1
|
Liu N, Odinot E, David H, Vita N, Otalvaro FM, Parsiegla G, Denis Y, Faulds C, Fierobe HP, Perret S. Intracellular removal of acetyl, feruloyl and p-coumaroyl decorations on arabinoxylo-oligosaccharides imported from lignocellulosic biomass degradation by Ruminiclostridium cellulolyticum. Microb Cell Fact 2024; 23:151. [PMID: 38789996 PMCID: PMC11127375 DOI: 10.1186/s12934-024-02423-z] [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: 02/13/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Xylans are polysaccharides that are naturally abundant in agricultural by-products, such as cereal brans and straws. Microbial degradation of arabinoxylan is facilitated by extracellular esterases that remove acetyl, feruloyl, and p-coumaroyl decorations. The bacterium Ruminiclostridium cellulolyticum possesses the Xua (xylan utilization associated) system, which is responsible for importing and intracellularly degrading arabinoxylodextrins. This system includes an arabinoxylodextrins importer, four intracellular glycosyl hydrolases, and two intracellular esterases, XuaH and XuaJ which are encoded at the end of the gene cluster. RESULTS Genetic studies demonstrate that the genes xuaH and xuaJ are part of the xua operon, which covers xuaABCDD'EFGHIJ. This operon forms a functional unit regulated by the two-component system XuaSR. The esterases encoded at the end of the cluster have been further characterized: XuaJ is an acetyl esterase active on model substrates, while XuaH is a xylan feruloyl- and p-coumaryl-esterase. This latter is active on oligosaccharides derived from wheat bran and wheat straw. Modelling studies indicate that XuaH has the potential to interact with arabinoxylobiose acylated with mono- or diferulate. The intracellular esterases XuaH and XuaJ are believed to allow the cell to fully utilize the complex acylated arabinoxylo-dextrins imported into the cytoplasm during growth on wheat bran or straw. CONCLUSIONS This study reports for the first time that a cytosolic feruloyl esterase is part of an intracellular arabinoxylo-dextrin import and degradation system, completing its cytosolic enzymatic arsenal. This system represents a new pathway for processing highly-decorated arabinoxylo-dextrins, which could provide a competitive advantage to the cell and may have interesting biotechnological applications.
Collapse
Affiliation(s)
- Nian Liu
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Elise Odinot
- OléoInnov, 19 rue du Musée, Marseille, 13001, France
| | - Hélène David
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Nicolas Vita
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Felipe Mejia Otalvaro
- Technical University of Denmark, The Novo Nordisk Foundation Center for Biosustainability, Konges Lyngby, 2800, Denmark
| | - Goetz Parsiegla
- Aix-Marseille Université, CNRS, BIP-UMR7281, Marseille, France
| | - Yann Denis
- Aix-Marseille Université, CNRS, IMM, Marseille, France
| | - Craig Faulds
- Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, UMR1163, 13009, France
| | | | | |
Collapse
|
2
|
Fosses A, Franche N, Parsiegla G, Denis Y, Maté M, de Philip P, Fierobe HP, Perret S. Role of the Solute-Binding Protein CuaD in the Signaling and Regulating Pathway of Cellobiose and Cellulose Utilization in Ruminiclostridium cellulolyticum. Microorganisms 2023; 11:1732. [PMID: 37512904 PMCID: PMC10384115 DOI: 10.3390/microorganisms11071732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
In Ruminiclostridium cellulolyticum, cellobiose is imported by the CuaABC ATP-binding cassette transporter containing the solute-binding protein (SBP) CuaA and is further degraded in the cytosol by the cellobiose phosphorylase CbpA. The genes encoding these proteins have been shown to be essential for cellobiose and cellulose utilization. Here, we show that a second SBP (CuaD), whose gene is adjacent to two genes encoding a putative two-component regulation system (CuaSR), forms a three-component system with CuaS and CuaR. Studies of mutant and recombinant strains of R. cellulolyticum have indicated that cuaD is important for the growth of strains on cellobiose and cellulose. Furthermore, the results of our RT-qPCR experiments suggest that both the three (CuaDSR)- and the two (CuaSR)-component systems are able to perceive the cellobiose signal. However, the strain producing the three-component system is more efficient in its cellobiose and cellulose utilization. As CuaD binds to CuaS, we propose an in-silico model of the complex made up of two extracellular domains of CuaS and two of CuaD. CuaD allows microorganisms to detect very low concentrations of cellobiose due to its high affinity and specificity for this disaccharide, and together with CuaSR, it triggers the expression of the cuaABC-cbpA genes involved in cellodextrins uptake.
Collapse
Affiliation(s)
| | | | | | - Yann Denis
- Aix Marseille Univ, CNRS, Plateforme Transcriptome, Marseille, France
| | - Maria Maté
- CNRS, Aix Marseille Univ, UMR7257 AFMB, Marseille, France
| | | | | | | |
Collapse
|
3
|
Lee SM, Ahn YM, Park SH, Shin S, Jung J. Reshaping the gut microbiome and bile acid composition by Gyejibongnyeong-hwan ameliorates western diet-induced dyslipidemia. Biomed Pharmacother 2023; 163:114826. [PMID: 37148862 DOI: 10.1016/j.biopha.2023.114826] [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: 03/16/2023] [Revised: 04/22/2023] [Accepted: 04/30/2023] [Indexed: 05/08/2023] Open
Abstract
Gyejibongnyeong-hwan (GBH), a traditional Chinese medicine, is used in clinical practice to treat blood stasis in metabolic diseases. Herein, we examined the effects of GBH on dyslipidemia and investigated the underlying mechanisms by focusing on modulation of the gut microbiota-bile acid axis by GBH. We utilized a Western diet-induced dyslipidemia mouse model and divided animals into the following four groups (n = 5 each): the normal chow diet, vehicle control (WD), simvastatin (Sim, 10 mg/kg/day simvastatin; positive control), and GBH (GBH, 300 mg/kg/day) groups. The drugs were administered for 10 weeks, and morphological changes in the liver and aorta were analyzed. The mRNA expression of genes related to cholesterol metabolism, gut microbiota, and bile acid profiles were also evaluated. The GBH group showed significantly lower levels of total cholesterol, accumulation of lipids, and inflammatory markers in the liver and aorta of Western diet-fed mice. Low-density lipoprotein cholesterol levels were significantly lower in the GBH group than in the WD group (P < 0.001). The expression of cholesterol excretion-associated genes such as liver X receptor alpha and ATP-binding cassette subfamily G member 8, as well as the bile acid synthesis gene cholesterol 7 alpha-hydroxylase, which lowers cholesterol in circulation, was increased. Furthermore, GBH inhibited the intestinal farnesoid X receptor (FXR)-fibroblast growth factor 15 signaling pathway through the interactions of gut microbiota with bile acids acting as FXR ligands, which included chenodeoxycholic acid and lithocholic acid. Overall, GBH improved dyslipidemia induced by a Western diet by modulating the gut microbiota-bile acid axis.
Collapse
Affiliation(s)
- So Min Lee
- KM Science Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
| | - You Mee Ahn
- KM Convergence Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
| | - Seong-Hwan Park
- KM Convergence Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
| | - Sarah Shin
- KM Convergence Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
| | - Jeeyoun Jung
- KM Convergence Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea.
| |
Collapse
|
4
|
Liu N, Gagnot S, Denis Y, Byrne D, Faulds C, Fierobe HP, Perret S. Selfish uptake versus extracellular arabinoxylan degradation in the primary degrader Ruminiclostridium cellulolyticum, a new string to its bow. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:127. [PMID: 36403068 PMCID: PMC9675976 DOI: 10.1186/s13068-022-02225-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Primary degraders of polysaccharides play a key role in anaerobic biotopes, where plant cell wall accumulates, providing extracellular enzymes to release fermentable carbohydrates to fuel themselves and other non-degrader species. Ruminiclostridium cellulolyticum is a model primary degrader growing amongst others on arabinoxylan. It produces large multi-enzymatic complexes called cellulosomes, which efficiently deconstruct arabinoxylan into fermentable monosaccharides. RESULTS Complete extracellular arabinoxylan degradation was long thought to be required to fuel the bacterium during this plant cell wall deconstruction stage. We discovered and characterized a second system of "arabinoxylan" degradation in R. cellulolyticum, which challenged this paradigm. This "selfish" system is composed of an ABC transporter dedicated to the import of large and possibly acetylated arabinoxylodextrins, and a set of four glycoside hydrolases and two esterases. These enzymes show complementary action modes on arabinoxylo-dextrins. Two α-L-arabinofuranosidases target the diverse arabinosyl side chains, and two exo-xylanases target the xylo-oligosaccharides backbone either at the reducing or the non-reducing end. Together, with the help of two different esterases removing acetyl decorations, they achieve the depolymerization of arabinoxylo-dextrins in arabinose, xylose and xylobiose. The in vivo study showed that this new system is strongly beneficial for the fitness of the bacterium when grown on arabinoxylan, leading to the conclusion that a part of arabinoxylan degradation is achieved in the cytosol, even if monosaccharides are efficiently provided by the cellulosomes in the extracellular space. These results shed new light on the strategies used by anaerobic primary degrader bacteria to metabolize highly decorated arabinoxylan in competitive environments. CONCLUSION The primary degrader model Ruminiclostridium cellulolyticum has developed a "selfish" strategy consisting of importing into the bacterium, large arabinoxylan-dextrin fractions released from a partial extracellular deconstruction of arabinoxylan, thus complementing its efficient extracellular arabinoxylan degradation system. Genetic studies suggest that this system is important to support fitness and survival in a competitive biotope. These results provide a better understanding of arabinoxylan catabolism in the primary degrader, with biotechnological application for synthetic microbial community engineering for the production of commodity chemicals from lignocellulosic biomass.
Collapse
Affiliation(s)
- Nian Liu
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France
| | - Séverine Gagnot
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France
| | - Yann Denis
- Aix Marseille Univ, CNRS, IMM, Marseille, France
| | | | - Craig Faulds
- INRAE, Aix Marseille Univ, INRAE, BBF, Marseille, France, 13009, Marseille, France
| | - Henri-Pierre Fierobe
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France
| | - Stéphanie Perret
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France.
| |
Collapse
|
5
|
Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases. Int J Mol Sci 2022; 23:ijms23063043. [PMID: 35328479 PMCID: PMC8950772 DOI: 10.3390/ijms23063043] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Among carbohydrate active enzymes, glycoside phosphorylases (GPs) are valuable catalysts for white biotechnologies, due to their exquisite capacity to efficiently re-modulate oligo- and poly-saccharides, without the need for costly activated sugars as substrates. The reversibility of the phosphorolysis reaction, indeed, makes them attractive tools for glycodiversification. However, discovery of new GP functions is hindered by the difficulty in identifying them in sequence databases, and, rather, relies on extensive and tedious biochemical characterization studies. Nevertheless, recent advances in automated tools have led to major improvements in GP mining, activity predictions, and functional screening. Implementation of GPs into innovative in vitro and in cellulo bioproduction strategies has also made substantial advances. Herein, we propose to discuss the latest developments in the strategies employed to efficiently discover GPs and make the best use of their exceptional catalytic properties for glycoside bioproduction.
Collapse
|
6
|
Bai S, Yang L, Wang H, Yang C, Hou X, Gao J, Zhang Z. Cellobiose phosphorylase from Caldicellulosiruptor bescii catalyzes reversible phosphorolysis via different kinetic mechanisms. Sci Rep 2022; 12:3978. [PMID: 35273293 PMCID: PMC8913831 DOI: 10.1038/s41598-022-08036-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/01/2022] [Indexed: 01/01/2023] Open
Abstract
In the process of yielding biofuels from cellulose degradation, traditional enzymatic hydrolysis, such as β-glucosidase catalyzing cellobiose, can barely resolve the contradiction between cellulose degradation and bioenergy conservation. However, it has been shown that cellobiose phosphorylase provides energetic advantages for cellobiose degradation through a phosphorolytic pathway, which has attracted wide attention. Here, the cellobiose phosphorylase gene from Caldicellulosiruptor bescii (CbCBP) was cloned, expressed, and purified. Analysis of the enzymatic properties and kinetic mechanisms indicated that CbCBP catalyzed reversible phosphorolysis and had good thermal stability and broad substrate selectivity. In addition, the phosphorolytic reaction of cellobiose by CbCBP proceeded via an ordered Bi Bi mechanism, while the synthetic reaction proceeded via a ping pong Bi Bi mechanism. The present study lays the foundation for optimizing the degradation of cellulose and the synthesis of functional oligosaccharides.
Collapse
Affiliation(s)
- Shaowei Bai
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, 130012, China
| | - Liangzhen Yang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, 130012, China
| | - Honglei Wang
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, 130012, China
| | - Chao Yang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, 130012, China
| | - Xuechen Hou
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, 130012, China
| | - Jingjie Gao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, 130012, China
| | - Zuoming Zhang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, 130012, China.
| |
Collapse
|
7
|
Gabrielli V, Muñoz-García JC, Pergolizzi G, de Andrade P, Khimyak YZ, Field RA, Angulo J. Molecular Recognition of Natural and Non-Natural Substrates by Cellodextrin Phosphorylase from Ruminiclostridium Thermocellum Investigated by NMR Spectroscopy. Chemistry 2021; 27:15688-15698. [PMID: 34436794 PMCID: PMC9293210 DOI: 10.1002/chem.202102039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 11/08/2022]
Abstract
β‐1→4‐Glucan polysaccharides like cellulose, derivatives and analogues, are attracting attention due to their unique physicochemical properties, as ideal candidates for many different applications in biotechnology. Access to these polysaccharides with a high level of purity at scale is still challenging, and eco‐friendly alternatives by using enzymes in vitro are highly desirable. One prominent candidate enzyme is cellodextrin phosphorylase (CDP) from Ruminiclostridium thermocellum, which is able to yield cellulose oligomers from short cellodextrins and α‐d‐glucose 1‐phosphate (Glc‐1‐P) as substrates. Remarkably, its broad specificity towards donors and acceptors allows the generation of highly diverse cellulose‐based structures to produce novel materials. However, to fully exploit this CDP broad specificity, a detailed understanding of the molecular recognition of substrates by this enzyme in solution is needed. Herein, we provide a detailed investigation of the molecular recognition of ligands by CDP in solution by saturation transfer difference (STD) NMR spectroscopy, tr‐NOESY and protein‐ligand docking. Our results, discussed in the context of previous reaction kinetics data in the literature, allow a better understanding of the structural basis of the broad binding specificity of this biotechnologically relevant enzyme.
Collapse
Affiliation(s)
- Valeria Gabrielli
- School of Pharmacy, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Juan C Muñoz-García
- School of Pharmacy, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Giulia Pergolizzi
- Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich, NR4 7TH, UK
| | - Peterson de Andrade
- Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich, NR4 7TH, UK.,Present address, Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Yaroslav Z Khimyak
- School of Pharmacy, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich, NR4 7TH, UK.,Present address, Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK.,Department of Organic Chemistry, Faculty of Chemistry, University of Seville, 41012, Seville, Spain.,Instituto de Investigaciones Químicas (CSIC-US), Avda. Américo Vespucio, 49, 41092, Sevilla, Spain
| |
Collapse
|
8
|
Handling Several Sugars at a Time: a Case Study of Xyloglucan Utilization by Ruminiclostridium cellulolyticum. mBio 2021; 12:e0220621. [PMID: 34749527 PMCID: PMC8576529 DOI: 10.1128/mbio.02206-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xyloglucan utilization by Ruminiclostridium cellulolyticum was formerly shown to imply the uptake of large xylogluco-oligosaccharides, followed by cytosolic depolymerization into glucose, galactose, xylose, and cellobiose. This raises the question of how the anaerobic bacterium manages the simultaneous presence of multiple sugars. Using genetic and biochemical approaches targeting the corresponding metabolic pathways, we observed that, surprisingly, all sugars are catabolized, collectively, but glucose consumption is prioritized. Most selected enzymes display unusual features, especially the GTP-dependent hexokinase of glycolysis, which appeared reversible and crucial for xyloglucan utilization. In contrast, mutant strains lacking either galactokinase, cellobiose-phosphorylase, or xylulokinase still catabolize xyloglucan but display variably altered growth. Furthermore, the xylogluco-oligosaccharide depolymerization process appeared connected to the downstream pathways through an intricate network of competitive and noncompetitive inhibitions. Altogether, our data indicate that xyloglucan utilization by R. cellulolyticum relies on an energy-saving central carbon metabolism deviating from current bacterial models, which efficiently prevents carbon overflow. IMPORTANCE The study of the decomposition of recalcitrant plant biomass is of great interest as the limiting step of terrestrial carbon cycle and to produce plant-derived valuable chemicals and energy. While extracellular cellulose degradation and catabolism have been studied in detail, few publications describe the complete metabolism of hemicelluloses and, to date, the published models are limited to the extracellular degradation and sequential entry of simple sugars. Here, we describe how the model anaerobic bacterium Ruminiclostridium cellulolyticum deals with the synchronous intracellular release of glucose, galactose, xylose, and cellobiose upon cytosolic depolymerization of imported xyloglucan oligosaccharides. The described novel metabolic strategy involves the simultaneous activity of different metabolic pathways coupled to a network of inhibitions controlling the carbon flux and is distinct from the ubiquitously observed sequential uptake and metabolism of carbohydrates known as the diauxic shift. Our results highlight the diversity of cellular responses related to a complex environment.
Collapse
|
9
|
Li Y, Zhao J, Zhang Z. Implementing metatranscriptomics to unveil the mechanism of bioaugmentation adopted in a continuous anaerobic process treating cow manure. BIORESOURCE TECHNOLOGY 2021; 330:124962. [PMID: 33740585 DOI: 10.1016/j.biortech.2021.124962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to investigate the effect of bioaugmentation on microbial community and function in a continuous anaerobic process treating lignocellulosic cow manure. One reactor (Rb) received bioaugmentation dosage for a certain period (d100-d170) and stopped afterward (d170-d220), while the same applied to the control (Rc) except sterilized bioaugmentation dosage was introduced. Samples were taken on day130, 170 and 220 from both reactors for metatranscriptomic analysis. The results underlined the promotive effect of bioaugmentation on indigenous microorganisms regarding hydrolysis and methanogenesis. Bioaugmentation contributed to the enrichment of Clostridium, Cellvibrio, Cellulomonas, Bacillus, Fibrobacter, resulting in enhanced cellulase activity (Rb: 0.917-1.081; Rc: 0.551-0.677). Moreover, bioaugmentation brought Rb the prosperity of uncultured_ Bathyarchaeia, a prominent archaeal group responsible for the improved methyl-coenzyme M reductase activity, thus accelerated methanogenesis. Unique metabolic pathways (autotrophic carbon fixation and methanogenesis) in uncultured_ Bathyarchaeia broadened the horizon of its fundamental role as acetogens and methanogens in anaerobic digestion.
Collapse
Affiliation(s)
- Yu Li
- Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| | - Jing Zhao
- Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Zhenhua Zhang
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| |
Collapse
|
10
|
β-Glucan phosphorylases in carbohydrate synthesis. Appl Microbiol Biotechnol 2021; 105:4073-4087. [PMID: 33970317 PMCID: PMC8140972 DOI: 10.1007/s00253-021-11320-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 01/02/2023]
Abstract
Abstract β-Glucan phosphorylases are carbohydrate-active enzymes that catalyze the reversible degradation of β-linked glucose polymers, with outstanding potential for the biocatalytic bottom-up synthesis of β-glucans as major bioactive compounds. Their preference for sugar phosphates (rather than nucleotide sugars) as donor substrates further underlines their significance for the carbohydrate industry. Presently, they are classified in the glycoside hydrolase families 94, 149, and 161 (www.cazy.org). Since the discovery of β-1,3-oligoglucan phosphorylase in 1963, several other specificities have been reported that differ in linkage type and/or degree of polymerization. Here, we present an overview of the progress that has been made in our understanding of β-glucan and associated β-glucobiose phosphorylases, with a special focus on their application in the synthesis of carbohydrates and related molecules. Key points • Discovery, characteristics, and applications of β-glucan phosphorylases. • β-Glucan phosphorylases in the production of functional carbohydrates.
Collapse
|
11
|
Borne R, Vita N, Franche N, Tardif C, Perret S, Fierobe HP. Engineering of a new Escherichia coli strain efficiently metabolizing cellobiose with promising perspectives for plant biomass-based application design. Metab Eng Commun 2021; 12:e00157. [PMID: 33457204 PMCID: PMC7797564 DOI: 10.1016/j.mec.2020.e00157] [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: 08/17/2020] [Revised: 11/24/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022] Open
Abstract
The necessity to decrease our fossil energy dependence requests bioprocesses based on biomass degradation. Cellobiose is the main product released by cellulases when acting on the major plant cell wall polysaccharide constituent, the cellulose. Escherichia coli, one of the most common model organisms for the academy and the industry, is unable to metabolize this disaccharide. In this context, the remodeling of E. coli to catabolize cellobiose should thus constitute an important progress for the design of such applications. Here, we developed a robust E. coli strain able to metabolize cellobiose by integration of a small set of modifications in its genome. Contrary to previous studies that use adaptative evolution to achieve some growth on this sugar by reactivating E. coli cryptic operons coding for cellobiose metabolism, we identified easily insertable modifications impacting the cellobiose import (expression of a gene coding a truncated variant of the maltoporin LamB, modification of the expression of lacY encoding the lactose permease) and its intracellular degradation (genomic insertion of a gene encoding either a cytosolic β-glucosidase or a cellobiose phosphorylase). Taken together, our results provide an easily transferable set of mutations that confers to E. coli an efficient growth phenotype on cellobiose (doubling time of 2.2 h in aerobiosis) without any prior adaptation. Production of a cytosolic β-glucosidase or cellobiose phosphorylase allows E. coli to metabolize cellobiose. Optimization of cellobiose uptake through E. coli enveloppe to sustain an efficient growth on this carbon source. Genetic engineering of E. coli can provide the capacity of an efficient cellobiose catabolism.
Collapse
Affiliation(s)
- Romain Borne
- Aix-Marseille Université, CNRS, UMR7283, 31 ch. Joseph Aiguier, F-13402, Marseille, France
| | - Nicolas Vita
- Aix-Marseille Université, CNRS, UMR7283, 31 ch. Joseph Aiguier, F-13402, Marseille, France
| | - Nathalie Franche
- Aix-Marseille Université, CNRS, UMR7283, 31 ch. Joseph Aiguier, F-13402, Marseille, France
| | - Chantal Tardif
- Aix-Marseille Université, CNRS, UMR7283, 31 ch. Joseph Aiguier, F-13402, Marseille, France
| | - Stéphanie Perret
- Aix-Marseille Université, CNRS, UMR7283, 31 ch. Joseph Aiguier, F-13402, Marseille, France
| | - Henri-Pierre Fierobe
- Aix-Marseille Université, CNRS, UMR7283, 31 ch. Joseph Aiguier, F-13402, Marseille, France
| |
Collapse
|
12
|
A Need for Improved Cellulase Identification from Metagenomic Sequence Data. Appl Environ Microbiol 2020; 87:AEM.01928-20. [PMID: 33067195 DOI: 10.1128/aem.01928-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Improved sequencing technologies and the maturation of metagenomic approaches allow the identification of gene variants with potential industrial applications, including cellulases. Cellulase identification from metagenomic environmental surveys is complicated by inconsistent nomenclature and multiple categorization systems. Here, we summarize the current classification and nomenclature systems, with recommendations for improvements to these systems. Addressing the issues described will strengthen the annotation of cellulose-active enzymes from environmental sequence data sets-a rapidly growing resource in environmental and applied microbiology.
Collapse
|
13
|
A Novel Two-Component System, XygS/XygR, Positively Regulates Xyloglucan Degradation, Import, and Catabolism in Ruminiclostridium cellulolyticum. Appl Environ Microbiol 2020; 86:AEM.01357-20. [PMID: 32769189 DOI: 10.1128/aem.01357-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022] Open
Abstract
Cellulolytic microorganisms play a key role in the global carbon cycle by decomposing structurally diverse plant biopolymers from dead plant matter. These microorganisms, in particular anaerobes such as Ruminiclostridium cellulolyticum that are capable of degrading and catabolizing several different polysaccharides, require a fine-tuned regulation of the biosynthesis of their polysaccharide-degrading enzymes. In this study, we present a bacterial regulatory system involved in the regulation of genes enabling the metabolism of the ubiquitous plant polysaccharide xyloglucan. The characterization of R. cellulolyticum knockout mutants suggests that the response regulator XygR and its cognate histidine kinase XygS are essential for growth on xyloglucan. Using in vitro and in vivo analyses, we show that XygR binds to the intergenic region and activates the expression of two polycistronic transcriptional units encoding an ABC transporter dedicated to the uptake of xyloglucan oligosaccharides and the two-component system itself together with three intracellular glycoside hydrolases responsible for the sequential intracellular degradation of the imported oligosaccharides into mono- and disaccharides. Interestingly, XygR also upregulates the expression of a distant gene coding for the most active extracellular cellulosomal xyloglucanase of R. cellulolyticum by binding to the upstream intergenic region.IMPORTANCE Ruminiclostridium cellulolyticum is a Gram-positive, mesophilic, anaerobic, cellulolytic, and hemicellulolytic bacterium. The last property qualifies this species as a model species for the study of hemicellulose degradation, import of degradation products, and overall regulation of these phenomena. In this study, we focus on the regulation of xyloglucan dextrin import and intracellular degradation and show that the two components of the two-component regulation system XygSR are essential for growth on xyloglucan and that the response regulator XygR regulates the transcription of genes involved in the extracellular degradation of the polysaccharide, the import of degradation products, and their intracellular degradation.
Collapse
|
14
|
Navarro SL, Levy L, Curtis KR, Elkon I, Kahsai OJ, Ammar HS, Randolph TW, Hong NN, Carnevale Neto F, Raftery D, Chapkin RS, Lampe JW, Hullar MAJ. Effect of a Flaxseed Lignan Intervention on Circulating Bile Acids in a Placebo-Controlled Randomized, Crossover Trial. Nutrients 2020; 12:E1837. [PMID: 32575611 PMCID: PMC7374341 DOI: 10.3390/nu12061837] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
Plant lignans and their microbial metabolites, e.g., enterolactone (ENL), may affect bile acid (BA) metabolism through interaction with hepatic receptors. We evaluated the effects of a flaxseed lignan extract (50 mg/day secoisolariciresinol diglucoside) compared to a placebo for 60 days each on plasma BA concentrations in 46 healthy men and women (20-45 years) using samples from a completed randomized, crossover intervention. Twenty BA species were measured in fasting plasma using LC-MS. ENL was measured in 24-h urines by GC-MS. We tested for (a) effects of the intervention on BA concentrations overall and stratified by ENL excretion; and (b) cross-sectional associations between plasma BA and ENL. We also explored the overlap in bacterial metabolism at the genus level and conducted in vitro anaerobic incubations of stool with lignan substrate to identify genes that are enriched in response to lignan metabolism. There were no intervention effects, overall or stratified by ENL at FDR < 0.05. In the cross-sectional analysis, irrespective of treatment, five secondary BAs were associated with ENL excretion (FDR < 0.05). In vitro analyses showed positive associations between ENL production and bacterial gene expression of the bile acid-inducible gene cluster and hydroxysteroid dehydrogenases. These data suggest overlap in community bacterial metabolism of secondary BA and ENL.
Collapse
Affiliation(s)
- Sandi L. Navarro
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Lisa Levy
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Keith R. Curtis
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Isaac Elkon
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Orsalem J. Kahsai
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Hamza S. Ammar
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Timothy W. Randolph
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Natalie N. Hong
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA; (N.N.H.); (F.C.N.)
| | - Fausto Carnevale Neto
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA; (N.N.H.); (F.C.N.)
| | - Daniel Raftery
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA; (N.N.H.); (F.C.N.)
| | - Robert S. Chapkin
- Program in Integrative Nutrition & Complex Diseases, Texas A&M University, College Station, TX 77843, USA;
| | - Johanna W. Lampe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Meredith A. J. Hullar
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| |
Collapse
|
15
|
Li J, Gu S, Zhao Z, Chen B, Liu Q, Sun T, Sun W, Tian C. Dissecting cellobiose metabolic pathway and its application in biorefinery through consolidated bioprocessing in Myceliophthora thermophila. Fungal Biol Biotechnol 2019; 6:21. [PMID: 31754437 PMCID: PMC6852783 DOI: 10.1186/s40694-019-0083-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/04/2019] [Indexed: 02/08/2023] Open
Abstract
Background Lignocellulosic biomass has long been recognized as a potential sustainable source for industrial applications. The costs associated with conversion of plant biomass to fermentable sugar represent a significant barrier to the production of cost-competitive biochemicals. Consolidated bioprocessing (CBP) is considered a potential breakthrough for achieving cost-efficient production of biomass-based fuels and commodity chemicals. During the degradation of cellulose, cellobiose (major end-product of cellulase activity) is catabolized by hydrolytic and phosphorolytic pathways in cellulolytic organisms. However, the details of the two intracellular cellobiose metabolism pathways in cellulolytic fungi remain to be uncovered. Results Using the engineered malic acid production fungal strain JG207, we demonstrated that the hydrolytic pathway by β-glucosidase and the phosphorolytic pathway by phosphorylase are both used for intracellular cellobiose metabolism in Myceliophthora thermophila, and the yield of malic acid can benefit from the energy advantages of phosphorolytic cleavage. There were obvious differences in regulation of the two cellobiose catabolic pathways depending on whether M. thermophila JG207 was grown on cellobiose or Avicel. Disruption of Mtcpp in strain JG207 led to decreased production of malic acid under cellobiose conditions, while expression levels of all three intracellular β-glucosidase genes were significantly up-regulated to rescue the impairment of the phosphorolytic pathway under Avicel conditions. When the flux of the hydrolytic pathway was reduced, we found that β-glucosidase encoded by bgl1 was the dominant enzyme in the hydrolytic pathway and deletion of bgl1 resulted in significant enhancement of protein secretion but reduction of malate production. Combining comprehensive manipulation of both cellobiose utilization pathways and enhancement of cellobiose uptake by overexpression of a cellobiose transporter, the final strain JG412Δbgl2Δbgl3 produced up to 101.2 g/L and 77.4 g/L malic acid from cellobiose and Avicel, respectively, which corresponded to respective yields of 1.35 g/g and 1.03 g/g, representing significant improvement over the starting strain JG207. Conclusions This is the first report of detailed investigation of intracellular cellobiose catabolism in cellulolytic fungus M. thermophila. These results provide insights that can be applied to industrial fungi for production of biofuels and biochemicals from cellobiose and cellulose.
Collapse
Affiliation(s)
- Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Shuying Gu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Zhen Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Bingchen Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Tao Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| |
Collapse
|