1
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Metatranscriptome Profiling of a Specialized Microbial Consortium during the Degradation of Nixtamalized Maize Pericarp. Microbiol Spectr 2022; 10:e0231821. [PMID: 34985337 PMCID: PMC8729791 DOI: 10.1128/spectrum.02318-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lignocellulose degradation by microbial consortia is multifactorial; hence, it must be analyzed from a holistic perspective. In this study, the temporal transcriptional activity of consortium PM-06, a nixtamalized maize pericarp (NMP) degrader, was determined and related to structural and physicochemical data to give insights into the mechanism used to degrade this substrate. Transcripts were described in terms of metabolic profile, carbohydrate-active enzyme (CAZyme) annotation, and taxonomic affiliation. The PM-06 gene expression pattern was closely related to the differential rates of degradation. The environmental and physiological conditions preceding high-degradation periods were crucial for CAZyme expression. The onset of degradation preceded the period with the highest degradation rate in the whole process, and in this time, several CAZymes were upregulated. Functional analysis of expressed CAZymes indicated that PM-06 overcomes NMP recalcitrance through modular enzymes operating at the proximity of the insoluble substrate. Increments in the diversity of expressed modular CAZymes occurred in the last stages of degradation where the substrate is more recalcitrant and environmental conditions are stressing. Taxonomic affiliation of CAZyme transcripts indicated that Paenibacillus macerans was fundamental for degradation. This microorganism established synergistic relationships with Bacillus thuringiensis for the degradation of cellulose and hemicellulose and with Microbacterium, Leifsonia, and Nocardia for the saccharification of oligosaccharides. IMPORTANCE Nixtamalized maize pericarp is an abundant residue of the tortilla industry. Consortium PM-06 efficiently degraded this substrate in 192 h. In this work, the temporal transcriptional profile of PM-06 was determined. Findings indicated that differential degradation rates are important sample selection criteria since they were closely related to the expression of carbohydrate-active enzymes (CAZymes). The initial times of degradation were crucial for the consumption of nixtamalized pericarp. A transcriptional profile at the onset of degradation is reported for the first time. Diverse CAZyme genes were rapidly transcribed after inoculation to produce different enzymes that participated in the stage with the highest degradation rate in the whole process. This study provides information about the regulation of gene expression and mechanisms used by PM-06 to overcome recalcitrance. These findings are useful in the design of processes and enzyme cocktails for the degradation of this abundant substrate.
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2
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Hoke AK, Reynoso G, Smith MR, Gardner MI, Lockwood DJ, Gilbert NE, Wilhelm SW, Becker IR, Brennan GJ, Crider KE, Farnan SR, Mendoza V, Poole AC, Zimmerman ZP, Utz LK, Wurch LL, Steffen MM. Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere. PLoS One 2021; 16:e0257017. [PMID: 34550975 PMCID: PMC8457463 DOI: 10.1371/journal.pone.0257017] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/20/2021] [Indexed: 11/18/2022] Open
Abstract
Microbial interactions in harmful algal bloom (HAB) communities have been examined in marine systems, but are poorly studied in fresh waters. To investigate HAB-microbe interactions, we isolated bacteria with close associations to bloom-forming cyanobacteria, Microcystis spp., during a 2017 bloom in the western basin of Lake Erie. The genomes of five isolates (Exiguobacterium sp. JMULE1, Enterobacter sp. JMULE2, Deinococcus sp. JMULE3, Paenibacillus sp. JMULE4, and Acidovorax sp. JMULE5.) were sequenced on a PacBio Sequel system. These genomes ranged in size from 3.1 Mbp (Exiguobacterium sp. JMULE1) to 5.7 Mbp (Enterobacter sp. JMULE2). The genomes were analyzed for genes relating to critical metabolic functions, including nitrogen reduction and carbon utilization. All five of the sequenced genomes contained genes that could be used in potential signaling and nutrient exchange between the bacteria and cyanobacteria such as Microcystis. Gene expression signatures of algal-derived carbon utilization for two isolates were identified in Microcystis blooms in Lake Erie and Lake Tai (Taihu) at low levels, suggesting these organisms are active and may have a functional role during Microcystis blooms in aggregates, but were largely missing from whole water samples. These findings build on the growing evidence that the bacterial microbiome associated with bloom-forming algae have the functional potential to contribute to nutrient exchange within bloom communities and interact with important bloom formers like Microcystis.
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Affiliation(s)
- Alexa K. Hoke
- James Madison University, Harrisonburg, VA, United States of America
| | - Guadalupe Reynoso
- James Madison University, Harrisonburg, VA, United States of America
- Virginia Tech, Blacksburg, VA, United States of America
| | - Morgan R. Smith
- James Madison University, Harrisonburg, VA, United States of America
- Texas A&M University, College Station, TX, United States of America
| | - Malia I. Gardner
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Naomi E. Gilbert
- James Madison University, Harrisonburg, VA, United States of America
- University of Tennessee, Knoxville, TN, United States of America
| | | | | | - Grant J. Brennan
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Shannon R. Farnan
- James Madison University, Harrisonburg, VA, United States of America
| | - Victoria Mendoza
- James Madison University, Harrisonburg, VA, United States of America
| | - Alison C. Poole
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Lucy K. Utz
- James Madison University, Harrisonburg, VA, United States of America
| | - Louie L. Wurch
- James Madison University, Harrisonburg, VA, United States of America
| | - Morgan M. Steffen
- James Madison University, Harrisonburg, VA, United States of America
- * E-mail:
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3
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Talens-Perales D, Jiménez-Ortega E, Sánchez-Torres P, Sanz-Aparicio J, Polaina J. Phylogenetic, functional and structural characterization of a GH10 xylanase active at extreme conditions of temperature and alkalinity. Comput Struct Biotechnol J 2021; 19:2676-2686. [PMID: 34093984 PMCID: PMC8148631 DOI: 10.1016/j.csbj.2021.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 01/31/2023] Open
Abstract
Endoxylanases active under extreme conditions of
temperature and alkalinity can replace the use of highly pollutant chemicals in
the pulp and paper industry. Searching for enzymes with these properties, we
carried out a comprehensive bioinformatics study of the GH10 family. The
phylogenetic analysis allowed the construction of a radial cladogram in which
protein sequences putatively ascribed as thermophilic and alkaliphilic appeared
grouped in a well-defined region of the cladogram, designated TAK Cluster. One
among five TAK sequences selected for experimental analysis (Xyn11) showed
extraordinary xylanolytic activity under simultaneous conditions of high
temperature (90 °C) and alkalinity (pH 10.5). Addition of a carbohydrate binding
domain (CBM2) at the C-terminus of the protein sequence further improved the
activity of the enzyme at high pH. Xyn11 structure, which has been solved at
1.8 Å resolution by X-ray crystallography, reveals an unusually high number of
hydrophobic, ionic and hydrogen bond atomic interactions that could account for
the enzyme’s extremophilic nature.
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Affiliation(s)
- David Talens-Perales
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
| | - Elena Jiménez-Ortega
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Paloma Sánchez-Torres
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
| | - Julia Sanz-Aparicio
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Julio Polaina
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
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4
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Draft genome sequence data of Paenbacillus curdlanolyticus B-6 possessing a unique xylanolytic-cellulolytic multienzyme system. Data Brief 2020; 32:106213. [PMID: 32923539 PMCID: PMC7476223 DOI: 10.1016/j.dib.2020.106213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/18/2020] [Indexed: 11/23/2022] Open
Abstract
Paenibacillus curdlanolyticus B-6 is a facultative anaerobic bacterium that efficiently produces a lignocellulolytic multienzyme complex. The whole genome of P. curdlanolyticus B-6 was sequenced on an Ion GeneStudio S5 system, which yielded 74 contigs with a total size of 4,875,097 bp, 4,473 protein-coding sequences, and a G+C content of 49.7%. The genome data have been deposited in DDBJ/ENA/GenBank under accession numbers BLWM01000001–BLWM01000074. Analyses of average nucleotide identities and phylogenetic relationships of 16S rRNA sequences of Paenibacillus species revealed that strain B-6 is most closely related to Paenibacillus xylaniclasticus TW1. P. curdlanolyticus B-6 should thus be reclassified as a strain of P. xylaniclasticus.
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5
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Significance of a family-6 carbohydrate-binding module in a modular feruloyl esterase for removing ferulic acid from insoluble wheat arabinoxylan. Enzyme Microb Technol 2020; 138:109546. [DOI: 10.1016/j.enzmictec.2020.109546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/23/2020] [Accepted: 03/03/2020] [Indexed: 11/21/2022]
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6
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Limsakul P, Phitsuwan P, Waeonukul R, Pason P, Tachaapaikoon C, Poomputsa K, Kosugi A, Sakka M, Sakka K, Ratanakhanokchai K. A novel AA10 from Paenibacillus curdlanolyticus and its synergistic action on crystalline and complex polysaccharides. Appl Microbiol Biotechnol 2020; 104:7533-7550. [PMID: 32651597 DOI: 10.1007/s00253-020-10758-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/24/2020] [Indexed: 02/08/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) play an important role in the degradation of complex polysaccharides in lignocellulosic biomass. In the present study, we characterized a modular LPMO (PcAA10A), consisting of a family 10 auxiliary activity of LPMO (AA10) catalytic domain, and non-catalytic domains including a family 5 carbohydrate-binding module, two fibronectin type-3 domains, and a family 3 carbohydrate-binding module from Paenibacillus curdlanolyticus B-6, which was expressed in a recombinant Escherichia coli. Comparison of activities between full-length PcAA10A and the catalytic domain polypeptide (PcAA10A_CD) indicates that the non-catalytic domains are important for the deconstruction of crystalline cellulose and complex polysaccharides contained in untreated lignocellulosic biomass. Interestingly, PcAA10A_CD acted not only on cellulose and chitin, but also on xylan, mannan, and xylan and cellulose contained in lignocellulosic biomass, which has not been reported for the AA10 family. Mutation of the key residues, Trp51 located at subsite - 2 and Phe171 located at subsite +2, in the substrate-binding site of PcAA10A_CD revealed that these residues are substantially involved in broad substrate specificity toward cellulose, xylan, and mannan, albeit with a low effect toward chitin. Furthermore, PcAA10A had a boosting effect on untreated corn hull degradation by P. curdlanolyticus B-6 endo-xylanase Xyn10D and Clostridium thermocellum endo-glucanase Cel9A. These results suggest that PcAA10A is a unique LPMO capable of cleaving and enhancing lignocellulosic biomass degradation, making it a good candidate for biotechnological applications. KEY POINTS: • PcAA10A is a novel modular LPMO family 10 from Paenibacillus curdlanolyticus. • PcAA10A showed broad substrate specificity on β-1,4 glycosidic linkage substrates. • Non-catalytic domains are important for degrading complex polysaccharides. • PcAA10A is a unique LPMO capable of enhancing lignocellulosic biomass degradation.
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Affiliation(s)
- Puangpen Limsakul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paripok Phitsuwan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Kanokwan Poomputsa
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, 305-8686, Japan
| | - Makiko Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
| | - Kazuo Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan.
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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7
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A novel multifunctional GH9 enzyme from Paenibacillus curdlanolyticus B-6 exhibiting endo/exo functions of cellulase, mannanase and xylanase activities. Appl Microbiol Biotechnol 2020; 104:2079-2096. [DOI: 10.1007/s00253-020-10388-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 12/13/2022]
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8
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Han Z, Shang-Guan F, Yang J. Molecular and Biochemical Characterization of a Bimodular Xylanase From Marinifilaceae Bacterium Strain SPP2. Front Microbiol 2019; 10:1507. [PMID: 31312196 PMCID: PMC6614494 DOI: 10.3389/fmicb.2019.01507] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 06/17/2019] [Indexed: 01/31/2023] Open
Abstract
In this study, the first xylantic enzyme from the family Marinifilaceae, XynSPP2, was identified from Marinifilaceae bacterium strain SPP2. Amino acid sequence analysis revealed that XynSPP2 is a rare Fn3-fused xylanase, consisting of a signal peptide, a fibronectin type-III domain (Fn3), and a C-terminal catalytic domain belonging to glycoside hydrolase family 10 (GH10). The catalytic domain shared 17–46% identities to those of biochemically characterized GH10 xylanases. Structural analysis revealed that the conserved asparagine and glutamine at the glycone −2/−3 subsite of GH10 xylanases are substituted by a tryptophan and a serine, respectively, in XynSPP2. Full-length XynSPP2 and its Fn3-deleted variant (XynSPP2ΔFn3) were overexpressed in Escherichia coli and purified by Ni-affinity chromatography. The optimum temperature and pH for both recombinant enzymes were 50°C and 6, respectively. The enzymes were stable under alkaline condition and at temperature lower than 50°C. With beechwood xylan as the substrate, XynSPP2 showed 2.8 times the catalytic efficiency of XynSPP2ΔFn3, indicating that the Fn3 module promotes xylanase activity. XynSPP2 was active toward xylooligosaccharides (XOSs) longer than xylotriose. Such a substrate preference can be explained by the unique −2/−3 subsite composition in the enzyme which provides new insight into subsite interaction within the GH10 family. XynSPP2 hydrolyzed beechwood xylan into small XOSs (xylotriose and xylotetraose as major products). No monosaccharide was detected by thin-layer chromatography which may be ascribed to putative transxylosylation activity of XynSPP2. Preferring long XOS substrate and lack of monosaccharide production suggest its potential in probiotic XOS manufacture.
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Affiliation(s)
- Zhenggang Han
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Fang Shang-Guan
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jiangke Yang
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
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9
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Sakka M, Kunitake E, Kimura T, Sakka K. Function of a laminin_G_3 module as a carbohydrate-binding module in an arabinofuranosidase from Ruminiclostridium josui. FEBS Lett 2018; 593:42-51. [PMID: 30403289 DOI: 10.1002/1873-3468.13283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/23/2018] [Accepted: 10/30/2018] [Indexed: 11/09/2022]
Abstract
Laminin_G_3 modules can exist together with family-43 catalytic modules of glycoside hydrolase (GH43), but their functions are unknown. Here, a laminin_G_3 module and a GH43 module derived from a Ruminiclostridium josui modular arabinofuranosidase Abf43A-Abf43B-Abf43C were produced individually as RjLG3 and RjGH43_22, respectively, or combined as RjGH43-1 to gain insights into their activities. Isothermal calorimetry analysis showed that RjLG3 has high affinity toward 32 -α-l-arabinofuranosyl-(1,5)-α-l-arabinotriose but not for α-1,5-linked arabinooligosaccharides, which suggests that RjLG3 interacts specifically with a branched arabinofuranosyl residue of an arabinooligosaccharide but not an arabinofuranosyl residue at the end of α-1,5-linked arabinooligosaccharides. RjGH43-1 (with CBM) shows higher activity toward sugar beet arabinan than RjGH43_22 (without CBM), which suggests that the LG3 module in RjGH43-1 plays an important role in substrate hydrolysis as a carbohydrate-binding module.
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Affiliation(s)
- Makiko Sakka
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Emi Kunitake
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Tetsuya Kimura
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Kazuo Sakka
- Graduate School of Bioresources, Mie University, Tsu, Japan
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10
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A New Group of Modular Xylanases in Glycoside Hydrolase Family 8 from Marine Bacteria. Appl Environ Microbiol 2018; 84:AEM.01785-18. [PMID: 30217847 DOI: 10.1128/aem.01785-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 09/12/2018] [Indexed: 11/20/2022] Open
Abstract
Xylanases play a crucial role in the degradation of xylan in both terrestrial and marine environments. The endoxylanase XynB from the marine bacterium Glaciecola mesophila KMM 241 is a modular enzyme comprising a long N-terminal domain (NTD) (E44 to T562) with xylan-binding ability and a catalytic domain (CD) (T563 to E912) of glycoside hydrolase family 8 (GH8). In this study, the long NTD is confirmed to contain three different functional regions, which are NTD1 (E44 to D136), NTD2 (Y137 to A193), and NTD3 (L194 to T562). NTD1, mainly composed of eight β-strands, functions as a new type of carbohydrate-binding module (CBM), which has xylan-binding ability but no sequence similarity to any known CBM. NTD2, mainly forming two α-helices, contains one of the α-helices of the catalytic domain's (α/α)6 barrel and therefore is essential for the activity of XynB, although it is far away from the catalytic domain in sequence. NTD3, next to the catalytic domain in sequence, is shown to be helpful in maintaining the thermostability of XynB. Thus, XynB represents a kind of xylanase with a new domain architecture. There are four other predicted glycoside hydrolase sequences with the same domain architecture and high sequence identity (≥80%) with XynB, all of which are from marine bacteria. Phylogenetic analysis shows that XynB and these homologs form a new group in GH8, representing a new class of marine bacterial xylanases. Our results shed light on xylanases, especially marine xylanases.IMPORTANCE Xylanases play a crucial role in natural xylan degradation and have been extensively used in industries such as food processing, animal feed, and kraft pulp biobleaching. Some marine bacteria have been found to secrete xylanases. Characterization of novel xylanases from marine bacteria has significance for both the clarification of xylan degradation mechanisms in the sea and the development of new enzymes for industrial application. With G. mesophila XynB as a representative, this study reveals a new group of the GH8 xylanases from marine bacteria, which have a distinct domain architecture and contain a novel carbohydrate-binding module. Thus, this study offers new knowledge on marine xylanases.
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11
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Orita T, Sakka M, Kimura T, Sakka K. Recombinant cellulolytic or xylanolytic complex comprising the full-length scaffolding protein RjCipA and cellulase RjCel5B or xylanase RjXyn10C of Ruminiclostridium josui. Enzyme Microb Technol 2017; 97:63-70. [DOI: 10.1016/j.enzmictec.2016.10.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/14/2016] [Accepted: 10/30/2016] [Indexed: 11/26/2022]
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12
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Sermsathanaswadi J, Baramee S, Tachaapaikoon C, Pason P, Ratanakhanokchai K, Kosugi A. The family 22 carbohydrate-binding module of bifunctional xylanase/β-glucanase Xyn10E from Paenibacillus curdlanolyticus B-6 has an important role in lignocellulose degradation. Enzyme Microb Technol 2017; 96:75-84. [DOI: 10.1016/j.enzmictec.2016.09.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/05/2016] [Accepted: 09/24/2016] [Indexed: 10/20/2022]
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13
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Kim DR, Lim HK, Lee KI, Hwang IT. Identification of a novel cellulose-binding domain within the endo -β-1,4-xylanase KRICT PX-3 from Paenibacillus terrae HPL-003. Enzyme Microb Technol 2016; 93-94:166-173. [DOI: 10.1016/j.enzmictec.2016.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/19/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
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14
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Baramee S, Teeravivattanakit T, Phitsuwan P, Waeonukul R, Pason P, Tachaapaikoon C, Kosugi A, Sakka K, Ratanakhanokchai K. A novel GH6 cellobiohydrolase from Paenibacillus curdlanolyticus B-6 and its synergistic action on cellulose degradation. Appl Microbiol Biotechnol 2016; 101:1175-1188. [PMID: 27743043 DOI: 10.1007/s00253-016-7895-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/12/2016] [Accepted: 09/25/2016] [Indexed: 11/30/2022]
Abstract
We recently discovered a novel glycoside hydrolase family 6 (GH6) cellobiohydrolase from Paenibacillus curdlanolyticus B-6 (PcCel6A), which is rarely found in bacteria. This enzyme is a true exo-type cellobiohydrolase which exhibits high substrate specificity on amorphous cellulose and low substrate specificity on crystalline cellulose, while this showed no activity on substitution substrates, carboxymethyl cellulose and xylan, distinct from all other known GH6 cellobiohydrolases. Product profiles, HPLC analysis of the hydrolysis products and a schematic drawing of the substrate-binding subsites catalysing cellooligosaccharides can explain the new mode of action of this enzyme which prefers to hydrolyse cellopentaose. PcCel6A was not inhibited by glucose or cellobiose at concentrations up to 300 and 100 mM, respectively. A good synergistic effect for glucose production was found when PcCel6A acted together with processive endoglucanase Cel9R from Clostridium thermocellum and β-glucosidase CglT from Thermoanaerobacter brockii. These properties of PcCel6A make it a suitable candidate for industrial application in the cellulose degradation process.
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Affiliation(s)
- Sirilak Baramee
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Thitiporn Teeravivattanakit
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paripok Phitsuwan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, 305-8686, Japan
| | - Kazuo Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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15
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Zhang Q, Li H, Zhu X, Lai F, Zhai Z, Wang Y. Exploration of the key functional proteins from an efficient cellulolytic microbial consortium using dilution-to-extinction approach. J Environ Sci (China) 2016; 43:199-207. [PMID: 27155425 DOI: 10.1016/j.jes.2015.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/21/2015] [Accepted: 09/23/2015] [Indexed: 06/05/2023]
Abstract
In the present study, the cellulose binding proteins (CBPs) secreted by a putative cellulolytic microbial consortium were isolated and purified by affinity digestion. The purified CBPs were subsequently separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Using mass spectrometric analyses, eight CBPs were identified and annotated to be similar to known proteins secreted by Clostridium clariflavum DSM 19732 and Paenibacillus sp. W-61. In addition, in combination with dilution-to-extinction approach and zymogram analysis technique, CBPs 6 (97kDa) and 12 (52kDa) were confirmed to be the key functional proteins that influence cellulolytic activities. Moreover, structural domain analyses and enzymatic activity detection indicated that CBPs 6 and 12 contained glycoside hydrolase families (GH) 9 and 48 catalytic modules, which both revealed endoglucandase and xylanase activities. It was suggested that the coexistence of GH9 and GH48 catalytic domains present in these two proteins could synergistically promote the efficient degradation of cellulose.
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Affiliation(s)
- Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Hanguang Li
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Xiangdong Zhu
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fenju Lai
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhijun Zhai
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yuanxiu Wang
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
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Mollerup F, Parikka K, Vuong TV, Tenkanen M, Master E. Influence of a family 29 carbohydrate binding module on the activity of galactose oxidase from Fusarium graminearum. Biochim Biophys Acta Gen Subj 2015; 1860:354-62. [PMID: 26518347 DOI: 10.1016/j.bbagen.2015.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 10/02/2015] [Accepted: 10/23/2015] [Indexed: 11/26/2022]
Abstract
BACKGROUND Galactose oxidase (GaO) selectively oxidizes the primary hydroxyl of galactose to a carbonyl, facilitating targeted chemical derivatization of galactose-containing polysaccharides, leading to renewable polymers with tailored physical and chemical properties. Here we investigate the impact of a family 29 glucomannan binding module on the activity and binding of GaO towards various polysaccharides. Specifically, CBM29-1-2 from Piromyces equi was separately linked to the N- and C-termini of GaO. RESULTS Both GaO-CBM29 and CBM29-GaO were successfully expressed in Pichia pastoris, and demonstrated enhanced binding to galactomannan, galactoglucomannan and galactoxyloglucan. The position of the CBM29 fusion affected the enzyme function. Particularly, C-terminal fusion led to greatest increases in galactomannan binding and catalytic efficiency, where relative to wild-type GaO, kcat/Km values increased by 7.5 and 19.8 times on guar galactomannan and locust bean galactomannan, respectively. The fusion of CBM29 also induced oligomerization of GaO-CBM29. MAJOR CONCLUSIONS Similar to impacts of cellulose-binding modules associated with cellulolytic enzymes, increased substrate binding impeded the action of GaO fusions on more concentrated preparations of galactomannan, galactoglucomannan and galactoxyloglucan; this was especially true for GaO-CBM29. Given the N-terminal positioning of the native galactose-binding CBM32 in GaO, the varying impacts of N-terminal versus C-terminal fusion of CBM29-1-2 may reflect competing action of neighboring CBMs. GENERAL SIGNIFICANCE This study thoroughly examines and discusses the effects of CBM fusion to non-lignocellulytic enzymes on soluble polysaccharides. Herein kinetics of GaO on galactose containing polysaccharides is presented for the first time.
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Affiliation(s)
- Filip Mollerup
- Department of Biotechnology and Chemical Technology, Aalto University, 00076 Aalto, Finland
| | - Kirsti Parikka
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki 00014, Finland
| | - Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki 00014, Finland
| | - Emma Master
- Department of Biotechnology and Chemical Technology, Aalto University, 00076 Aalto, Finland; Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada.
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Ojima Y, Suparman A, Nguyen MH, Sakka M, Sakka K, Taya M. Exopolysaccharide assay in Escherichia coli microcolonies using a cleavable fusion protein of GFP-labeled carbohydrate-binding module. J Microbiol Methods 2015; 114:75-7. [DOI: 10.1016/j.mimet.2015.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 05/11/2015] [Accepted: 05/11/2015] [Indexed: 11/28/2022]
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18
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Paenibacillus curdlanolyticus B-6 xylanase Xyn10C capable of producing a doubly arabinose-substituted xylose, α-l-Araf-(1→2)-[α-l-Araf-(1→3)]-d-Xylp, from rye arabinoxylan. Enzyme Microb Technol 2015; 72:1-9. [DOI: 10.1016/j.enzmictec.2015.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 01/31/2015] [Accepted: 02/05/2015] [Indexed: 11/18/2022]
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19
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Molecular and Biochemical Characterization of a Novel Multidomain Xylanase from Arthrobacter sp. GN16 Isolated from the Feces of Grus nigricollis. Appl Biochem Biotechnol 2014; 175:573-88. [DOI: 10.1007/s12010-014-1295-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/10/2014] [Indexed: 11/26/2022]
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20
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Nguyen MH, Ojima Y, Sakka M, Sakka K, Taya M. Probing of exopolysaccharides with green fluorescence protein-labeled carbohydrate-binding module in Escherichia coli biofilms and flocs induced by bcsB overexpression. J Biosci Bioeng 2014; 118:400-5. [PMID: 24746734 DOI: 10.1016/j.jbiosc.2014.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/11/2014] [Accepted: 03/13/2014] [Indexed: 01/30/2023]
Abstract
Polysaccharides are major structural constituents to develop the three-dimensional architecture of Escherichia coli biofilms. In this study, confocal laser scanning microscopy was applied in combination with a fluorescent probe to analyze the location and arrangement of exopolysaccharide (EPSh) in microcolonies of E. coli K-12 derived strains, formed as biofilms on solid surfaces and flocs in the liquid phase. For this purpose, a novel fluorescent probe was constructed by conjugating a carbohydrate-binding module 3, from Paenibacillus curdlanolyticus, with the green fluorescence protein (GFP-CBM3). The GFP-CBM3 fused protein exhibited strong affinity to microcrystalline cellulose. Moreover, GFP-CBM3 specifically bound to cell-dense microcolonies in the E. coli biofilms, and to their flocs induced by bcsB overexpression. Therefore, the fused protein presents as a novel marker for EPSh produced by E. coli cells. Overexpression of bcsB was associated with abundant EPSh production and enhanced E. coli biofilm formation, which was similarly detectable by GFP-CBM3 probing.
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Affiliation(s)
- Minh Hong Nguyen
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan
| | - Yoshihiro Ojima
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan
| | - Makiko Sakka
- Applied Microbiology Laboratory, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Kazuo Sakka
- Applied Microbiology Laboratory, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Masahito Taya
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan.
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21
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Mizutani K, Sakka M, Kimura T, Sakka K. Essential role of a family-32 carbohydrate-binding module in substrate recognition byClostridium thermocellummannanaseCtMan5A. FEBS Lett 2014; 588:1726-30. [DOI: 10.1016/j.febslet.2014.03.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/28/2014] [Accepted: 03/12/2014] [Indexed: 11/27/2022]
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22
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Song HY, Lim HK, Kim DR, Lee KI, Hwang IT. A new bi-modular endo-β-1,4-xylanase KRICT PX-3 from whole genome sequence of Paenibacillus terrae HPL-003. Enzyme Microb Technol 2014; 54:1-7. [DOI: 10.1016/j.enzmictec.2013.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 10/26/2022]
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23
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Ashida T, Ojima Y, Sakai S, Sakka M, Sakka K, Kawakami K, Taya M. Designing Fusion Proteins with Carbohydrate-Binding Modules Having Affinity to Enzymatically Gellable Carboxymethylcellulose Derivative Hydrogel. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2014. [DOI: 10.1252/jcej.14we080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tomoaki Ashida
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University
| | - Yoshihiro Ojima
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University
| | - Shinji Sakai
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University
| | - Makiko Sakka
- Applied Microbiology Laboratory, Graduate School of Bioresources, Mie University
| | - Kazuo Sakka
- Applied Microbiology Laboratory, Graduate School of Bioresources, Mie University
| | - Koei Kawakami
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University
| | - Masahito Taya
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University
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Guo N, Zheng J, Wu LS, Tian J, Zhou HB. Engineered bifunctional enzymes of endo-1,4-β-xylanase/endo-1,4-β-mannanase were constructed for synergistically hydrolyzing hemicellulose. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.06.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Present and potential applications of cellulases in agriculture, biotechnology, and bioenergy. Folia Microbiol (Praha) 2012; 58:163-76. [DOI: 10.1007/s12223-012-0184-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 07/10/2012] [Indexed: 11/27/2022]
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26
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Sakka M, Tachino S, Katsuzaki H, van Dyk JS, Pletschke BI, Kimura T, Sakka K. Characterization of Xyn30A and Axh43A of Bacillus licheniformis SVD1 identified by its genomic analysis. Enzyme Microb Technol 2012; 51:193-9. [PMID: 22883553 DOI: 10.1016/j.enzmictec.2012.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 06/14/2012] [Accepted: 06/21/2012] [Indexed: 11/18/2022]
Abstract
The genome sequence of Bacillus licheniformis SVD1, that produces a cellulolytic and hemi-cellulolytic multienzyme complex, was partially determined, indicating that the glycoside hydrolase system of this strain is highly similar to that of B. licheniformis ATCC14580. All of the fifty-six genes encoding glycoside hydrolases identified in B. licheniformis ATCC14580 were conserved in strain SVD1. In addition, two new genes, xyn30A and axh43A, were identified in the B. licheniformis SVD1 genome. The xyn30A gene was highly similar to Bacillus subtilis subsp. subtilis 168 xynC encoding for a glucuronoarabinoxylan endo-1,4-β-xylanase. Xyn30A, produced by a recombinant Escherichia coli, had high activity toward 4-O-methyl-D-glucurono-D-xylan but showed definite activity toward oat-spelt xylan and unsubstituted xylooligosaccharides. Recombinant Axh43A, consisting of a family-43 catalytic module of the glycoside hydrolases and a family-6 carbohydrate-binding module (CBM), was an arabinoxylan arabinofuranohydrolase (α-L-arabinofuranosidase) classified as AXH-m23 and capable of releasing arabinosyl residues, which are linked to the C-2 or C-3 position of singly substituted xylose residues in arabinoxylan or arabinoxylan oligomers. The isolated CBM polypeptide had an affinity for soluble and insoluble xylans and removal of the CBM from Axh43A abolished the catalytic activity of the enzyme, indicating that the CBM plays an essential role in hydrolysis of arabinoxylan.
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Affiliation(s)
- Makiko Sakka
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu 514-8507, Japan
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Influence of a mannan binding family 32 carbohydrate binding module on the activity of the appended mannanase. Appl Environ Microbiol 2012; 78:4781-7. [PMID: 22562994 DOI: 10.1128/aem.07457-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In general, cellulases and hemicellulases are modular enzymes in which the catalytic domain is appended to one or more noncatalytic carbohydrate binding modules (CBMs). CBMs, by concentrating the parental enzyme at their target polysaccharide, increase the capacity of the catalytic module to bind the substrate, leading to a potentiation in catalysis. Clostridium thermocellum hypothetical protein Cthe_0821, defined here as C. thermocellum Man5A, is a modular protein comprising an N-terminal signal peptide, a family 5 glycoside hydrolase (GH5) catalytic module, a family 32 CBM (CBM32), and a C-terminal type I dockerin module. Recent proteomic studies revealed that Cthe_0821 is one of the major cellulosomal enzymes when C. thermocellum is cultured on cellulose. Here we show that the GH5 catalytic module of Cthe_0821 displays endomannanase activity. C. thermocellum Man5A hydrolyzes soluble konjac glucomannan, soluble carob galactomannan, and insoluble ivory nut mannan but does not attack the highly galactosylated mannan from guar gum, suggesting that the enzyme prefers unsubstituted β-1,4-mannoside linkages. The CBM32 of C. thermocellum Man5A displays a preference for the nonreducing ends of mannooligosaccharides, although the protein module exhibits measurable affinity for the termini of β-1,4-linked glucooligosaccharides such as cellobiose. CBM32 potentiates the activity of C. thermocellum Man5A against insoluble mannans but has no significant effect on the capacity of the enzyme to hydrolyze soluble galactomannans and glucomannans. The product profile of C. thermocellum Man5A is affected by the presence of CBM32.
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Modular glucuronoxylan-specific xylanase with a family CBM35 carbohydrate-binding module. Appl Environ Microbiol 2012; 78:3923-31. [PMID: 22447606 DOI: 10.1128/aem.07932-11] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xyn30D from the xylanolytic strain Paenibacillus barcinonensis has been identified and characterized. The enzyme shows a modular structure comprising a catalytic module family 30 (GH30) and a carbohydrate-binding module family 35 (CBM35). Like GH30 xylanases, recombinant Xyn30D efficiently hydrolyzed glucuronoxylans and methyl-glucuronic acid branched xylooligosaccharides but showed no catalytic activity on arabinose-substituted xylans. Kinetic parameters of Xyn30D were determined on beechwood xylan, showing a K(m) of 14.72 mg/ml and a k(cat) value of 1,510 min(-1). The multidomain structure of Xyn30D clearly distinguishes it from the GH30 xylanases characterized to date, which are single-domain enzymes. The modules of the enzyme were individually expressed in a recombinant host and characterized. The isolated GH30 catalytic module showed specific activity, mode of action on xylan, and kinetic parameters that were similar to those of the full-length enzyme. Computer modeling of the three-dimensional structure of Xyn30D showed that the catalytic module is comprised of a common (β/α)(8) barrel linked to a side-associated β-structure. Several derivatives of the catalytic module with decreasing deletions of this associated structure were constructed. None of them showed catalytic activity, indicating the importance of the side β-structure in the catalysis of Xyn30D. Binding properties of the isolated carbohydrate-binding module were analyzed by affinity gel electrophoresis, which showed that the CBM35 of the enzyme binds to soluble glucuronoxylans and arabinoxylans. Analysis by isothermal titration calorimetry showed that CBM35 binds to glucuronic acid and requires calcium ions for binding. Occurrence of a CBM35 in a glucuronoxylan-specific xylanase is a differential trait of the enzyme characterized.
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