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Costa P, Usai G, Re A, Manfredi M, Mannino G, Bertea CM, Pessione E, Mazzoli R. Clostridium cellulovorans Proteomic Responses to Butanol Stress. Front Microbiol 2021; 12:674639. [PMID: 34367082 PMCID: PMC8336468 DOI: 10.3389/fmicb.2021.674639] [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: 03/01/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Combination of butanol-hyperproducing and hypertolerant phenotypes is essential for developing microbial strains suitable for industrial production of bio-butanol, one of the most promising liquid biofuels. Clostridium cellulovorans is among the microbial strains with the highest potential for direct production of n-butanol from lignocellulosic wastes, a process that would significantly reduce the cost of bio-butanol. However, butanol exhibits higher toxicity compared to ethanol and C. cellulovorans tolerance to this solvent is low. In the present investigation, comparative gel-free proteomics was used to study the response of C. cellulovorans to butanol challenge and understand the tolerance mechanisms activated in this condition. Sequential Window Acquisition of all Theoretical fragment ion spectra Mass Spectrometry (SWATH-MS) analysis allowed identification and quantification of differentially expressed soluble proteins. The study data are available via ProteomeXchange with the identifier PXD024183. The most important response concerned modulation of protein biosynthesis, folding and degradation. Coherent with previous studies on other bacteria, several heat shock proteins (HSPs), involved in protein quality control, were up-regulated such as the chaperones GroES (Cpn10), Hsp90, and DnaJ. Globally, our data indicate that protein biosynthesis is reduced, likely not to overload HSPs. Several additional metabolic adaptations were triggered by butanol exposure such as the up-regulation of V- and F-type ATPases (involved in ATP synthesis/generation of proton motive force), enzymes involved in amino acid (e.g., arginine, lysine, methionine, and branched chain amino acids) biosynthesis and proteins involved in cell envelope re-arrangement (e.g., the products of Clocel_4136, Clocel_4137, Clocel_4144, Clocel_4162 and Clocel_4352, involved in the biosynthesis of saturated fatty acids) and a redistribution of carbon flux through fermentative pathways (acetate and formate yields were increased and decreased, respectively). Based on these experimental findings, several potential gene targets for metabolic engineering strategies aimed at improving butanol tolerance in C. cellulovorans are suggested. This includes overexpression of HSPs (e.g., GroES, Hsp90, DnaJ, ClpC), RNA chaperone Hfq, V- and F-type ATPases and a number of genes whose function in C. cellulovorans is currently unknown.
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Affiliation(s)
- Paolo Costa
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giulia Usai
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy.,Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Angela Re
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Marcello Manfredi
- Center for Translational Research on Autoimmune and Allergic Diseases, Università del Piemonte Orientale, Novara, Italy.,Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Giuseppe Mannino
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Cinzia Margherita Bertea
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Enrica Pessione
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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Mazzoli R, Olson D. Clostridium thermocellum: A microbial platform for high-value chemical production from lignocellulose. ADVANCES IN APPLIED MICROBIOLOGY 2020; 113:111-161. [PMID: 32948265 DOI: 10.1016/bs.aambs.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Second generation biorefining, namely fermentation processes based on lignocellulosic feedstocks, has attracted tremendous interest (owing to the large availability and low cost of this biomass) as a strategy to produce biofuels and commodity chemicals that is an alternative to oil refining. However, the innate recalcitrance of lignocellulose has slowed progress toward economically viable processes. Consolidated bioprocessing (CBP), i.e., single-step fermentation of lignocellulose may dramatically reduce the current costs of 2nd generation biorefining. Metabolic engineering has been used as a tool to develop improved microbial strains supporting CBP. Clostridium thermocellum is among the most efficient cellulose degraders isolated so far and one of the most promising host organisms for application of CBP. The development of efficient and reliable genetic tools has allowed significant progress in metabolic engineering of this strain aimed at expanding the panel of growth substrates and improving the production of a number of commodity chemicals of industrial interest such as ethanol, butanol, isobutanol, isobutyl acetate and lactic acid. The present review aims to summarize recent developments in metabolic engineering of this organism which currently represents a reference model for the development of biocatalysts for 2nd generation biorefining.
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Pontonio E, Mahony J, Di Cagno R, O'Connell Motherway M, Lugli GA, O'Callaghan A, De Angelis M, Ventura M, Gobbetti M, van Sinderen D. Cloning, expression and characterization of a β-D-xylosidase from Lactobacillus rossiae DSM 15814(T). Microb Cell Fact 2016; 15:72. [PMID: 27142164 PMCID: PMC4855831 DOI: 10.1186/s12934-016-0473-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/24/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Among the oligosaccharides that may positively affect the gut microbiota, xylo-oligosaccharides (XOS) and arabinoxylan oligosaccharides (AXOS) possess promising functional properties. Ingestion of XOS has been reported to contribute to anti-oxidant, anti-bacterial, immune-modulatory and anti-diabetic activities. Because of the structural complexity and chemical heterogeneity, complete degradation of xylan-containing plant polymers requires the synergistic activity of several enzymes. Endo-xylanases and β-D-xylosidases, collectively termed xylanases, represent the two key enzymes responsible for the sequential hydrolysis of xylan. Xylanase cocktails are used on an industrial scale for biotechnological purposes. Lactobacillus rossiae DSM 15814(T) can utilize an extensive set of carbon sources, an ability that is likely to contribute to its adaptive ability. In this study, the capacity of this strain to utilize XOS, xylan, D-xylose and L-arabinose was investigated. RESULTS Genomic and transcriptomic analyses revealed the presence of two gene clusters, designated xyl and ara, encoding proteins predicted to be responsible for XOS uptake and hydrolysis and D-xylose utilization, and L-arabinose metabolism, respectively. The deduced amino acid sequence of one of the genes of the xyl gene cluster, LROS_1108 (designated here as xylA), shows high similarity to (predicted) β-D-xylosidases encoded by various lactic acid bacteria, and belongs to glycosyl hydrolase family 43. Heterologously expressed XylA was shown to completely hydrolyse XOS to xylose and showed optimal activity at pH 6.0 and 40 °C. Furthermore, β-D-xylosidase activity of L. rossiae DSM 15814(T) was also measured under sourdough conditions. CONCLUSIONS This study highlights the ability of L. rossiae DSM 15814(T) to utilize XOS, which is a very useful trait when selecting starters with specific metabolic performances for sourdough fermentation or as probiotics.
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Affiliation(s)
- Erica Pontonio
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126, Bari, Italy
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
| | - Raffaella Di Cagno
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126, Bari, Italy.
| | - Mary O'Connell Motherway
- School of Microbiology, University College Cork, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Amy O'Callaghan
- School of Microbiology, University College Cork, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126, Bari, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Marco Gobbetti
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126, Bari, Italy
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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Teng L, Wang K, Xu J, Xu C. Flavin mononucleotide (FMN)-based fluorescent protein (FbFP) as reporter for promoter screening in Clostridium cellulolyticum. J Microbiol Methods 2015; 119:37-43. [PMID: 26427827 DOI: 10.1016/j.mimet.2015.09.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/28/2015] [Accepted: 09/28/2015] [Indexed: 12/13/2022]
Abstract
Conventional methods for screening promoters in anaerobic bacteria are generally based on detection of enzymatic reactions and thus usually complicated or strain specific. Therefore a more efficient and universal method will be valuable. Here, using cellulolytic bacteria Clostridium cellulolyticum H10 as a model, we employed an oxygen-independent flavin-based fluorescent protein (FbFP) derived from Pseudomonas putida as a quantitative reporter for the screening of promoter via monitoring fluorescence intensity. The stability and reliability of FbFP fluorescence were proven by the high correlation (R(2)=0.87) between fluorescence intensity and abundance of FbFP. Moreover, two endogenous promoters with exceptional performance were identified and characterized, including a constitutive promoter p3398 and an inducible promoter p1133. Compared to the existing reporter systems widely used in clostridia, this FbFP-based method is more rapid, intuitive and versatile, and the endogenous promoters reported here should enrich the synthetic biology toolbox for this and related organisms.
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Affiliation(s)
- Lin Teng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Wang
- Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.
| | - Chenggang Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.
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5
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Li YK, Chu SH, Sung YH. Purification, Characterization and Mechanistic Study of β-Glucosidase fromFlavobacterium meningosepticum(ATCC 13253). J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199800091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Xu C, Huang R, Teng L, Wang D, Hemme CL, Borovok I, He Q, Lamed R, Bayer EA, Zhou J, Xu J. Structure and regulation of the cellulose degradome in Clostridium cellulolyticum. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:73. [PMID: 23657055 PMCID: PMC3656788 DOI: 10.1186/1754-6834-6-73] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 05/01/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Many bacteria efficiently degrade lignocellulose yet the underpinning genome-wide metabolic and regulatory networks remain elusive. Here we revealed the "cellulose degradome" for the model mesophilic cellulolytic bacterium Clostridium cellulolyticum ATCC 35319, via an integrated analysis of its complete genome, its transcriptomes under glucose, xylose, cellobiose, cellulose, xylan or corn stover and its extracellular proteomes under glucose, cellobiose or cellulose. RESULTS Proteins for core metabolic functions, environment sensing, gene regulation and polysaccharide metabolism were enriched in the cellulose degradome. Analysis of differentially expressed genes revealed a "core" set of 48 CAZymes required for degrading cellulose-containing substrates as well as an "accessory" set of 76 CAZymes required for specific non-cellulose substrates. Gene co-expression analysis suggested that Carbon Catabolite Repression (CCR) related regulators sense intracellular glycolytic intermediates and control the core CAZymes that mainly include cellulosomal components, whereas 11 sets of Two-Component Systems (TCSs) respond to availability of extracellular soluble sugars and respectively regulate most of the accessory CAZymes and associated transporters. Surprisingly, under glucose alone, the core cellulases were highly expressed at both transcript and protein levels. Furthermore, glucose enhanced cellulolysis in a dose-dependent manner, via inducing cellulase transcription at low concentrations. CONCLUSION A molecular model of cellulose degradome in C. cellulolyticum (Ccel) was proposed, which revealed the substrate-specificity of CAZymes and the transcriptional regulation of core cellulases by CCR where the glucose acts as a CCR inhibitor instead of a trigger. These features represent a distinct environment-sensing strategy for competing while collaborating for cellulose utilization, which can be exploited for process and genetic engineering of microbial cellulolysis.
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Affiliation(s)
- Chenggang Xu
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Ranran Huang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Lin Teng
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Dongmei Wang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Christopher L Hemme
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73072, USA
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73072, USA
| | - Jian Xu
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
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Lasrado LD, Gudipati M. Purification and characterization of β-D-xylosidase from Lactobacillus brevis grown on xylo-oligosaccharides. Carbohydr Polym 2012; 92:1978-83. [PMID: 23399247 DOI: 10.1016/j.carbpol.2012.11.081] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/25/2012] [Accepted: 11/26/2012] [Indexed: 11/24/2022]
Abstract
In the recent years there has been a growing interest in the use of oligosaccharides as prebiotics to modulate gut microbiota with an aim to improve the gut health. Though xylo-oligosaccharides (XOS) have been increasingly used as prebiotics, information pertaining to the enzymes used by lactobacilli to degrade these substrates is scanty. Present investigation reports the purification and characterization of β-D-xylosidase from Lactobacillus brevis NCDC01 grown on XOS. Three sequential steps consisting of ultra-filtration, DEAE cellulose ion-exchange and Sephacryl S-100 gel filtration chromatographies were employed to purify the enzyme to apparent homogeneity and it was found to be monomeric on SDS-PAGE with an apparent molecular mass of ~58.0 kDa. The pH and temperature optima were 6.0 and 40 °C respectively. The enzyme remained stable over a pH range of 5.5-7.5 and up to 50 °C for 30 min. Under optimum pH and temperature with p-nitrophenyl β-D-xylopyranoside as a substrate, the enzyme exhibited a K(m) of 0.87 mM. The enzyme does not require any metal ion for activity or stability but is completely inhibited by Hg(2+), Pb(2+), p-chloromercuribenzoate (PCMB), oxalic acid and citric acid. This is perhaps the first report on the purification and characterization of β-D-xylosidase from Lactobacillus brevis NCDC01.
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Affiliation(s)
- Lyned D Lasrado
- Department of Biochemistry and Nutrition, Council of Scientific and Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysore 570020, Karnataka, India
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Fekete CA, Kiss L. Purification and Characterization of a Recombinant β-d-xylosidase from Thermobifida fusca TM51. Protein J 2012; 31:641-50. [DOI: 10.1007/s10930-012-9440-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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9
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Characterization of two β-xylosidases from Bifidobacterium adolescentis and their contribution to the hydrolysis of prebiotic xylooligosaccharides. Appl Microbiol Biotechnol 2011; 92:1179-85. [PMID: 21691791 DOI: 10.1007/s00253-011-3396-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 05/15/2011] [Accepted: 05/17/2011] [Indexed: 10/18/2022]
Abstract
Xylooligosaccharides have strong bifidogenic properties and are increasingly used as a prebiotic. Nonetheless, little is known about the degradation of these substrates by bifidobacteria. We characterized two recombinant β-xylosidases, XylB and XylC, with different substrate specificities from Bifidobacterium adolescentis. XylB is a novel β-xylosidase that belongs to the recently introduced glycoside hydrolase family 120. In contrast to most reported β-xylosidases, it shows only weak activity on xylobiose and prefers xylooligosaccharides with a degree of polymerization above two. The remaining xylobiose is efficiently hydrolyzed by the second B. adolescentis β-xylosidase, XylC, a glycoside hydrolase of family 43. Furthermore, XylB releases more xylose from arabinose-substituted xylooligosaccharides than XylC (30% and 20%, respectively). The different specificities of XylB, XylC, and the recently described reducing-end xylose-releasing exo-oligoxylanase RexA show how B. adolescentis can efficiently degrade prebiotic xylooligosaccharides.
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Yan QJ, Wang L, Jiang ZQ, Yang SQ, Zhu HF, Li LT. A xylose-tolerant beta-xylosidase from Paecilomyces thermophila: characterization and its co-action with the endogenous xylanase. BIORESOURCE TECHNOLOGY 2008; 99:5402-5410. [PMID: 18180153 DOI: 10.1016/j.biortech.2007.11.033] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2007] [Revised: 11/06/2007] [Accepted: 11/07/2007] [Indexed: 05/25/2023]
Abstract
An extracellular beta-xylosidase from the thermophilic fungus Paecilomyces thermophila J18 was purified 31.9-fold to homogeneity with a recovery yield of 2.27% from the cell-free culture supernatant. It appeared as a single protein band on SDS-PAGE with a molecular mass of approx 53.5 kDa. The molecular mass of beta-xylosidase was 51.8 kDa determined by Superdex 75 gel filtration. The enzyme was a glycoprotein with a carbohydrate content of 61.5%. It exhibited an optimal activity at 55 degrees C and pH 6.5, respectively. The enzyme was stable in the range of pH 6.0-9.0 and at 55 degrees C. The purified enzyme hydrolyzed xylobiose and higher xylooligosaccharides but was inactive against xylan substrates. It released xylose from xylooligosaccharides with a degree of polymerization ranging between 2 and 5. The rate of xylose released from xylooligosaccharides by the purified enzyme increased with increasing chain length. It had a K(m) of 4.3mM for p-nitrophenol-beta-d-xylopyranoside and was competitively inhibited by xylose with a K(i) value of 139 mM. Release of reducing sugars from xylans by a purified xylanase produced by the same organism increased markedly in the presence of beta-xylosidase. During 24-hour hydrolysis, the amounts of reducing sugar released in the presence of added beta-xylosidase were about 1.5-1.73 times that of the reaction employing the xylanase alone. This is the first report on the purification and characterization of a beta-xylosidase from Paecilomyces thermophila.
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Affiliation(s)
- Q J Yan
- Bioresource Utilization Laboratory, College of Engineering, China Agricultural University, Beijing 100083, China
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12
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Desvaux M. Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia. FEMS Microbiol Rev 2004; 29:741-64. [PMID: 16102601 DOI: 10.1016/j.femsre.2004.11.003] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Revised: 04/27/2004] [Accepted: 11/01/2004] [Indexed: 11/22/2022] Open
Abstract
Clostridium cellulolyticum ATCC 35319 is a non-ruminal mesophilic cellulolytic bacterium originally isolated from decayed grass. As with most truly cellulolytic clostridia, C. cellulolyticum possesses an extracellular multi-enzymatic complex, the cellulosome. The catalytic components of the cellulosome release soluble cello-oligosaccharides from cellulose providing the primary carbon substrates to support bacterial growth. As most cellulolytic bacteria, C. cellulolyticum was initially characterised by limited carbon consumption and subsequent limited growth in comparison to other saccharolytic clostridia. The first metabolic studies performed in batch cultures suggested nutrient(s) limitation and/or by-product(s) inhibition as the reasons for this limited growth. In most recent investigations using chemostat cultures, metabolic flux analysis suggests a self-intoxication of bacterial metabolism resulting from an inefficiently regulated carbon flow. The investigation of C. cellulolyticum physiology with cellobiose, as a model of soluble cellodextrin, and with pure cellulose, as a carbon source more closely related to lignocellulosic compounds, strengthen the idea of a bacterium particularly well adapted, and even restricted, to a cellulolytic lifestyle. The metabolic flux analysis from continuous cultures revealed that (i) in comparison to cellobiose, the cellulose hydrolysis by the cellulosome introduces an extra regulation of entering carbon flow resulting in globally lower metabolic fluxes on cellulose than on cellobiose, (ii) the glucose 1-phosphate/glucose 6-phosphate branch point controls the carbon flow directed towards glycolysis and dissipates carbon excess towards the formation of cellodextrins, glycogen and exopolysaccharides, (iii) the pyruvate/acetyl-CoA metabolic node is essential to the regulation of electronic and energetic fluxes. This in-depth analysis of C. cellulolyticum metabolism has permitted the first attempt to engineer metabolically a cellulolytic microorganism.
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Affiliation(s)
- Mickaël Desvaux
- Institute for Biomedical Research, The University of Birmingham - The Medical School, Edgbaston, UK.
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Kosugi A, Murashima K, Doi RH. Characterization of xylanolytic enzymes in Clostridium cellulovorans: expression of xylanase activity dependent on growth substrates. J Bacteriol 2001; 183:7037-43. [PMID: 11717260 PMCID: PMC95550 DOI: 10.1128/jb.183.24.7037-7043.2001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylanase activity of Clostridium cellulovorans, an anaerobic, mesophilic, cellulolytic bacterium, was characterized. Most of the activity was secreted into the growth medium when the bacterium was grown on xylan. Furthermore, when the extracellular material was separated into cellulosomal and noncellulosomal fractions, the activity was present in both fractions. Each of these fractions contained at least two major and three minor xylanase activities. In both fractions, the pattern of xylan hydrolysis products was almost identical based on thin-layer chromatography analysis. The major xylanase activities in both fractions were associated with proteins with molecular weights of about 57,000 and 47,000 according to zymogram analyses, and the minor xylanases had molecular weights ranging from 45,000 to 28,000. High alpha-arabinofuranosidase activity was detected exclusively in the noncellulosomal fraction. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis revealed that cellulosomes derived from xylan-, cellobiose-, and cellulose-grown cultures had different subunit compositions. Also, when xylanase activity in the cellulosomes from the xylan-grown cultures was compared with that of cellobiose- and cellulose-grown cultures, the two major xylanases were dramatically increased in the presence of xylan. These results strongly indicated that C. cellulovorans is able to regulate the expression of xylanase activity and to vary the cellulosome composition depending on the growth substrate.
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Affiliation(s)
- A Kosugi
- Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
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Erlandson KA, Delamarre SC, Batt CA. Genetic evidence for a defective xylan degradation pathway in Lactococcus lactis. Appl Environ Microbiol 2001; 67:1445-52. [PMID: 11282589 PMCID: PMC92753 DOI: 10.1128/aem.67.4.1445-1452.2001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetic and biochemical evidence for a defective xylan degradation pathway was found linked to the xylose operon in three lactococcal strains, Lactococcus lactis 210, L. lactis IO-1, and L. lactis NRRL B-4449. Immediately downstream of the xylulose kinase gene (xylB) (K. A. Erlandson, J.-H. Park, W. El Khal, H.-H. Kao, P. Basaran, S. Brydges, and C. A. Batt, Appl. Environ. Microbiol. 66:3974-3980, 1999) are two open reading frames encoding a mutarotase (xylM) and a xyloside transporter (xynT) and a partial open reading frame encoding a beta-xylosidase (xynB). These are functions previously unreported for lactococci or lactobacilli. The mutarotase activity of the putative xylM gene product was confirmed by overexpression of the L. lactis enzyme in Escherichia coli and purification of recombinant XylM. We hypothesize that the mutarotase links xylan degradation to xylose metabolism due to the anomeric preference of xylose isomerase. In addition, Northern hybridization experiments suggested that the xylM and xynTB genes are cotranscribed with the xylRAB genes, responsible for xylose metabolism. Although none of the three strains appeared to metabolize xylan or xylobiose, they exhibited xylosidase activity, and L. lactis IO-1 and L. lactis NRRL B-4449 had functional mutarotases.
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Affiliation(s)
- K A Erlandson
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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Abstract
beta-Xylosidase (1,4-beta-D-xylan xylohydrolase EC 3.2.1.37) and xylose isomerase (D-xylose ketol-isomerase EC 5.3.1.5) produced by Streptomyces sp. strain EC 10, were cell-bound enzymes induced by xylan, straw, and xylose. Enzyme production was subjected to a form of carbon catabolite repression by glycerol. beta-Xylosidase and xylose isomerase copurified strictly, and the preparation was found homogeneous by gel electrophoresis after successive chromatography on DEAE-Sephacel and gel filtration on Biogel A. Streptomyces sp. produced apparently a bifunctional beta-xylosidase-xylose isomerase enzyme. The molecular weight of the enzyme was measured to be 163,000 by gel filtration and 42,000 by SDS-PAGE, indicating that the enzyme behaved as a tetramer of identical subunits. The Streptomyces sp. beta-xylosidase was a typical glycosidase acting as an exoenzyme on xylooligosaccharides, and working optimally at pH 7.5 and 45 degrees C. The xylose isomerase optimal temperature was 70 degrees C and maximal activity was observed in a broad range pH (5-8). Enhanced saccharification of arabinoxylan caused by the addition of the enzyme to endoxylanase suggested a cooperative enzyme action. The first 35 amino acids of the N-terminal sequence of the enzyme showed strong analogies with N-terminal sequences of xylose isomerase produced by other microorganisms but not with other published N-terminal sequences of beta-xylosidases.
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Mohand-Oussaid O, Payot S, Guedon E, Gelhaye E, Youyou A, Petitdemange H. The extracellular xylan degradative system in Clostridium cellulolyticum cultivated on xylan: evidence for cell-free cellulosome production. J Bacteriol 1999; 181:4035-40. [PMID: 10383972 PMCID: PMC93894 DOI: 10.1128/jb.181.13.4035-4040.1999] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/1999] [Accepted: 04/27/1999] [Indexed: 11/20/2022] Open
Abstract
In this study, we demonstrate that the cellulosome of Clostridium cellulolyticum grown on xylan is not associated with the bacterial cell. Indeed, the large majority of the activity (about 90%) is localized in the cell-free fraction when the bacterium is grown on xylan. Furthermore, about 70% of the detected xylanase activity is associated with cell-free high-molecular-weight complexes containing avicelase activity and the cellulosomal scaffolding protein CipC. The same repartition is observed with carboxymethyl cellulase activity. The cellulose adhesion of xylan-grown cells is sharply reduced in comparison with cellulose-grown cells. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis revealed that cellulosomes derived from xylan- and cellulose-grown cells have different compositions. In both cases, the scaffolding protein CipC is present, but the relative proportions of the other components is dramatically changed depending on the growth substrate. We propose that, depending on the growth substrate, C. cellulolyticum is able to regulate the cell association and cellulose adhesion of cellulosomes and regulate cellulosomal composition.
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Affiliation(s)
- O Mohand-Oussaid
- Laboratoire de Microbiologie URBAF, Institut des Sciences de la Nature, Université Mouloud Mammeri, Tizi-Ouzou, Algeria
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Pitson SM, Mutter M, van den Broek LA, Voragen AG, Beldman G. Stereochemical course of hydrolysis catalysed by alpha-L-rhamnosyl and alpha-D-galacturonosyl hydrolases from Aspergillus aculeatus. Biochem Biophys Res Commun 1998; 242:552-9. [PMID: 9464254 DOI: 10.1006/bbrc.1997.8009] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The stereochemical course of hydrolysis catalysed by four Aspergillus aculeatus enzymes acting on alpha-L-rhamnosyl and alpha-D-galacturonosyl linkages in the hairy regions of pectins has been determined using 1H-NMR. Exogalacturonase acts with inversion of anomeric configuration (e-->a), shown by the initial release of beta-D-GalpA from the non-reducing end of polygalacturonic acid. Similarly, rhamnogalacturonan (RG) hydrolase also acts with inversion of anomeric configuration (e-->a) during hydrolysis of alpha-D-GalpA-(1-->2)-alpha-L-Rhap linkages in RG, initially releasing oligosaccharides with beta-D-GalpA at the reducing end. This result is consistent with the recently solved crystal structure of this enzyme, as well as its classification based on amino acid sequence similarity into glycosyl hydrolase family 28. alpha-L-Rhamnosidase and RG-rhamnohydrolase also act with inversion of configuration (a-->e), initially releasing beta-L-Rhap from p-nitrophenyl alpha-L-rhamnopyranoside and RG oligosaccharides, respectively. Thus, all four enzymes examined are inverting hydrolases which probably catalyse hydrolysis via single displacement mechanisms.
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Affiliation(s)
- S M Pitson
- Department of Food Science, Wageningen Agricultural University, The Netherlands.
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Gal L, Pages S, Gaudin C, Belaich A, Reverbel-Leroy C, Tardif C, Belaich JP. Characterization of the cellulolytic complex (cellulosome) produced by Clostridium cellulolyticum. Appl Environ Microbiol 1997; 63:903-9. [PMID: 9055408 PMCID: PMC168382 DOI: 10.1128/aem.63.3.903-909.1997] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The cellulolytic complex was isolated from Clostridium cellulolyticum grown on cellulose. Upon gel filtration, the complex was found to consist mainly of 600-kDa units, along with a 16-MDa aggregate. Its ability to degrade various substrates and its capacity to bind to the crystalline cellulose were measured. The results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis, N-terminal sequencing, and blotting analysis showed that all of the known cellulases of this organism are present in this complex. Three major components were observed: the first component, a noncatalytic, large (160-kDa) protein, was identified based on its ability to bind to the dockerin-containing cellulases as scaffolding protein CipC. The other two components, which had molecular masses of 94 and 80.6 kDa, were identified as CelE and CelF, respectively. The identified cellulases and some other components of the cellulosome were able to bind to a miniCipC1 construct. In addition to providing an extensive description of the system, the results of the present study confirm that the dockerin-cohesin domain interaction plays an essential role in the constitution of the cellulosome.
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Affiliation(s)
- L Gal
- Laboratoire de Bioénergétique et Ingéniérie des Protéines, IFR C1, Centre National de la Recherche Scientifique, Marseille, France
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Beldman G, Schols H, Pitson S, Searle-van Leeuwen M, Voragen A. Arabinans and arabinan degrading enzymes. ADVANCES IN MACROMOLECULAR CARBOHYDRATE RESEARCH 1997. [DOI: 10.1016/s1874-5261(97)80003-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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