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Berlemont R. The supragenic organization of glycoside hydrolase encoding genes reveals distinct strategies for carbohydrate utilization in bacteria. Front Microbiol 2023; 14:1179206. [PMID: 37333644 PMCID: PMC10272396 DOI: 10.3389/fmicb.2023.1179206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
Glycoside hydrolases (GHs) are carbohydrate-active enzymes essential for many environmental (e.g., carbon cycling) and biotechnological (e.g., biofuels) processes. The complete processing of carbohydrates by bacteria requires many enzymes acting synergistically. Here, I investigated the clustered or scattered distribution of 406,337 GH-genes and their association with transporter genes identified in 15,640 completely sequenced bacterial genomes. Different bacterial lineages displayed conserved levels of clustered or scattered GH-genes, but overall, the GH-genes clustering was generally higher than in randomized genomes. In lineages with highly clustered GH-genes (e.g., Bacteroides, Paenibacillus), clustered genes shared the same orientation. These codirectional gene clusters potentially facilitate the genes' co-expression by allowing transcriptional read-through and, at least in some cases, forming operons. In several taxa, the GH-genes clustered with distinct types of transporter genes. The type of transporter genes and the distribution of the so-called GH:TR-genes clusters were conserved in selected lineages. Globally, the phylogenetically conserved clustering of the GH-genes with transporter genes highlights the central function of carbohydrate processing across bacterial lineages. In addition, in bacteria with the most identified GH-genes, the genomic adaptations for carbohydrate processing also mirrored the broad environmental origin of the sequenced strains (e.g., soil and mammal gut) suggesting that a combination of evolutionary history and the environment selects for the specific supragenic organization of the GH-genes supporting the carbohydrate processing in bacterial genomes.
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Affiliation(s)
- Renaud Berlemont
- Department of Biological Sciences, California State University – Long Beach, Long Beach, CA, United States
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Multifunctionality and mechanism of processivity of family GH5 endoglucanase, RfGH5_4 from Ruminococcus flavefaciens on lignocellulosic polymers. Int J Biol Macromol 2022; 224:1395-1411. [DOI: 10.1016/j.ijbiomac.2022.10.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/15/2022] [Accepted: 10/24/2022] [Indexed: 11/05/2022]
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Wu M, Lv K, Li J, Wu B, He B. Coevolutionary analysis reveals a distal amino acid residue pair affecting the catalytic activity of GH5 processive endoglucanase from Bacillus subtilis BS-5. Biotechnol Bioeng 2022; 119:2105-2114. [PMID: 35438195 DOI: 10.1002/bit.28113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/06/2022]
Abstract
EG5C-1, processive endoglucanase from Bacillus subtilis, is a typical bifunctional cellulase with endoglucanase and exoglucanase activities. The engineering of processive endoglucanase focuses on the catalytic pocket or carbohydrate-binding module tailoring based on sequence/structure information. Herein, a computational strategy was applied to identify the desired mutants in the enzyme molecule by evolutionary coupling analysis; subsequently, four residue pairs were selected as evolutionary mutational hotspots. Based on iterative-saturation mutagenesis and subsequent enzymatic activity analysis, a superior mutant K51T/L93T was identified away from the active center. This variant had increased specific activity from 4170 U/µmol of wild-type (WT) to 5678 U/µmol towards CMC-Na and an increase towards the substrate Avicel from 320 U/µmol in WT to 521 U/µmol. In addition, kinetic measurements suggested that superior mutant K51T/L93T had a high substrate affinity (Km ) and a remarkable improvement in catalytic efficiency (kcat /Km ). Furthermore, molecular dynamics simulations revealed that the K51T/L93T mutation altered the spatial conformation at the active site cleft, enhancing the interaction frequency between active site residues and substrate, improving catalytic efficiency and substrate affinity. The current studies provided some perspectives on the effects of distal residue substitution, which might assist in the engineering of processive endoglucanase or other glycoside hydrolases. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mujunqi Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
| | - Kemin Lv
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
| | - Jiahuang Li
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
| | - Bingfang He
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
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Lv K, Shao W, Pedroso MM, Peng J, Wu B, Li J, He B, Schenk G. Enhancing the catalytic activity of a GH5 processive endoglucanase from Bacillus subtilis BS-5 by site-directed mutagenesis. Int J Biol Macromol 2020; 168:442-452. [PMID: 33310097 DOI: 10.1016/j.ijbiomac.2020.12.060] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 11/16/2022]
Abstract
Processive endoglucanases possess both endo- and exoglucanase activity, making them attractive discovery and engineering targets. Here, a processive endoglucanase EG5C-1 from Bacillus subtilis was employed as the starting point for enzyme engineering. Referring to the complex structure information of EG5C-1 and cellohexaose, the amino acid residues in the active site architecture were identified and subjected to alanine scanning mutagenesis. The residues were chosen for a saturation mutagenesis since their variants showed similar activities to EG5C-1. Variants D70Q and S235W showed increased activity towards the substrates CMC and Avicel, an increase was further enhanced in D70Q/S235W double mutant, which displayed a 2.1- and 1.7-fold improvement in the hydrolytic activity towards CMC and Avicel, respectively. In addition, kinetic measurements showed that double mutant had higher substrate affinity (Km) and a significantly higher catalytic efficiency (kcat/Km). The binding isotherms of wild-type EG5C-1 and double mutant D70Q/S235W suggested that the binding capability of EG5C-1 for the insoluble substrate was weaker than that of D70Q/S235W. Molecular dynamics simulations suggested that the collaborative substitutions of D70Q and S235W altered the hydrogen bonding network within the active site architecture and introduced new hydrogen bonds between the enzyme and cellohexaose, thus enhancing both substrate affinity and catalytic efficiency.
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Affiliation(s)
- Kemin Lv
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Wenyu Shao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jiayu Peng
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China.
| | - Jiahuang Li
- School of Life Science, Nanjing University, Nanjing 210023, Jiangsu, China.
| | - Bingfang He
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
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Jiang N, Ma XD, Fu LH, Li CX, Feng JX, Duan CJ. Identification of a unique 1,4-β-D-glucan glucohydrolase of glycoside hydrolase family 9 from Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2020; 104:7051-7066. [PMID: 32577801 DOI: 10.1007/s00253-020-10731-8] [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] [Received: 12/29/2019] [Revised: 05/25/2020] [Accepted: 06/07/2020] [Indexed: 10/24/2022]
Abstract
Cytophaga hutchinsonii is an aerobic cellulolytic soil bacterium that rapidly digests crystalline cellulose. The predicted mechanism by which C. hutchinsonii digests cellulose differs from that of other known cellulolytic bacteria and fungi. The genome of C. hutchinsonii contains 22 glycoside hydrolase (GH) genes, which may be involved in cellulose degradation. One predicted GH with uncertain specificity, CHU_0961, is a modular enzyme with several modules. In this study, phylogenetic tree of the catalytic modules of the GH9 enzymes showed that CHU_0961 and its homologues formed a new group (group C) of GH9 enzymes. The catalytic module of CHU_0961 (CHU_0961B) was identified as a 1,4-β-D-glucan glucohydrolase (EC 3.2.1.74) that has unique properties compared with known GH9 cellulases. CHU_0961B showed highest activity against barley glucan, but low activity against other polysaccharides. Interestingly, CHU_0961B showed similar activity against ρ-nitrophenyl β-D-cellobioside (ρ-NPC) and ρ-nitrophenyl β-D-glucopyranoside. CHU_0961B released glucose from the nonreducing end of cello-oligosaccharides, ρ-NPC, and barley glucan in a nonprocessive exo-type mode. CHU_0961B also showed same hydrolysis mode against deacetyl-chitooligosaccharides as against cello-oligosaccharides. The kcat/Km values for CHU_0961B against cello-oligosaccharides increased as the degree of polymerization increased, and its kcat/Km for cellohexose was 750 times higher than that for cellobiose. Site-directed mutagenesis showed that threonine 321 in CHU_0961 played a role in hydrolyzing cellobiose to glucose. CHU_0961 may act synergistically with other cellulases to convert cellulose to glucose on the bacterial cell surface. The end product, glucose, may initiate cellulose degradation to provide nutrients for bacterial proliferation in the early stage of C. hutchinsonii growth. KEY POINTS: • CHU_0961 and its homologues formed a novel group (group C) of GH9 enzymes. • CHU_0961 was identified as a 1,4-β-d-glucan glucohydrolase with unique properties. • CHU_0961 may play an important role in the early stage of C. hutchinsonii growth.
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Affiliation(s)
- Nan Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Xiao-Dan Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Li-Hao Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Cheng-Jie Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China.
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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Wang W, Archbold T, Lam JS, Kimber MS, Fan MZ. A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota. Sci Rep 2019; 9:13630. [PMID: 31541154 PMCID: PMC6754456 DOI: 10.1038/s41598-019-50050-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 09/05/2019] [Indexed: 02/08/2023] Open
Abstract
Cellulases play important roles in the dietary fibre digestion in pigs, and have multiple industrial applications. The porcine intestinal microbiota display a unique feature in rapid cellulose digestion. Herein, we have expressed a cellulase gene, p4818Cel5_2A, which singly encoded a catalytic domain belonging to glycoside hydrolase family 5 subfamily 2, and was previously identified from a metagenomic expression library constructed from porcine gut microbiome after feeding grower pigs with a cellulose-supplemented diet. The activity of purified p4818Cel5_2A was maximal at pH 6.0 and 50 °C and displayed resistance to trypsin digestion. This enzyme exhibited activities towards a wide variety of plant polysaccharides, including cellulosic substrates of avicel and solka-Floc®, and the hemicelluloses of β-(1 → 4)/(1 → 3)-glucans, xyloglucan, glucomannan and galactomannan. Viscosity, reducing sugar distribution and hydrolysis product analyses further revealed that this enzyme was a processive endo-β-(1 → 4)-glucanase capable of hydrolyzing cellulose into cellobiose and cellotriose as the primary end products. These catalytic features of p4818Cel5_2A were further explored in the context of a three-dimensional homology model. Altogether, results of this study report a microbial processive endoglucanase identified from the porcine gut microbiome, and it may be tailored as an efficient biocatalyst candidate for potential industrial applications.
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Affiliation(s)
- Weijun Wang
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Tania Archbold
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Joseph S Lam
- Department of Cellular and Molecular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Matthew S Kimber
- Department of Cellular and Molecular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Ming Z Fan
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
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Identification and characterization of an Endo-glucanase secreted from cellulolytic Escherichia coli ZH-4. BMC Biotechnol 2019; 19:63. [PMID: 31455320 PMCID: PMC6712877 DOI: 10.1186/s12896-019-0556-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 08/22/2019] [Indexed: 12/20/2022] Open
Abstract
Background In the previous study, the cellulolytic Escherichia coli ZH-4 isolated from bovine rumen was found to show extracellular cellulase activity and could degrade cellulose in the culture. The goal of this work was to identify and characterize the secreted cellulase of E. coli ZH-4. It will be helpful to re-understand E. coli and extend its application in industry. Results A secreted cellulase was confirmed to be endo-glucanase BcsZ which was encoded by bcsZ gene and located in the cellulose synthase operon bcsABZC in cellulolytic E. coli ZH-4 by western blotting. Characterization of BcsZ indicated that a broad range of pH and temperature tolerance with optima at pH 6.0 and 50 °C, respectively. The apparent Michaelis–Menten constant (Km) and maximal reaction rate (Vmax) for BcsZ were 8.86 mg/mL and 0.3 μM/min·mg, respectively. Enzyme activity of BcsZ was enhanced by Mg2+ and inhibited by Zn2+, Cu2+ and Fe3+. BcsZ could hydrolyze carboxymethylcellulose (CMC) to produce cello-oligosaccharides, cellotriose, cellobiose and glucose. Conclusions It is confirmed that extracellular cellulolytic capability of E. coli ZH-4 was attributed to BcsZ, which explained why E. coli ZH-4 can grow on cellulose. The endo-glucanase BcsZ from E. coli-ZH4 has some new characteristics which will extend the understanding of endo-glucanase. Analysis of the secretion characteristics of BcsZ provided a great reference for applying E. coli in multiple industrial fields.
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Processivity and the Mechanisms of Processive Endoglucanases. Appl Biochem Biotechnol 2019; 190:448-463. [DOI: 10.1007/s12010-019-03096-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/18/2019] [Indexed: 11/26/2022]
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Nguyen SN, Flores A, Talamantes D, Dar F, Valdez A, Schwans J, Berlemont R. GeneHunt for rapid domain-specific annotation of glycoside hydrolases. Sci Rep 2019; 9:10137. [PMID: 31300677 PMCID: PMC6626019 DOI: 10.1038/s41598-019-46290-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/26/2019] [Indexed: 12/20/2022] Open
Abstract
The identification of glycoside hydrolases (GHs) for efficient polysaccharide deconstruction is essential for the development of biofuels. Here, we investigate the potential of sequential HMM-profile identification for the rapid and precise identification of the multi-domain architecture of GHs from various datasets. First, as a validation, we successfully reannotated >98% of the biochemically characterized enzymes listed on the CAZy database. Next, we analyzed the 43 million non-redundant sequences from the M5nr data and identified 322,068 unique GHs. Finally, we searched 129 assembled metagenomes retrieved from MG-RAST for environmental GHs and identified 160,790 additional enzymes. Although most identified sequences corresponded to single domain enzymes, many contained several domains, including known accessory domains and some domains never identified in association with GH. Several sequences displayed multiple catalytic domains and few of these potential multi-activity proteins combined potentially synergistic domains. Finally, we produced and confirmed the biochemical activities of a GH5-GH10 cellulase-xylanase and a GH11-CE4 xylanase-esterase. Globally, this "gene to enzyme pipeline" provides a rationale for mining large datasets in order to identify new catalysts combining unique properties for the efficient deconstruction of polysaccharides.
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Affiliation(s)
- S N Nguyen
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - A Flores
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - D Talamantes
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - F Dar
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - A Valdez
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - J Schwans
- Department of Chemistry and Biochemistry, California State University Long Beach, Long Beach, California, USA
| | - R Berlemont
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA.
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Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling Bacteroidetes. mSystems 2018; 3:mSystems00240-18. [PMID: 30505945 PMCID: PMC6247017 DOI: 10.1128/msystems.00240-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/02/2018] [Indexed: 11/20/2022] Open
Abstract
Bacteria of the phylum Bacteroidetes are regarded as highly efficient carbohydrate metabolizers, but most species are limited to (semi)soluble glycans. The soil Bacteroidetes species Cytophaga hutchinsonii and Sporocytophaga myxococcoides have long been known as efficient cellulose metabolizers, but neither species conforms to known cellulolytic mechanisms. Both species require contact with their substrate but do not encode cellulosomal systems of cell surface-attached enzyme complexes or the polysaccharide utilization loci found in many other Bacteroidetes species. Here, we have fractionated the cellular compartments of each species from cultures growing on crystalline cellulose and pectin, respectively, and analyzed them using label-free quantitative proteomics as well as enzymatic activity assays. The combined results enabled us to highlight enzymes likely to be important for cellulose conversion and to infer their cellular localization. The combined proteomes represent a wide array of putative cellulolytic enzymes and indicate specific and yet highly redundant mechanisms for cellulose degradation. Of the putative endoglucanases, especially enzymes of hitherto-unstudied glycoside hydrolase family, 8 were abundant, indicating an overlooked important role during cellulose metabolism. Furthermore, both species generated a large number of abundant hypothetical proteins during cellulose conversion, providing a treasure trove of targets for future enzymology studies. IMPORTANCE Cellulose is the most abundant renewable polymer on earth, but its recalcitrance limits highly efficient conversion methods for energy-related and material applications. Though microbial cellulose conversion has been studied for decades, recent advances showcased that large knowledge gaps still exist. Bacteria of the phylum Bacteroidetes are regarded as highly efficient carbohydrate metabolizers, but most species are limited to (semi)soluble glycans. A few species, including the soil bacteria C. hutchinsonii and S. myxococcoides, are regarded as cellulose specialists, but their cellulolytic mechanisms are not understood, as they do not conform to the current models for enzymatic cellulose turnover. By unraveling the proteome setups of these two bacteria during growth on both crystalline cellulose and pectin, we have taken a significant step forward in understanding their idiosyncratic mode of cellulose conversion. This report provides a plethora of new enzyme targets for improved biomass conversion.
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Guan Z, Wang Y, Gao L, Zhang W, Lu X. Effects of the histone-like protein HU on cellulose degradation and biofilm formation of Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2018; 102:6593-6611. [PMID: 29876607 DOI: 10.1007/s00253-018-9071-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/26/2018] [Accepted: 04/29/2018] [Indexed: 01/23/2023]
Abstract
Cytophaga hutchinsonii, belonging to Bacteroidetes, is speculated to use a novel cell-contact mode to digest cellulose. In this study, we identified a histone-like protein HU, CHU_2750, in C. hutchinsonii, whose transcription could be induced by crystalline but not amorphous cellulose. We constructed a CHU_2750-deleted mutant and expressed CHU_2750 in Escherichia coli to study the gene's functions. Our results showed that although the deletion of CHU_2750 was not lethal to C. hutchinsonii, the mutant displayed an abnormal filamentous morphology, loose nucleoid, and obvious defects in the degradation of crystalline cellulose and cell motility. Further study indicated that the mutant displayed significantly decreased cell surface and intracellular endoglucanase activities but with β-glucosidase activities similar to the wild-type strain. Analyses by real-time quantitative PCR revealed that the transcription levels of many genes involved in cellulose degradation and/or cell motility were significantly downregulated in the mutant. In addition, we found that CHU_2750 was important for biofilm formation of C. hutchinsonii. The main extracellular components of the biofilm were analyzed, and the results showed that the mutant yielded significantly less exopolysaccharide but more extracellular DNA and protein than the wild-type strain. Collectively, our findings demonstrated that CHU_2750 is important for cellulose degradation, cell motility, and biofilm formation of C. hutchinsonii by modulating transcription of certain related genes, and it is the first identified transcriptional regulator in these processes of C. hutchinsonii. Our study shed more light on the mechanisms of cellulose degradation, cell motility, and biofilm formation by C. hutchinsonii.
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Affiliation(s)
- Zhiwei Guan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.,School of Life Science, Qilu Normal University, Jinan, 250200, China
| | - Ying Wang
- Central Laboratory, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China
| | - Lijuan Gao
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
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Kundu S, Sharma R. Origin, evolution, and divergence of plant class C GH9 endoglucanases. BMC Evol Biol 2018; 18:79. [PMID: 29848310 PMCID: PMC5977491 DOI: 10.1186/s12862-018-1185-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycoside hydrolases of the GH9 family encode cellulases that predominantly function as endoglucanases and have wide applications in the food, paper, pharmaceutical, and biofuel industries. The partitioning of plant GH9 endoglucanases, into classes A, B, and C, is based on the differential presence of transmembrane, signal peptide, and the carbohydrate binding module (CBM49). There is considerable debate on the distribution and the functions of these enzymes which may vary in different organisms. In light of these findings we examined the origin, emergence, and subsequent divergence of plant GH9 endoglucanases, with an emphasis on elucidating the role of CBM49 in the digestion of crystalline cellulose by class C members. RESULTS Since, the digestion of crystalline cellulose mandates the presence of a well-defined set of aromatic and polar amino acids and/or an attributable domain that can mediate this conversion, we hypothesize a vertical mode of transfer of genes that could favour the emergence of class C like GH9 endoglucanase activity in land plants from potentially ancestral non plant taxa. We demonstrated the concomitant occurrence of a GH9 domain with CBM49 and other homologous carbohydrate binding modules, in putative endoglucanase sequences from several non-plant taxa. In the absence of comparable full length CBMs, we have characterized several low strength patterns that could approximate the CBM49, thereby, extending support for digestion of crystalline cellulose to other segments of the protein. We also provide data suggestive of the ancestral role of putative class C GH9 endoglucanases in land plants, which includes detailed phylogenetics and the presence and subsequent loss of CBM49, transmembrane, and signal peptide regions in certain populations of early land plants. These findings suggest that classes A and B of modern vascular land plants may have emerged by diverging directly from CBM49 encompassing putative class C enzymes. CONCLUSION Our detailed phylogenetic and bioinformatics analysis of putative GH9 endoglucanase sequences across major taxa suggests that plant class C enzymes, despite their recent discovery, could function as the last common ancestor of classes A and B. Additionally, research into their ability to digest or inter-convert crystalline and amorphous forms of cellulose could make them lucrative candidates for engineering biofuel feedstock.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Government of NCT of Delhi, Dr. Baba Saheb Ambedkar Medical College & Hospital, New Delhi, 110085, India. .,Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Rita Sharma
- Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Naas AE, Solden LM, Norbeck AD, Brewer H, Hagen LH, Heggenes IM, McHardy AC, Mackie RI, Paša-Tolić L, Arntzen MØ, Eijsink VGH, Koropatkin NM, Hess M, Wrighton KC, Pope PB. "Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system. MICROBIOME 2018; 6:44. [PMID: 29490697 PMCID: PMC5831590 DOI: 10.1186/s40168-018-0421-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/07/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family ("Candidatus MH11") composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa. RESULTS The first metabolic reconstruction of Ca. MH11-affiliated genome bins, with a particular focus on the provisionally named "Candidatus Paraporphyromonas polyenzymogenes", illustrated their capacity to degrade various lignocellulosic substrates via comprehensive inventories of singular and multi-modular carbohydrate active enzymes (CAZymes). Closer examination revealed an absence of archetypical polysaccharide utilization loci found in human gut microbiota. Instead, we identified many multi-modular CAZymes putatively secreted via the Bacteroidetes-specific type IX secretion system (T9SS). This included cellulases with two or more catalytic domains, which are modular arrangements that are unique to Bacteroidetes species studied to date. Core metabolic proteins from Ca. P. polyenzymogenes were detected in metaproteomic data and were enriched in rumen-incubated plant biomass, indicating that active saccharification and fermentation of complex carbohydrates could be assigned to members of this novel family. Biochemical analysis of selected Ca. P. polyenzymogenes CAZymes further iterated the cellulolytic activity of this hitherto uncultured bacterium towards linear polymers, such as amorphous and crystalline cellulose as well as mixed linkage β-glucans. CONCLUSION We propose that Ca. P. polyenzymogene genotypes and other Ca. MH11 members actively degrade plant biomass in the rumen of cows, sheep and most likely other ruminants, utilizing singular and multi-domain catalytic CAZymes secreted through the T9SS. The discovery of a prominent role of multi-modular cellulases in the Gram-negative Bacteroidetes, together with similar findings for Gram-positive cellulosomal bacteria (Ruminococcus flavefaciens) and anaerobic fungi (Orpinomyces sp.), suggests that complex enzymes are essential and have evolved within all major cellulolytic dominions inherent to the rumen.
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Affiliation(s)
- A E Naas
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - L M Solden
- Department of Microbiology, The Ohio State University, Columbus, OH, 43201, USA
| | - A D Norbeck
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - H Brewer
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - L H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - I M Heggenes
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - A C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraβe 7, 38124, Braunschweig, Germany
| | - R I Mackie
- Institute for Genomic Biology and Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - L Paša-Tolić
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - M Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - V G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - N M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - M Hess
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - K C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, 43201, USA
| | - P B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway.
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15
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Wu B, Zheng S, Pedroso MM, Guddat LW, Chang S, He B, Schenk G. Processivity and enzymatic mechanism of a multifunctional family 5 endoglucanase from Bacillus subtilis BS-5 with potential applications in the saccharification of cellulosic substrates. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:20. [PMID: 29422948 PMCID: PMC5787917 DOI: 10.1186/s13068-018-1022-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/11/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Presently, enzymes still constitute a major part of the cost of biofuel production from lignocellulosic biomass. Processive endoglucanases, which possess both endoglucanase and exoglucanase activity, have the potential to reduce the costs of biomass saccharification when used together with commercial cellulases. Therefore, the exploration of new processive endoglucanases has attracted much attention with a view to accelerating the industrialization of biofuels and biochemicals. RESULTS The endoglucanase EG5C and its truncated form EG5C-1 from Bacillus subtilis BS-5 were expressed and characterized. EG5C was a typical endoglucanase, comprised of a family 5 catalytic domain and family 3 carbohydrate-binding domain, and which had high activity toward soluble cellulosic substrates, but low activity toward insoluble cellulosic substrates. Importantly, the truncated form EG5C-1 was a processive endoglucanase that hydrolyzed not only carboxymethyl cellulose (CMC), but also insoluble cellulosic substrates. The hydrolytic activities of EG5C-1 towards CMC, phosphoric acid-swollen cellulose (PASC), p-nitrophenyl-β-d-cellobioside, filter paper and Avicel are 4170, 700, 2550, 405 and 320 U/μmol, respectively. These data demonstrated that EG5C-1 had higher activity ratio of exoglucanase to endoglucanase than other known processive endoglucanases. When PASC was degraded by EG5C-1, the ratio of soluble to insoluble reducing sugars was about 3.7 after 3 h of incubation with cellobiose and cellotriose as the main products. Importantly, EG5C-1 alone was able to hydrolyze filter paper and PASC. At 5% substrate concentration and 10 FPU/g PASC enzyme loading, the saccharification yield was 76.5% after 60 h of incubation. Replacement of a phenylalanine residue (F238) by an alanine at the entrance/exit of the substrate binding cleft significantly reduces the ability of EG5C-1 to degrade filter paper and Avicel, but this mutation has little impact on CMCase activity. The processivity of this mutant was also greatly reduced while its cellulose binding ability was markedly enhanced. CONCLUSIONS The processive endoglucanase EG5C-1 from B. subtilis BS-5 exhibits excellent properties that render it a suitable candidate for use in biofuel and biochemical production from lignocellulosic biomass. In addition, our studies also provide useful information for research on enzyme processivity at the molecular level.
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Affiliation(s)
- Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
- China Jiangsu National Synergetic Innovation Center for Advanced Materials, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
| | - Shan Zheng
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
| | - Siyuan Chang
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
| | - Bingfang He
- China Jiangsu National Synergetic Innovation Center for Advanced Materials, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
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16
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Wei YD, Li Y, Deng C, Wu SH, Huang CJ, Yi Y. Expression and biochemical characterization of a multifunctional glycosidase from the thermophilic Bacillus licheniformis SR01. J GEN APPL MICROBIOL 2017; 63:259-265. [PMID: 28835594 DOI: 10.2323/jgam.2016.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A gene (gkdA) (741 bp) encoding a putative protein of 247 amino acids was cloned from the Bacillus licheniformis SR01. The protein was expressed in Escherichia coli BL21 with a molecular mass estimated by SDS-PAGE of approximately 28.03 kDa and showed a calculating isoelectric point (pI) of 6.42. Structure analysis and function identification showed that the enzyme was a multifunctional glycosidase. Its specific activity was 0.013 U/μg. The recombinant glycosidase showed a maximum activity at 50°C and pH 7.0. It was very stable below 90°C and may have heat activation at higher temperatures. The relative residual activity was still more than 80% after 120 min at pH 5.0-10.0. The enzyme activity was inhibited by Cu2+, Fe2+, Ca2+, Mg2+, Co2+, Li+, SDS and EDTA, activated by Ca2+, and not affected by Mn2+ and K+. Under simulated stomach, and in vitro intestine, conditions, the enzyme retained 80%, and more than 100%, activity, respectively, after incubation for 90 min. The excellent properties of this enzyme, specifically its thermal stability and multifunctional abilities, give it potential application in the field of feed processing and other high-temperature processing industries.
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Affiliation(s)
- Yang-Dao Wei
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology.,Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology.,Key Laboratory for Processing of Sugar Resources of Guangxi Higher Education Institutes, Guangxi University of Science and Technology
| | - Ya Li
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology.,Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology.,Key Laboratory for Processing of Sugar Resources of Guangxi Higher Education Institutes, Guangxi University of Science and Technology
| | - Chun Deng
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology.,Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology.,Key Laboratory for Processing of Sugar Resources of Guangxi Higher Education Institutes, Guangxi University of Science and Technology
| | - Shi-Hua Wu
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology.,Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology.,Key Laboratory for Processing of Sugar Resources of Guangxi Higher Education Institutes, Guangxi University of Science and Technology
| | - Cui-Ji Huang
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology.,Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology.,Key Laboratory for Processing of Sugar Resources of Guangxi Higher Education Institutes, Guangxi University of Science and Technology
| | - Yi Yi
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology.,Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology.,Key Laboratory for Processing of Sugar Resources of Guangxi Higher Education Institutes, Guangxi University of Science and Technology
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17
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The unusual cellulose utilization system of the aerobic soil bacterium Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2017; 101:7113-7127. [PMID: 28849247 DOI: 10.1007/s00253-017-8467-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 08/05/2017] [Indexed: 10/19/2022]
Abstract
Cellulolytic microorganisms play important roles in global carbon cycling and have evolved diverse strategies to digest cellulose. Some are 'generous,' releasing soluble sugars from cellulose extracellularly to feed both themselves and their neighbors. The gliding soil bacterium Cytophaga hutchinsonii exhibits a more 'selfish' strategy. It digests crystalline cellulose using cell-associated cellulases and releases little soluble sugar outside of the cell. The mechanism of C. hutchinsonii cellulose utilization is still poorly understood. In this review, we discuss novel aspects of the C. hutchinsonii cellulolytic system. Recently developed genetic manipulation tools allowed the identification of proteins involved in C. hutchinsonii cellulose utilization. These include periplasmic and cell-surface endoglucanases and novel cellulose-binding proteins. The recently discovered type IX secretion system is needed for cellulose utilization and appears to deliver some of the cellulolytic enzymes and other proteins to the cell surface. The requirement for periplasmic endoglucanases for cellulose utilization is unusual and suggests that cello-oligomers must be imported across the outer membrane before being further digested. Cellobiohydrolases or other predicted processive cellulases that play important roles in many other cellulolytic bacteria appear to be absent in C. hutchinsonii. Cells of C. hutchinsonii attach to and glide along cellulose fibers, which may allow them to find sites most amenable to attack. A model of C. hutchinsonii cellulose utilization summarizing recent progress is proposed.
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18
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Wang X, Han Q, Chen G, Zhang W, Liu W. A Putative Type II Secretion System Is Involved in Cellulose Utilization in Cytophaga hutchisonii. Front Microbiol 2017; 8:1482. [PMID: 28848505 PMCID: PMC5553014 DOI: 10.3389/fmicb.2017.01482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/24/2017] [Indexed: 11/23/2022] Open
Abstract
Cytophaga hutchinsonii is a gliding cellulolytic bacterium that degrades cellulose in a substrate contact-dependent manner. Specific proteins are speculated to be translocated to its extracellular milieu or outer membrane surface to participate in adhesion to cellulose and further digestion. In this study, we show that three orthologous genes encoding the major components (T2S-D, -F, and -G) of type II secretion system (T2SS) are involved in cellulose degradation but not in cell motility. The individual disruption of the three t2s genes results in a significantly retarded growth on cellobiose, regenerated amorphous cellulose, and Avicel cellulose. Enzymatic analyses demonstrate that, whereas the endoglucanase activity of the t2s mutant cells is increased, the β-glucosidase activity is remarkably reduced compared to that of WT cells. Further analyses reveal that the t2s mutant cells not only exhibit a different profile of cellulose-bound outer membrane proteins from that of wild-type cells, but also display a significant decrease in their capability to adhere to cellulose. These results indicate that a functional link exits between the putative T2SS and cellulose utilization in C. hutchinsonii, and thus provide a conceptual framework to understand the unique strategy deployed by C. hutchinsonii to assimilate cellulose.
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Affiliation(s)
- Xia Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China
| | - Qingqing Han
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China
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19
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Bai X, Wang X, Wang S, Ji X, Guan Z, Zhang W, Lu X. Functional Studies of β-Glucosidases of Cytophaga hutchinsonii and Their Effects on Cellulose Degradation. Front Microbiol 2017; 8:140. [PMID: 28210251 PMCID: PMC5288383 DOI: 10.3389/fmicb.2017.00140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/19/2017] [Indexed: 11/17/2022] Open
Abstract
Cytophaga hutchinsonii can rapidly digest crystalline cellulose without free cellulases or cellulosomes. Its cell-contact cellulose degradation mechanism is unknown. In this study, the four β-glucosidase (bgl) genes in C. hutchinsonii were singly and multiply deleted, and the functions of these β-glucosidases in cellobiose and cellulose degradation were investigated. We found that the constitutively expressed BglB played a key role in cellobiose utilization, while BglA which was induced by cellobiose could partially make up for the deletion of bglB. The double deletion mutant ΔbglA/bglB lost the ability to digest cellobiose and could not thrive in cellulose medium, indicating that β-glucosidases were important for cellulose degradation. When cultured in cellulose medium, a small amount of glucose accumulated in the medium in the initial stage of growth for the wild type, while almost no glucose accumulated for ΔbglA/bglB. When supplemented with a small amount of glucose, ΔbglA/bglB started to degrade cellulose and grew in cellulose medium. We inferred that glucose might be essential for initiating cellulose degradation, and with additional glucose, C. hutchinsonii could partially utilize cellulose without β-glucosidases. We also found that there were both cellulose binding cells and free cells when cultured in cellulose. Since direct contact between C. hutchinsonii cells and cellulose is necessary for cellulose degradation, we deduced that the free cells which were convenient to explore new territory in the environment might be fed by the adherent cells which could produce cello-oligosaccharide and glucose into the environment. This study enriched our knowledge of the cellulolytic pathway of C. hutchinsonii.
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Affiliation(s)
- Xinfeng Bai
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Xifeng Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Sen Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Xiaofei Ji
- Department of Pathogenic Biology, Binzhou Medical University Yantai, China
| | - Zhiwei Guan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
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20
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Identification and Characterization of a Large Protein Essential for Degradation of the Crystalline Region of Cellulose by Cytophaga hutchinsonii. Appl Environ Microbiol 2016; 83:AEM.02270-16. [PMID: 27742681 DOI: 10.1128/aem.02270-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/04/2016] [Indexed: 12/22/2022] Open
Abstract
Cytophaga hutchinsonii is a Gram-negative bacterium that can efficiently degrade crystalline cellulose by a unique mechanism different from the free cellulase or cellulosome strategy. In this study, chu_3220, encoding the hypothetical protein CHU_3220 (205 kDa), was identified by insertional mutation and gene deletion as the first gene essential for degradation of the crystalline region but not the amorphous region of cellulose by C. hutchinsonii A chu_3220 deletion mutant was defective in the degradation of crystalline cellulose and increased the degree of crystallinity of Avicel PH101 but could still degrade amorphous cellulose completely. CHU_3220 was found to be located on the outer surface of the outer membrane and could bind to cellulose. It contains 15 PbH1 domains and a C-terminal domain (CHU_C) that was proved to be critical for the localization of CHU_3220 on the cell surface and the function of CHU_3220 in crystalline cellulose degradation. Moreover, the degradation of crystalline cellulose was intact-cell dependent and inhibited by NaN3 Further study showed that chu_3220 was induced by cellulose and that the endoglucanase activity on the cell surface was significantly reduced without chu_3220 Real-time PCR revealed that the transcription of most genes encoding endoglucanases located on the cell surface was decreased in the chu_3220 deletion mutant, indicating that chu_3220 might also play a role in the regulation of the expression of some endoglucanases. IMPORTANCE Cytophaga hutchinsonii could efficiently degrade crystalline cellulose with a unique mechanism without cellulosomes and free cellulases. It lacks proteins that are thought to play important roles in disruption of the crystalline region of cellulose, including exoglucanases, lytic polysaccharide monooxygenases, expansins, expansin-like proteins, or swollenins, and most of its endoglucanases lack carbohydrate binding modules. The mechanism of the degradation of crystalline cellulose is still unknown. In this study, chu_3220 was identified as the first gene essential for the degradation of the crystalline region but not the amorphous region of cellulose. CHU_3220 is a high-molecular-weight protein located on the outer surface of the outer membrane and could bind to cellulose. We proposed that CHU_3220 might be an essential component of a protein complex on the cell surface in charge of the decrystallization of crystalline cellulose. The degradation of crystalline cellulose by C. hutchinsonii was not only dependent on intact cells but also required the energy supplied by the cells. This was obviously different from other known cellulose depolymerization system. Our study has shed more light on the novel strategy of crystalline cellulose degradation by C. hutchinsonii.
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21
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Expression and characterization of a glucose-tolerant β-1,4-glucosidase with wide substrate specificity from Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2016; 101:1919-1926. [PMID: 27822737 DOI: 10.1007/s00253-016-7927-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 10/01/2016] [Accepted: 10/09/2016] [Indexed: 10/20/2022]
Abstract
Cytophaga hutchinsonii is a gram-negative bacterium that can efficiently degrade crystalline cellulose by a novel strategy without cell-free cellulases or cellulosomes. Genomic analysis implied that C. hutchinsonii had endoglucanases and β-glucosidases but no exoglucanases which could processively digest cellulose and produce cellobiose. In this study, BglA was functionally expressed in Escherichia coli and found to be a β-glucosidase with wide substrate specificity. It can hydrolyze pNPG, pNPC, cellobiose, and cellodextrins. Moreover, unlike most β-glucosidases whose activity greatly decreases with increasing length of the substrate chains, BglA has similar activity on cellobiose and larger cellodextrins. The K m values of BglA on cellobiose, cellotriose, and cellotetraose were calculated to be 4.8 × 10-2, 5.6 × 10-2, and 5.3 × 10-2 mol/l, respectively. These properties give BglA a great advantage to cooperate with endoglucanases in C. hutchinsonii in cellulose degradation. We proposed that C. hutchinsonii could utilize a simple cellulase system which consists of endoglucanases and β-glucosidases to completely digest amorphous cellulose into glucose. Moreover, BglA was also found to be highly tolerant to glucose as it retained 40 % activity when the concentration of glucose was 100 times higher than that of the substrate, showing potential application in the bioenergy industry.
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22
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Lee HJ, Kim IJ, Youn HJ, Yun EJ, Choi IG, Kim KH. Cellotriose-hydrolyzing activity conferred by truncating the carbohydrate-binding modules of Cel5 from Hahella chejuensis. Bioprocess Biosyst Eng 2016; 40:241-249. [PMID: 27761654 DOI: 10.1007/s00449-016-1692-8] [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: 06/20/2016] [Accepted: 10/07/2016] [Indexed: 01/30/2023]
Abstract
Processivity is a typical characteristic of cellobiohydrolases (CBHs); it enables the enzyme to successively hydrolyze the ends of cellulose chains and to produce cellobiose as the major product. Some microbes, which do not have CBHs, utilize endoglucanases (EGs) that exhibit processivity, commonly referred to as processive EGs. A processive EG identified from Hahella chejuensis, HcCel5, has a catalytic domain (CD) belonging to the glycoside hydrolase family 5 (GH5) and two carbohydrate-binding modules (CBM6s). In this study, we compared HcCel5-CD with the CD of Saccharophagus degradans Cel5H (SdCel5H-CD), which is a processive EG reported previously. Our results showed that in comparison to SdCel5H-CD, HcCel5-CD has more suitable characteristics for cellulose hydrolysis, such as higher hydrolytic activity, thermostability (40-80 °C), and processivity. Noticeably, HcCel5-CD is capable of hydrolyzing cellotriose, unlike HcCel5. These features of HcCel5-CD for cellulose hydrolysis could be employed for efficient saccharification of lignocellulose to produce cellobiose and glucose, which may be used to produce renewable fuels and chemicals.
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Affiliation(s)
- Hee Jin Lee
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea.,Ildong Pharmaceutical, Hwaseong, 18449, South Korea
| | - In Jung Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Hak Jin Youn
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Eun Ju Yun
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - In-Geol Choi
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea.
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23
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Extra carbohydrate binding module contributes to the processivity and catalytic activity of a non-modular hydrolase family 5 endoglucanase from Fomitiporia mediterranea MF3/22. Enzyme Microb Technol 2016; 91:42-51. [DOI: 10.1016/j.enzmictec.2016.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/12/2016] [Accepted: 06/01/2016] [Indexed: 11/23/2022]
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24
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Periplasmic Cytophaga hutchinsonii Endoglucanases Are Required for Use of Crystalline Cellulose as the Sole Source of Carbon and Energy. Appl Environ Microbiol 2016; 82:4835-4845. [PMID: 27260354 DOI: 10.1128/aem.01298-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/25/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The soil bacterium Cytophaga hutchinsonii actively digests crystalline cellulose by a poorly understood mechanism. Genome analyses identified nine genes predicted to encode endoglucanases with roles in this process. No predicted cellobiohydrolases, which are usually involved in the utilization of crystalline cellulose, were identified. Chromosomal deletions were performed in eight of the endoglucanase-encoding genes: cel5A, cel5B, cel5C, cel9A, cel9B, cel9C, cel9E, and cel9F Each mutant retained the ability to digest crystalline cellulose, although the deletion of cel9C caused a modest decrease in cellulose utilization. Strains with multiple deletions were constructed to identify the critical cellulases. Cells of a mutant lacking both cel5B and cel9C were completely deficient in growth on cellulose. Cell fractionation and biochemical analyses indicate that Cel5B and Cel9C are periplasmic nonprocessive endoglucanases. The requirement of periplasmic endoglucanases for cellulose utilization suggests that cellodextrins are transported across the outer membrane during this process. Bioinformatic analyses predict that Cel5A, Cel9A, Cel9B, Cel9D, and Cel9E are secreted across the outer membrane by the type IX secretion system, which has been linked to cellulose utilization. These secreted endoglucanases may perform the initial digestion within amorphous regions on the cellulose fibers, releasing oligomers that are transported into the periplasm for further digestion by Cel5B and Cel9C. The results suggest that both cell surface and periplasmic endoglucanases are required for the growth of C. hutchinsonii on cellulose and that novel cell surface proteins may solubilize and transport cellodextrins across the outer membrane. IMPORTANCE The bacterium Cytophaga hutchinsonii digests crystalline cellulose by an unknown mechanism. It lacks processive cellobiohydrolases that are often involved in cellulose digestion. Critical cellulolytic enzymes were identified by genetic analyses. Intracellular (periplasmic) nonprocessive endoglucanases performed an important role in cellulose utilization. The results suggest a model involving partial digestion at the cell surface, solubilization and uptake of cellodextrins across the outer membrane by an unknown mechanism, and further digestion within the periplasm. The ability to sequester cellodextrins and digest them intracellularly may limit losses of soluble cellobiose to other organisms. C. hutchinsonii uses an unusual approach to digest cellulose and is a potential source of novel proteins to increase the efficiency of conversion of cellulose into soluble sugars and biofuels.
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Loaces I, Bottini G, Moyna G, Fabiano E, Martínez A, Noya F. EndoG: A novel multifunctional halotolerant glucanase and xylanase isolated from cow rumen. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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An Outer Membrane Protein Involved in the Uptake of Glucose Is Essential for Cytophaga hutchinsonii Cellulose Utilization. Appl Environ Microbiol 2016; 82:1933-1944. [PMID: 26773084 DOI: 10.1128/aem.03939-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/08/2016] [Indexed: 11/20/2022] Open
Abstract
Cytophaga hutchinsonii specializes in cellulose digestion by employing a collection of novel cell-associated proteins. Here, we identified a novel gene locus, CHU_1276, that is essential for C. hutchinsonii cellulose utilization. Disruption of CHU_1276 in C. hutchinsonii resulted in complete deficiency in cellulose degradation, as well as compromised assimilation of cellobiose or glucose at a low concentration. Further analysis showed that CHU_1276 was an outer membrane protein that could be induced by cellulose and low concentrations of glucose. Transcriptional profiling revealed that CHU_1276 exerted a profound effect on the genome-wide response to both glucose and Avicel and that the mutant lacking CHU_1276 displayed expression profiles very different from those of the wild-type strain under different culture conditions. Specifically, comparison of their transcriptional responses to cellulose led to the identification of a gene set potentially regulated by CHU_1276. These results suggest that CHU_1276 plays an essential role in cellulose utilization, probably by coordinating the extracellular hydrolysis of cellulose substrate with the intracellular uptake of the hydrolysis product in C. hutchinsonii.
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A small periplasmic protein essential for Cytophaga hutchinsonii cellulose digestion. Appl Microbiol Biotechnol 2015; 100:1935-1944. [PMID: 26649736 DOI: 10.1007/s00253-015-7204-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022]
Abstract
Cytophaga hutchinsonii is a gliding cellulolytic bacterium that is ubiquitously distributed in soil. The mechanism by which C. hutchinsonii achieves cellulose digestion, however, is still largely unknown. In this study, we obtained a C. hutchinsonii mutant that was defective in utilizing filter paper or Avicel as the sole carbon source by transposon mutagenesis. The interrupted gene locus, CHU_2981, encodes a hypothetical protein with only 130 amino acids. Cell fractionation and western blot detection of CHU_2981 fused with a C-terminal green fluorescence protein (GFP) indicated that CHU_2981 is located in the periplasm. The CHU_2981-disrupted mutant cells exhibited a significant growth defect on Avicel but not on glucose and cellobiose. The absence of CHU_2981 also resulted in a significant defect in colony spreading and individual cell motility compared to wild-type cells. Further analysis demonstrated that the CHU_2981-disrupted mutant cells exhibited a different profile of cellulose-absorbed outer membrane proteins from that of wild-type cells, in which protein varieties and amounts were markedly decreased. Our results showed that CHU_2981, the periplasmic non-cellulolytic protein, plays an important role in both cellulose utilization and cell motility probably by being involved in the appropriate production of outer membrane proteins.
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Expression and characteristics of a Ca2+-dependent endoglucanase from Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2015; 99:9617-23. [DOI: 10.1007/s00253-015-6746-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
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Novel outer membrane protein involved in cellulose and cellooligosaccharide degradation by Cytophaga hutchinsonii. Appl Environ Microbiol 2015; 80:4511-8. [PMID: 24837387 DOI: 10.1128/aem.00687-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytophaga hutchinsonii is an aerobic cellulolytic soil bacterium which was reported to use a novel contact-dependent strategy to degrade cellulose. It was speculated that cellooligosaccharides were transported into the periplasm for further digestion. In this study, we reported that most of the endoglucanase and -glucosidase activity was distributed on the cell surface of C. hutchinsonii.Cellobiose and part of the cellulose could be hydrolyzed to glucose on the cell surface. However, the cell surface cellulolytic enzymes were not sufficient for cellulose degradation by C. hutchinsonii. An outer membrane protein, CHU_1277, was disrupted by insertional mutation. Although the mutant maintained the same endoglucanase activity and most of the -glucosidase activity,it failed to digest cellulose, and its cellooligosaccharide utilization ability was significantly reduced, suggesting that CHU_1277 was essential for cellulose degradation and played an important role in cellooligosaccharide utilization. Further study of cellobiose hydrolytic ability of the mutant on the enzymatic level showed that the -glucosidase activity in the outer membrane of the mutant was not changed. It revealed that CHU_1277 played an important role in assisting cell surface -glucosidase to exhibit its activity sufficiently. Studies on the outer membrane proteins involved in cellulose and cellooligosaccharide utilization could shed light on the mechanism of cellulose degradation by C. hutchinsonii.
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Zhu Y, Kwiatkowski KJ, Yang T, Kharade SS, Bahr CM, Koropatkin NM, Liu W, McBride MJ. Outer membrane proteins related to SusC and SusD are not required for Cytophaga hutchinsonii cellulose utilization. Appl Microbiol Biotechnol 2015; 99:6339-50. [DOI: 10.1007/s00253-015-6555-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 11/29/2022]
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