than SWG (0.1 mmol/Lh). C. saccharolyticus DSM 8903 was able to produce H2 directly from mechanically-comminuted SWG without any physicochemical or biological pretreatment. Combining four processing steps (pretreatment, enzyme production, saccharification and fermentation) into a single biorefinery operation makes C. saccharolyticus DSM 8903 a promising candidate for consolidated bioprocessing (CBP) of lignocellulosic biomass.
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Affiliation(s)
- Suvarna Talluri
- Center for Bioprocessing Research and Development, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
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44
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Isern NG, Xue J, Rao JV, Cort JR, Ahring BK. Novel monosaccharide fermentation products in Caldicellulosiruptor saccharolyticus identified using NMR spectroscopy. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:47. [PMID: 23552326 PMCID: PMC3637100 DOI: 10.1186/1754-6834-6-47] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/07/2013] [Indexed: 05/30/2023]
Abstract
BACKGROUND Caldicellulosiruptor saccharolyticus is a thermophilic, Gram-positive, non-spore forming, strictly anaerobic bacterium of interest in potential industrial applications, including the production of biofuels such as hydrogen or ethanol from lignocellulosic biomass through fermentation. High-resolution, solution-state nuclear magnetic resonance (NMR) spectroscopy is a useful method for the identification and quantification of metabolites that result from growth on different substrates. NMR allows facile resolution of isomeric (identical mass) constituents and does not destroy the sample. RESULTS Profiles of metabolites produced by the thermophilic cellulose-degrading bacterium Caldicellulosiruptor saccharolyticus DSM 8903 strain following growth on different monosaccharides (D-glucose, D-mannose, L-arabinose, D-arabinose, D-xylose, L-fucose, and D-fucose) as carbon sources revealed several unexpected fermentation products, suggesting novel metabolic capacities and unexplored metabolic pathways in this organism. Both 1H and 13C nuclear magnetic resonance (NMR) spectroscopy were used to determine intracellular and extracellular metabolite profiles. One dimensional 1H NMR spectral analysis was performed by curve fitting against spectral libraries provided in the Chenomx software; 2-D homonuclear and heteronuclear NMR experiments were conducted to further reduce uncertainties due to unassigned, overlapping, or poorly-resolved peaks. In addition to expected metabolites such as acetate, lactate, glycerol, and ethanol, several novel fermentation products were identified: ethylene glycol (from growth on D-arabinose), acetoin and 2,3-butanediol (from growth on D-glucose, L-arabinose, and D-xylose), and hydroxyacetone (from growth on D-mannose, L-arabinose, and D-xylose). Production of ethylene glycol from D-arabinose was particularly notable, with around 10% of the substrate carbon converted into this uncommon fermentation product. CONCLUSIONS The present research shows that C. saccharolyticus, already of substantial interest due to its capability for biological ethanol and hydrogen production, has further metabolic potential for production of higher molecular weight compounds, such as acetoin and 2,3-butanediol, as well as hydroxyacetone and the uncommon fermentation product ethylene glycol. In addition, application of nuclear magnetic resonance (NMR) spectroscopy facilitates identification of novel metabolites, which is instrumental for production of desirable bioproducts from biomass through microbial fermentation.
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Affiliation(s)
- Nancy G Isern
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Junfeng Xue
- Center for Bioproducts and Bioenergy, Washington State University, 2710 Crimson Way, Richland, WA, 99354, USA
| | - Jaya V Rao
- Center for Bioproducts and Bioenergy, Washington State University, 2710 Crimson Way, Richland, WA, 99354, USA
| | - John R Cort
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, PO Box 999, MSIN: K8-98, Richland, WA, 99352, USA
| | - Birgitte K Ahring
- Center for Bioproducts and Bioenergy, Washington State University, 2710 Crimson Way, Richland, WA, 99354, USA
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Svetlitchnyi VA, Kensch O, Falkenhan DA, Korseska SG, Lippert N, Prinz M, Sassi J, Schickor A, Curvers S. Single-step ethanol production from lignocellulose using novel extremely thermophilic bacteria. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:31. [PMID: 23448304 PMCID: PMC3598825 DOI: 10.1186/1754-6834-6-31] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 02/04/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Consolidated bioprocessing (CBP) of lignocellulosic biomass to ethanol using thermophilic bacteria provides a promising solution for efficient lignocellulose conversion without the need for additional cellulolytic enzymes. Most studies on the thermophilic CBP concentrate on co-cultivation of the thermophilic cellulolytic bacterium Clostridium thermocellum with non-cellulolytic thermophilic anaerobes at temperatures of 55°C-60°C. RESULTS We have specifically screened for cellulolytic bacteria growing at temperatures >70°C to enable direct conversion of lignocellulosic materials into ethanol. Seven new strains of extremely thermophilic anaerobic cellulolytic bacteria of the genus Caldicellulosiruptor and eight new strains of extremely thermophilic xylanolytic/saccharolytic bacteria of the genus Thermoanaerobacter isolated from environmental samples exhibited fast growth at 72°C, extensive lignocellulose degradation and high yield ethanol production on cellulose and pretreated lignocellulosic biomass. Monocultures of Caldicellulosiruptor strains degraded up to 89-97% of the cellulose and hemicellulose polymers in pretreated biomass and produced up to 72 mM ethanol on cellulose without addition of exogenous enzymes. In dual co-cultures of Caldicellulosiruptor strains with Thermoanaerobacter strains the ethanol concentrations rose 2- to 8.2-fold compared to cellulolytic monocultures. A co-culture of Caldicellulosiruptor DIB 087C and Thermoanaerobacter DIB 097X was particularly effective in the conversion of cellulose to ethanol, ethanol comprising 34.8 mol% of the total organic products. In contrast, a co-culture of Caldicellulosiruptor saccharolyticus DSM 8903 and Thermoanaerobacter mathranii subsp. mathranii DSM 11426 produced only low amounts of ethanol. CONCLUSIONS The newly discovered Caldicellulosiruptor sp. strain DIB 004C was capable of producing unexpectedly large amounts of ethanol from lignocellulose in fermentors. The established co-cultures of new Caldicellulosiruptor strains with new Thermoanaerobacter strains underline the importance of using specific strain combinations for high ethanol yields. These co-cultures provide an efficient CBP pathway for ethanol production and represent an ideal starting point for development of a highly integrated commercial ethanol production process.
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Affiliation(s)
| | - Oliver Kensch
- Direvo Industrial Biotechnology GmbH, Nattermannallee 1, D-50259, Köln, Germany
| | - Doris A Falkenhan
- Direvo Industrial Biotechnology GmbH, Nattermannallee 1, D-50259, Köln, Germany
| | - Svenja G Korseska
- Direvo Industrial Biotechnology GmbH, Nattermannallee 1, D-50259, Köln, Germany
| | - Nadine Lippert
- Direvo Industrial Biotechnology GmbH, Nattermannallee 1, D-50259, Köln, Germany
| | - Melanie Prinz
- Direvo Industrial Biotechnology GmbH, Nattermannallee 1, D-50259, Köln, Germany
| | - Jamaleddine Sassi
- Direvo Industrial Biotechnology GmbH, Nattermannallee 1, D-50259, Köln, Germany
| | - Anke Schickor
- Direvo Industrial Biotechnology GmbH, Nattermannallee 1, D-50259, Köln, Germany
| | - Simon Curvers
- Direvo Industrial Biotechnology GmbH, Nattermannallee 1, D-50259, Köln, Germany
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Biohydrogen Production by the Thermophilic Bacterium Caldicellulosiruptor saccharolyticus: Current Status and Perspectives. Life (Basel) 2013; 3:52-85. [PMID: 25371332 PMCID: PMC4187192 DOI: 10.3390/life3010052] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/06/2013] [Accepted: 01/07/2013] [Indexed: 01/24/2023] Open
Abstract
Caldicellulosiruptor saccharolyticus is one of the most thermophilic cellulolytic organisms known to date. This Gram-positive anaerobic bacterium ferments a broad spectrum of mono-, di- and polysaccharides to mainly acetate, CO2 and hydrogen. With hydrogen yields approaching the theoretical limit for dark fermentation of 4 mol hydrogen per mol hexose, this organism has proven itself to be an excellent candidate for biological hydrogen production. This review provides an overview of the research on C. saccharolyticus with respect to the hydrolytic capability, sugar metabolism, hydrogen formation, mechanisms involved in hydrogen inhibition, and the regulation of the redox and carbon metabolism. Analysis of currently available fermentation data reveal decreased hydrogen yields under non-ideal cultivation conditions, which are mainly associated with the accumulation of hydrogen in the liquid phase. Thermodynamic considerations concerning the reactions involved in hydrogen formation are discussed with respect to the dissolved hydrogen concentration. Novel cultivation data demonstrate the sensitivity of C. saccharolyticus to increased hydrogen levels regarding substrate load and nitrogen limitation. In addition, special attention is given to the rhamnose metabolism, which represents an unusual type of redox balancing. Finally, several approaches are suggested to improve biohydrogen production by C. saccharolyticus.
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Global microarray analysis of carbohydrate use in alkaliphilic hemicellulolytic bacterium Bacillus sp. N16-5. PLoS One 2013; 8:e54090. [PMID: 23326578 PMCID: PMC3542313 DOI: 10.1371/journal.pone.0054090] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 12/07/2012] [Indexed: 12/02/2022] Open
Abstract
The alkaliphilic hemicellulolytic bacterium Bacillus sp. N16-5 has a broad substrate spectrum and exhibits the capacity to utilize complex carbohydrates such as galactomannan, xylan, and pectin. In the monosaccharide mixture, sequential utilization by Bacillus sp. N16-5 was observed. Glucose appeared to be its preferential monosaccharide, followed by fructose, mannose, arabinose, xylose, and galactose. Global transcription profiles of the strain were determined separately for growth on six monosaccharides (glucose, fructose, mannose, galactose, arabinose, and xylose) and four polysaccharides (galactomannan, xylan, pectin, and sodium carboxymethylcellulose) using one-color microarrays. Numerous genes potentially related to polysaccharide degradation, sugar transport, and monosaccharide metabolism were found to respond to a specific substrate. Putative gene clusters for different carbohydrates were identified according to transcriptional patterns and genome annotation. Identification and analysis of these gene clusters contributed to pathway reconstruction for carbohydrate utilization in Bacillus sp. N16-5. Several genes encoding putative sugar transporters were highly expressed during growth on specific sugars, suggesting their functional roles. Two phosphoenolpyruvate-dependent phosphotransferase systems were identified as candidate transporters for mannose and fructose, and a major facilitator superfamily transporter was identified as a candidate transporter for arabinose and xylose. Five carbohydrate uptake transporter 1 family ATP-binding cassette transporters were predicted to participate in the uptake of hemicellulose and pectin degradation products. Collectively, microarray data improved the pathway reconstruction involved in carbohydrate utilization of Bacillus sp. N16-5 and revealed that the organism precisely regulates gene transcription in response to fluctuations in energy resources.
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48
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Xia Y, Fang HHP, Zhang T. Recent studies on thermophilic anaerobic bioconversion of lignocellulosic biomass. RSC Adv 2013. [DOI: 10.1039/c3ra40866c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Bhalla A, Bansal N, Kumar S, Bischoff KM, Sani RK. Improved lignocellulose conversion to biofuels with thermophilic bacteria and thermostable enzymes. BIORESOURCE TECHNOLOGY 2013; 128:751-9. [PMID: 23246299 DOI: 10.1016/j.biortech.2012.10.145] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 09/20/2012] [Accepted: 10/29/2012] [Indexed: 05/07/2023]
Abstract
Second-generation feedstock, especially nonfood lignocellulosic biomass is a potential source for biofuel production. Cost-intensive physical, chemical, biological pretreatment operations and slow enzymatic hydrolysis make the overall process of lignocellulosic conversion into biofuels less economical than available fossil fuels. Lignocellulose conversions carried out at ≤ 50 °C have several limitations. Therefore, this review focuses on the importance of thermophilic bacteria and thermostable enzymes to overcome the limitations of existing lignocellulosic biomass conversion processes. The influence of high temperatures on various existing lignocellulose conversion processes and those that are under development, including separate hydrolysis and fermentation, simultaneous saccharification and fermentation, and extremophilic consolidated bioprocess are also discussed.
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Affiliation(s)
- Aditya Bhalla
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
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Reconstitution of a thermostable xylan-degrading enzyme mixture from the bacterium Caldicellulosiruptor bescii. Appl Environ Microbiol 2012; 79:1481-90. [PMID: 23263957 DOI: 10.1128/aem.03265-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylose, the major constituent of xylans, as well as the side chain sugars, such as arabinose, can be metabolized by engineered yeasts into ethanol. Therefore, xylan-degrading enzymes that efficiently hydrolyze xylans will add value to cellulases used in hydrolysis of plant cell wall polysaccharides for conversion to biofuels. Heterogeneous xylan is a complex substrate, and it requires multiple enzymes to release its constituent sugars. However, the components of xylan-degrading enzymes are often individually characterized, leading to a dearth of research that analyzes synergistic actions of the components of xylan-degrading enzymes. In the present report, six genes predicted to encode components of the xylan-degrading enzymes of the thermophilic bacterium Caldicellulosiruptor bescii were expressed in Escherichia coli, and the recombinant proteins were investigated as individual enzymes and also as a xylan-degrading enzyme cocktail. Most of the component enzymes of the xylan-degrading enzyme mixture had similar optimal pH (5.5 to ∼6.5) and temperature (75 to ∼90°C), and this facilitated their investigation as an enzyme cocktail for deconstruction of xylans. The core enzymes (two endoxylanases and a β-xylosidase) exhibited high turnover numbers during catalysis, with the two endoxylanases yielding estimated k(cat) values of ∼8,000 and ∼4,500 s(-1), respectively, on soluble wheat arabinoxylan. Addition of side chain-cleaving enzymes to the core enzymes increased depolymerization of a more complex model substrate, oat spelt xylan. The C. bescii xylan-degrading enzyme mixture effectively hydrolyzes xylan at 65 to 80°C and can serve as a basal mixture for deconstruction of xylans in bioenergy feedstock at high temperatures.
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