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Chou KJ, Croft T, Hebdon SD, Magnusson LR, Xiong W, Reyes LH, Chen X, Miller EJ, Riley DM, Dupuis S, Laramore KA, Keller LM, Winkelman D, Maness PC. Engineering the cellulolytic bacterium, Clostridium thermocellum, to co-utilize hemicellulose. Metab Eng 2024; 83:193-205. [PMID: 38631458 DOI: 10.1016/j.ymben.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic biomass holds promise to realize economic production of second-generation biofuels/chemicals, and Clostridium thermocellum is a leading candidate for CBP due to it being one of the fastest degraders of crystalline cellulose and lignocellulosic biomass. However, CBP by C. thermocellum is approached with co-cultures, because C. thermocellum does not utilize hemicellulose. When compared with a single-species fermentation, the co-culture system introduces unnecessary process complexity that may compromise process robustness. In this study, we engineered C. thermocellum to co-utilize hemicellulose without the need for co-culture. By evolving our previously engineered xylose-utilizing strain in xylose, an evolved clonal isolate (KJC19-9) was obtained and showed improved specific growth rate on xylose by ∼3-fold and displayed comparable growth to a minimally engineered strain grown on the bacteria's naturally preferred substrate, cellobiose. To enable full xylan deconstruction to xylose, we recombinantly expressed three different β-xylosidase enzymes originating from Thermoanaerobacterium saccharolyticum into KJC19-9 and demonstrated growth on xylan with one of the enzymes. This recombinant strain was capable of co-utilizing cellulose and xylan simultaneously, and we integrated the β-xylosidase gene into the KJC19-9 genome, creating the KJCBXint strain. The strain, KJC19-9, consumed monomeric xylose but accumulated xylobiose when grown on pretreated corn stover, whereas the final KJCBXint strain showed significantly greater deconstruction of xylan and xylobiose. This is the first reported C. thermocellum strain capable of degrading and assimilating hemicellulose polysaccharide while retaining its cellulolytic capabilities, unlocking significant potential for CBP in advancing the bioeconomy.
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Affiliation(s)
- Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA.
| | - Trevor Croft
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Skyler D Hebdon
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lauren R Magnusson
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Wei Xiong
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Luis H Reyes
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA; Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Xiaowen Chen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Emily J Miller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Danielle M Riley
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Sunnyjoy Dupuis
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Kathrin A Laramore
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lisa M Keller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Dirk Winkelman
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
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Mendonça M, Barroca M, Collins T. Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities. Biotechnol Adv 2023; 65:108148. [PMID: 37030552 DOI: 10.1016/j.biotechadv.2023.108148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.
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de Camargo BR, Steindorff AS, da Silva LA, de Oliveira AS, Hamann PRV, Noronha EF. Expression profiling of Clostridium thermocellum B8 during the deconstruction of sugarcane bagasse and straw. World J Microbiol Biotechnol 2023; 39:105. [PMID: 36840776 DOI: 10.1007/s11274-023-03546-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023]
Abstract
The gram-positive bacterium Clostridium thermocellum contains a set of carbohydrate-active enzymes that can potentially be employed to generate high-value-added products from lignocellulose. In this study, the gene expression profiling of C. thermocellum B8 was provided during growth in the presence of sugarcane bagasse and straw as a carbon source in comparison to growth using microcrystalline cellulose. A total of 625 and 509 genes were up-regulated for growth in the presence of bagasse and straw, respectively. These genes were mainly grouped into carbohydrate-active enzymes (CAZymes), cell motility, chemotaxis, quorum sensing pathway and expression control of glycoside hydrolases. These results show that type of carbon source modulates the gene expression profiling of carbohydrate-active enzymes. In addition, highlight the importance of cell motility, attachment to the substrate and communication in deconstructing complex substrates. This present work may contribute to the development of enzymatic cocktails and industrial strains for biorefineries based on sugarcane residues as feedstock.
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Affiliation(s)
- Brenda Rabello de Camargo
- Laboratory of Enzymology, Department of Cell Biology, University of Brasília, Brasilia, DF, 70910-900, Brazil
| | | | - Leonardo Assis da Silva
- Laboratory of Virology, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Athos Silva de Oliveira
- Laboratory of Virology, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Pedro Ricardo Vieira Hamann
- São Carlos Institute of Physics, University of São Paulo, Avenida Trabalhador São-Carlense,400, Parque Arnold Schimidt, São Carlos, SP, 13566-590, Brazil
| | - Eliane Ferreira Noronha
- Laboratory of Enzymology, Department of Cell Biology, University of Brasília, Brasilia, DF, 70910-900, Brazil.
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Structure and function of microbial α-l-fucosidases: a mini review. Essays Biochem 2023; 67:399-414. [PMID: 36805644 PMCID: PMC10154630 DOI: 10.1042/ebc20220158] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 02/23/2023]
Abstract
Fucose is a monosaccharide commonly found in mammalian, insect, microbial and plant glycans. The removal of terminal α-l-fucosyl residues from oligosaccharides and glycoconjugates is catalysed by α-l-fucosidases. To date, glycoside hydrolases (GHs) with exo-fucosidase activity on α-l-fucosylated substrates (EC 3.2.1.51, EC 3.2.1.-) have been reported in the GH29, GH95, GH139, GH141 and GH151 families of the Carbohydrate Active Enzymes (CAZy) database. Microbes generally encode several fucosidases in their genomes, often from more than one GH family, reflecting the high diversity of naturally occuring fucosylated structures they encounter. Functionally characterised microbial α-l-fucosidases have been shown to act on a range of substrates with α-1,2, α-1,3, α-1,4 or α-1,6 fucosylated linkages depending on the GH family and microorganism. Fucosidases show a modular organisation with catalytic domains of GH29 and GH151 displaying a (β/α)8-barrel fold while GH95 and GH141 show a (α/α)6 barrel and parallel β-helix fold, respectively. A number of crystal structures have been solved in complex with ligands, providing structural basis for their substrate specificity. Fucosidases can also be used in transglycosylation reactions to synthesise oligosaccharides. This mini review provides an overview of the enzymatic and structural properties of microbial α-l-fucosidases and some insights into their biological function and biotechnological applications.
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Naumoff DG, Kulichevskaya IS, Dedysh SN. Genetic Determinants of Xylan Utilization in Humisphaera borealis M1803T, a Planctomycete of the Class Phycisphaerae. Microbiology (Reading) 2022. [DOI: 10.1134/s002626172230004x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Abstract—
Planctomycetes of the class Phycisphaerae are aerobic and anaerobic heterotrophic bacteria that colonize a wide range of marine and terrestrial habitats. Their functional roles in the environment, however, are still poorly understood. Humisphaera borealis M1803T is one of the very few characterized planctomycetes of this class. It is also the first described representative of the previously uncultured group WD2101, which is commonly detected in soils and peatlands. This work analyzed the genetic determinants that define the ability of Humisphaera borealis M1803T to grow on xylan, one of the plant cell wall polymers. The whole genome sequence analysis of this planctomycete resulted in identification of five genes encoding the proteins homologous to previously described endo-β-xylanases. For two of these proteins, evolutionarily closer experimentally characterized homologs with other substrate specificities were found. In a member of the GH10 family of glycoside hydrolases, the active center of the enzyme was destroyed. We consider two proteins from GH62 and GH141 families as the most likely candidates for the role of β-xylanase responsible for xylan utilization. Phylogenetic analysis of proteins of GH10, GH62, and GH141 families was carried out. The role of lateral transfers in the evolution of the genes for glycoside hydrolases and their close homologs is discussed.
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Biswal AK, Hengge NN, Black IM, Atmodjo MA, Mohanty SS, Ryno D, Himmel ME, Azadi P, Bomble YJ, Mohnen D. Composition and yield of non-cellulosic and cellulosic sugars in soluble and particulate fractions during consolidated bioprocessing of poplar biomass by Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:23. [PMID: 35227303 PMCID: PMC8887089 DOI: 10.1186/s13068-022-02119-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Terrestrial plant biomass is the primary renewable carbon feedstock for enabling transition to a sustainable bioeconomy. Consolidated bioprocessing (CBP) by the cellulolytic thermophile Clostridium thermocellum offers a single step microbial platform for production of biofuels and biochemicals via simultaneous solubilization of carbohydrates from lignocellulosic biomass and conversion to products. Here, solubilization of cell wall cellulosic, hemicellulosic, and pectic polysaccharides in the liquor and solid residues generated during CBP of poplar biomass by C. thermocellum was analyzed. RESULTS The total amount of biomass solubilized in the C. thermocellum DSM1313 fermentation platform was 5.8, 10.3, and 13.7% of milled non-pretreated poplar after 24, 48, and 120 h, respectively. These results demonstrate solubilization of 24% cellulose and 17% non-cellulosic sugars after 120 h, consistent with prior reports. The net solubilization of non-cellulosic sugars by C. thermocellum (after correcting for the uninoculated control fermentations) was 13 to 36% of arabinose (Ara), xylose (Xyl), galactose (Gal), mannose (Man), and glucose (Glc); and 15% and 3% of fucose and glucuronic acid, respectively. No rhamnose was solubilized and 71% of the galacturonic acid (GalA) was solubilized. These results indicate that C. thermocellum may be selective for the types and/or rate of solubilization of the non-cellulosic wall polymers. Xyl, Man, and Glc were found to accumulate in the fermentation liquor at levels greater than in uninoculated control fermentations, whereas Ara and Gal did not accumulate, suggesting that C. thermocellum solubilizes both hemicelluloses and pectins but utilizes them differently. After five days of fermentation, the relative amount of Rha in the solid residues increased 21% indicating that the Rha-containing polymer rhamnogalacturonan I (RG-I) was not effectively solubilized by C. thermocellum CBP, a result confirmed by immunoassays. Comparison of the sugars in the liquor versus solid residue showed that C. thermocellum solubilized hemicellulosic xylan and mannan, but did not fully utilize them, solubilized and appeared to utilize pectic homogalacturonan, and did not solubilize RG-I. CONCLUSIONS The significant relative increase in RG-I in poplar solid residues following CBP indicates that C. thermocellum did not solubilize RG-I. These results support the hypothesis that this pectic glycan may be one barrier for efficient solubilization of poplar by C. thermocellum.
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Affiliation(s)
- Ajaya K. Biswal
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Neal N. Hengge
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Ian M. Black
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Melani A. Atmodjo
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Sushree S. Mohanty
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - David Ryno
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Debra Mohnen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
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Verma D. Extremophilic Prokaryotic Endoxylanases: Diversity, Applicability, and Molecular Insights. Front Microbiol 2021; 12:728475. [PMID: 34566933 PMCID: PMC8458939 DOI: 10.3389/fmicb.2021.728475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Extremophilic endoxylanases grabbed attention in recent years due to their applicability under harsh conditions of several industrial processes. Thermophilic, alkaliphilic, and acidophilic endoxylanases found their employability in bio-bleaching of paper pulp, bioconversion of lignocellulosic biomass into xylooligosaccharides, bioethanol production, and improving the nutritious value of bread and other bakery products. Xylanases obtained from extremophilic bacteria and archaea are considered better than fungal sources for several reasons. For example, enzymatic activity under broad pH and temperature range, low molecular weight, cellulase-free activity, and longer stability under extreme conditions of prokaryotic derived xylanases make them a good choice. In addition, a short life span, easy cultivation/harvesting methods, higher yield, and rapid DNA manipulations of bacterial and archaeal cells further reduces the overall cost of the product. This review focuses on the diversity of prokaryotic endoxylanases, their characteristics, and their functional attributes. Besides, the molecular mechanisms of their extreme behavior have also been presented here.
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Affiliation(s)
- Digvijay Verma
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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Hamann PRV, de M B Silva L, Gomes TC, Noronha EF. Assembling mini-xylanosomes with Clostridium thermocellum XynA, and their properties in lignocellulose deconstruction. Enzyme Microb Technol 2021; 150:109887. [PMID: 34489040 DOI: 10.1016/j.enzmictec.2021.109887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 12/01/2022]
Abstract
Lignocellulose is a prominent source of carbohydrates to be used in biorefineries. One of the main challenges associated with its use is the low yields obtained during enzymatic hydrolysis, as well as the high cost associate with enzyme acquisition. Despite the great attention in using the fraction composed by hexoses, nowadays, there is a growing interest in enzymatic blends to deconstruct the pentose-rich fraction. Among the organisms studied as a source of enzymes to lignocellulose deconstruction, the anaerobic bacterium Clostridium thermocellum stands out. Most of the remarkable performance of C. thermocellum in degrading cellulose is related to its capacity to assemble enzymes into well-organized enzymatic complexes, cellulosomes. A mini-version of a cellulosome was designed in the present study, using the xylanase XynA and the N-terminus portion of scaffolding protein, mCipA, harboring one CBM3 and two cohesin I domains. The formed mini-xylanosome displayed maximum activity between 60 and 70 °C in a pH range from 6 to 8. Although biochemical properties of complexed/non-complexed enzymes were similar, the formed xylanosome displayed higher hydrolysis at 60 and 70 °C for alkali-treated sugarcane bagasse. Lignocellulose deconstruction using fungal secretome and the mini-xylanosome resulted in higher d-glucose yield, and the addition of the mCipA scaffolding protein enhanced cellulose deconstruction when coupled with fungal enzymes. Results obtained in this study demonstrated that the assembling of xylanases into mini-xylanosomes could improve sugarcane deconstruction, and the mCipA protein can work as a cellulose degradation enhancer.
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Affiliation(s)
- Pedro R V Hamann
- University of Brasilia, Cell Biology Department, Enzymology Laboratory, Brazil.
| | - Luísa de M B Silva
- University of Brasilia, Cell Biology Department, Enzymology Laboratory, Brazil
| | - Tainah C Gomes
- University of Brasilia, Cell Biology Department, Enzymology Laboratory, Brazil
| | - Eliane F Noronha
- University of Brasilia, Cell Biology Department, Enzymology Laboratory, Brazil.
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Biochemical characterization of a GH10 xylanase from the anaerobic rumen fungus Anaeromyces robustus and application in bread making. 3 Biotech 2021; 11:406. [PMID: 34471589 DOI: 10.1007/s13205-021-02956-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/04/2021] [Indexed: 01/03/2023] Open
Abstract
Anaeromyces robustus is an anaerobic rumen microorganism which can produce plant cell wall degrading enzymes. In this study, a new GH10 xylanase gene xylAr10 from A. robustus was identified, cloned and expressed in Pichia pastoris GS115. The recombinant protein ArXyn10 was characterized after being purified by Ni-NTA. The optimal pH and temperature of ArXyn10 was determined at 5.5 and 40 °C, respectively. ArXyn10 was stable at the pH range of 4.0-8.0, and could maintain high stability from 35 to 45 °C. The hydrolysis products released from beechwood xylan by ArXyn10 showed chromatographic mobility similar to xylobiose and xylotriose according to thin-layer chromatography analysis. It was shown that the addition of 7.5 mg of ArXyn10 in 100 g high-gluten wheat flour during bread making could increase the reducing sugar content by 10.80%, indicating that xylo-oligosaccharides were produced. With the addition of ArXyn10, the hardness and chewiness of the bread decreased and the quality was improved. The new discovered xylanase ArXyn10 have potential application prospect in bread making.
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Joseph RC, Kelley SQ, Kim NM, Sandoval NR. Metabolic Engineering and the Synthetic Biology Toolbox for
Clostridium. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Molecular modification, structural characterization, and biological activity of xylans. Carbohydr Polym 2021; 269:118248. [PMID: 34294285 DOI: 10.1016/j.carbpol.2021.118248] [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: 12/28/2020] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 12/17/2022]
Abstract
The differences in the source and structure of xylans make them have various biological activities. However, due to their inherent structural limitations, the various biological activities of xylans are far lower than those of commercial drugs. Currently, several types of molecular modification methods have been developed to address these limitations, and many derivatives with specific biological activity have been obtained. Further research on structural characteristics, structure-activity relationship and mechanism of action is of great significance for the development of xylan derivatives. Therefore, the major molecular modification methods of xylans are introduced in this paper, and the primary structure and conformation characteristics of xylans and their derivatives are summarized. In addition, the biological activity and structure-activity relationship of the modified xylans are also discussed.
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Dedysh SN, Beletsky AV, Ivanova AA, Kulichevskaya IS, Suzina NE, Philippov DA, Rakitin AL, Mardanov AV, Ravin NV. Wide distribution of Phycisphaera-like planctomycetes from WD2101 soil group in peatlands and genome analysis of the first cultivated representative. Environ Microbiol 2020; 23:1510-1526. [PMID: 33325093 DOI: 10.1111/1462-2920.15360] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022]
Abstract
Phycisphaera-like WD2101 'soil group' is one of the as-yet-uncultivated phylogenetic clades within the phylum Planctomycetes. Members of this clade are commonly detected in various terrestrial habitats. This study shows that WD2101 represented one of the major planctomycete groups in 10 boreal peatlands, comprising up to 76% and 36% of all Planctomycetes-affiliated 16S rRNA gene reads in raised bogs and eutrophic fens respectively. These types of peatlands displayed clearly distinct intra-group diversity of WD2101-affiliated planctomycetes. The first isolate of this enigmatic planctomycete group, strain M1803, was obtained from a humic lake surrounded by Sphagnum peat bogs. Strain M1803 displayed 89.2% 16S rRNA gene similarity to Tepidisphaera mucosa and was represented by motile cocci that divided by binary fission and grew under micro-oxic conditions. The complete 7.19 Mb genome of strain M1803 contained an array of genes encoding Planctomycetal type bacterial microcompartment organelle likely involved in l-rhamnose metabolism, suggesting participation of M1803-like planctomycetes in polysaccharide degradation in peatlands. The corresponding cellular microcompartments were revealed in ultrathin cell sections. Strain M1803 was classified as a novel genus and species, Humisphaera borealis gen. nov., sp. nov., affiliated with the formerly recognized WD2101 'soil group'.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Natalia E Suzina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitriy A Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Andrey L Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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Elcheninov AG, Podosokorskaya OA, Kovaleva OL, Novikov AA, Toshchakov SV, Bonch-Osmolovskaya EA, Kublanov IV. Thermogemmata fonticola gen. nov., sp. nov., the first thermophilic planctomycete of the order Gemmatales from a Kamchatka hot spring. Syst Appl Microbiol 2020; 44:126157. [PMID: 33220635 DOI: 10.1016/j.syapm.2020.126157] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/21/2020] [Accepted: 11/02/2020] [Indexed: 01/08/2023]
Abstract
A novel aerobic moderately thermophilic bacterium, designated strain 2918T, was isolated from a terrestrial hot spring of Kamchatka, Russian Federation. Gram-negative, motile, spherical cells were present singly, in pairs, or aggregates, and reproduced by budding. The strain grew at 25-60°C and within a pH range of 5.0-8.0 with an optimum at 54-60°C and pH 7.5. Strain 2918T did not require sodium chloride or yeast extract for growth. It was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (starch, lichenan, galactan, arabinan, xanthan gum, beta-glucan). No growth was observed under anaerobic conditions neither in the presence of sulfur, nitrate, or thiosulfate nor without adding any electron acceptor. Major cellular fatty acids were C18:0 and C20:0. The respiratory quinone was MK-6. The size of the genome of strain 2918T was 4.81 Mb. Genomic DNA G+C content was 60.4mol%. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, strain 2918T represented a distinct lineage of the order Gemmatales within Planctomycetes. Based on phylogenetic analysis and phenotypic features, the novel isolate was assigned to a novel genus in the Gemmatales for which the name Thermogemmata gen. nov. is proposed. Strain 2918T (=KCTC 72012T =VKM B-3161T) represents its first species Thermogemmata fonticola sp. nov.
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Affiliation(s)
- Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia.
| | - Olga A Podosokorskaya
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Olga L Kovaleva
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Andrei A Novikov
- Gubkin Russian State University of Oil and Gas, Leninskiy Prospect 65, 119991 Moscow, Russia
| | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Elizaveta A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia; Lomonosov State University, Leninskie Gory 1 Bldg 12, Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
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14
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Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, Fernandez-Guerra A, Liebeke M, Schweder T, Polz MF, Hehemann JH. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol 2020; 5:1026-1039. [PMID: 32451471 DOI: 10.1038/s41564-020-0720-2] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/06/2020] [Indexed: 12/16/2022]
Abstract
Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.
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Affiliation(s)
- Andreas Sichert
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany
| | - Christopher H Corzett
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Antonio Fernandez-Guerra
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany.
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15
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Hamann PR, Gomes TC, de M.B.Silva L, Noronha EF. Influence of lignin-derived phenolic compounds on the Clostridium thermocellum endo-β-1,4-xylanase XynA. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.02.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Krska D, Larsbrink J. Investigation of a thermostable multi-domain xylanase-glucuronoyl esterase enzyme from Caldicellulosiruptor kristjanssonii incorporating multiple carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:68. [PMID: 32308737 PMCID: PMC7151638 DOI: 10.1186/s13068-020-01709-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/02/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Efficient degradation of lignocellulosic biomass has become a major bottleneck in industrial processes which attempt to use biomass as a carbon source for the production of biofuels and materials. To make the most effective use of the source material, both the hemicellulosic as well as cellulosic parts of the biomass should be targeted, and as such both hemicellulases and cellulases are important enzymes in biorefinery processes. Using thermostable versions of these enzymes can also prove beneficial in biomass degradation, as they can be expected to act faster than mesophilic enzymes and the process can also be improved by lower viscosities at higher temperatures, as well as prevent the introduction of microbial contamination. RESULTS This study presents the investigation of the thermostable, dual-function xylanase-glucuronoyl esterase enzyme CkXyn10C-GE15A from the hyperthermophilic bacterium Caldicellulosiruptor kristjanssonii. Biochemical characterization of the enzyme was performed, including assays for establishing the melting points for the different protein domains, activity assays for the two catalytic domains, as well as binding assays for the multiple carbohydrate-binding domains present in CkXyn10C-GE15A. Although the enzyme domains are naturally linked together, when added separately to biomass, the expected boosting of the xylanase action was not seen. This lack of intramolecular synergy might suggest, together with previous data, that increased xylose release is not the main beneficial trait given by glucuronoyl esterases. CONCLUSIONS Due to its thermostability, CkXyn10C-GE15A is a promising candidate for industrial processes, with both catalytic domains exhibiting melting temperatures over 70 °C. Of particular interest is the glucuronoyl esterase domain, as it represents the first studied thermostable enzyme displaying this activity.
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Affiliation(s)
- Daniel Krska
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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17
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Bhardwaj N, Kumar B, Verma P. A detailed overview of xylanases: an emerging biomolecule for current and future prospective. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0276-2] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Xylan is the second most abundant naturally occurring renewable polysaccharide available on earth. It is a complex heteropolysaccharide consisting of different monosaccharides such as l-arabinose, d-galactose, d-mannoses and organic acids such as acetic acid, ferulic acid, glucuronic acid interwoven together with help of glycosidic and ester bonds. The breakdown of xylan is restricted due to its heterogeneous nature and it can be overcome by xylanases which are capable of cleaving the heterogeneous β-1,4-glycoside linkage. Xylanases are abundantly present in nature (e.g., molluscs, insects and microorganisms) and several microorganisms such as bacteria, fungi, yeast, and algae are used extensively for its production. Microbial xylanases show varying substrate specificities and biochemical properties which makes it suitable for various applications in industrial and biotechnological sectors. The suitability of xylanases for its application in food and feed, paper and pulp, textile, pharmaceuticals, and lignocellulosic biorefinery has led to an increase in demand of xylanases globally. The present review gives an insight of using microbial xylanases as an “Emerging Green Tool” along with its current status and future prospective.
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Passarinho ATP, Ventorim RZ, Maitan-Alfenas GP, de Oliveira EB, Guimarães VM. Engineered GH11 xylanases from Orpinomyces sp. PC-2 improve techno-functional properties of bread dough. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:741-747. [PMID: 29999533 DOI: 10.1002/jsfa.9242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/22/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Endo-1,4-β-xylanases have marked hydrolytic activity towards arabinoxylans. Xylanases (xynA) produced by the anaerobic fungus Orpinomyces sp. strain PC-2 have been shown to be superior in specific activity, which strongly suggests their applicability in the bakery industry for the processing of whole-wheat flour containing xylans. In the present study, two xylanases from this source, the small wild-type xylanase SWT and the small mutant xylanase SM2 (V108A, A199T), were expressed in Escherichia coli, purified, characterized, tested for their ability to hydrolyze whole-wheat flour and applied in dough processing. RESULTS Both purified SM2 and SWT showed high specific activity against oat spelt xylan and wheat arabinoxylan, exhibiting maximum activity at pH 3-7 and 60 °C. SM2 was more thermostable than SWT, which suggests that the mutations enhanced its stability. Both SWT and SM2 were able to hydrolyze whole-wheat flour, and evaluation of their applicability in dough processing by the sponge method indicated that use of these enzymes increased dough volume by 60% and reduced texture hardness by more than 50%, while gumminess and chewiness were reduced by 40%. CONCLUSION The recombinant xylanases showed potential for application in bakery processing and can improve techno-functional properties in sponges. © 2018 Society of Chemical Industry.
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Leis B, Held C, Andreeßen B, Liebl W, Graubner S, Schulte LP, Schwarz WH, Zverlov VV. Optimizing the composition of a synthetic cellulosome complex for the hydrolysis of softwood pulp: identification of the enzymatic core functions and biochemical complex characterization. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:220. [PMID: 30116297 PMCID: PMC6083626 DOI: 10.1186/s13068-018-1220-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/31/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND The development of efficient cellulase blends is a key factor for cost-effectively valorizing biomass in a new bio-economy. Today, the enzymatic hydrolysis of plant-derived polysaccharides is mainly accomplished with fungal cellulases, whereas potentially equally effective cellulose-degrading systems from bacteria have not been developed. Particularly, a thermostable multi-enzyme cellulase complex, the cellulosome from the anaerobic cellulolytic bacterium Clostridium thermocellum is promising of being applied as cellulolytic nano-machinery for the production of fermentable sugars from cellulosic biomass. RESULTS In this study, 60 cellulosomal components were recombinantly produced in E. coli and systematically permuted in synthetic complexes to study the function-activity relationship of all available enzymes on Kraft pulp from pine wood as the substrate. Starting from a basic exo/endoglucanase complex, we were able to identify additional functional classes such as mannanase and xylanase for optimal activity on the substrate. Based on these results, we predicted a synthetic cellulosome complex consisting of seven single components (including the scaffoldin protein and a β-glucosidase) and characterized it biochemically. We obtained a highly thermostable complex with optimal activity around 60-65 °C and an optimal pH in agreement with the optimum of the native cellulosome (pH 5.8). Remarkably, a fully synthetic complex containing 47 single cellulosomal components showed comparable activity with a commercially available fungal enzyme cocktail on the softwood pulp substrate. CONCLUSIONS Our results show that synthetic bacterial multi-enzyme complexes based on the cellulosome of C. thermocellum can be applied as a versatile platform for the quick adaptation and efficient degradation of a substrate of interest.
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Affiliation(s)
- Benedikt Leis
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Present Address: Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Winchester Str. 2, 35394 Gießen, Germany
| | - Claudia Held
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Björn Andreeßen
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Sigrid Graubner
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Louis-Philipp Schulte
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
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20
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Schwarz WH, Brunecky R, Broeker J, Liebl W, Zverlov VV. Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9A gene of Clostridium thermocellum. World J Microbiol Biotechnol 2018; 34:42. [PMID: 29480332 DOI: 10.1007/s11274-018-2424-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 02/20/2018] [Indexed: 01/11/2023]
Abstract
An increasing number of researchers working in biology, biochemistry, biotechnology, bioengineering, bioinformatics and other related fields of science are using biological molecules. As the scientific background of the members of different scientific communities is more diverse than ever before, the number of scientists not familiar with the rules for non-ambiguous designation of genetic elements is increasing. However, with biological molecules gaining importance through biotechnology, their functional and unambiguous designation is vital. Unfortunately, naming genes and proteins is not an easy task. In addition, the traditional concepts of bioinformatics are challenged with the appearance of proteins comprising different modules with a respective function in each module. This article highlights basic rules and novel solutions in designation recently used within the community of bacterial geneticists, and we discuss the present-day handling of gene and protein designations. As an example we will utilize a recent mischaracterization of gene nomenclature. We make suggestions for better handling of names in future literature as well as in databases and annotation projects. Our methodology emphasizes the hydrolytic function of multi-modular genes and extracellular proteins from bacteria.
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Affiliation(s)
- Wolfgang H Schwarz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany.
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Jannis Broeker
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany
| | - Vladimir V Zverlov
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany. .,Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182, Moscow, Russia.
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21
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Joseph RC, Kim NM, Sandoval NR. Recent Developments of the Synthetic Biology Toolkit for Clostridium. Front Microbiol 2018; 9:154. [PMID: 29483900 PMCID: PMC5816073 DOI: 10.3389/fmicb.2018.00154] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/23/2018] [Indexed: 12/15/2022] Open
Abstract
The Clostridium genus is a large, diverse group consisting of Gram-positive, spore-forming, obligate anaerobic firmicutes. Among this group are historically notorious pathogens as well as several industrially relevant species with the ability to produce chemical commodities, particularly biofuels, from renewable biomass. Additionally, other species are studied for their potential use as therapeutics. Although metabolic engineering and synthetic biology have been instrumental in improving product tolerance, titer, yields, and feed stock consumption capabilities in several organisms, low transformation efficiencies and lack of synthetic biology tools and genetic parts make metabolic engineering within the Clostridium genus difficult. Progress has recently been made to overcome challenges associated with engineering various Clostridium spp. For example, developments in CRISPR tools in multiple species and strains allow greater capability to produce edits with greater precision, faster, and with higher efficiencies. In this mini-review, we will highlight these recent advances and compare them to established methods for genetic engineering in Clostridium. In addition, we discuss the current state and development of Clostridium-based promoters (constitutive and inducible) and reporters. Future progress in this area will enable more rapid development of strain engineering, which would allow for the industrial exploitation of Clostridium for several applications including bioproduction of several commodity products.
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Affiliation(s)
- Rochelle C. Joseph
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, United States
| | - Nancy M. Kim
- Interdisciplinary Bioinnovation PhD Program, Tulane University, New Orleans, LA, United States
| | - Nicholas R. Sandoval
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, United States
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22
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Joseph RC, Kim NM, Sandoval NR. Recent Developments of the Synthetic Biology Toolkit for Clostridium. Front Microbiol 2018. [PMID: 29483900 DOI: 10.3389/fmicb.2018.00154/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
The Clostridium genus is a large, diverse group consisting of Gram-positive, spore-forming, obligate anaerobic firmicutes. Among this group are historically notorious pathogens as well as several industrially relevant species with the ability to produce chemical commodities, particularly biofuels, from renewable biomass. Additionally, other species are studied for their potential use as therapeutics. Although metabolic engineering and synthetic biology have been instrumental in improving product tolerance, titer, yields, and feed stock consumption capabilities in several organisms, low transformation efficiencies and lack of synthetic biology tools and genetic parts make metabolic engineering within the Clostridium genus difficult. Progress has recently been made to overcome challenges associated with engineering various Clostridium spp. For example, developments in CRISPR tools in multiple species and strains allow greater capability to produce edits with greater precision, faster, and with higher efficiencies. In this mini-review, we will highlight these recent advances and compare them to established methods for genetic engineering in Clostridium. In addition, we discuss the current state and development of Clostridium-based promoters (constitutive and inducible) and reporters. Future progress in this area will enable more rapid development of strain engineering, which would allow for the industrial exploitation of Clostridium for several applications including bioproduction of several commodity products.
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Affiliation(s)
- Rochelle C Joseph
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, United States
| | - Nancy M Kim
- Interdisciplinary Bioinnovation PhD Program, Tulane University, New Orleans, LA, United States
| | - Nicholas R Sandoval
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, United States
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