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Liu H, Huang M, Wei S, Wang X, Zhao Y, Han Z, Ye X, Li Z, Ji Y, Cui Z, Huang Y. Characterization of a multi-domain exo-β-1,3-galactanase from Paenibacillus xylanexedens. Int J Biol Macromol 2024; 266:131413. [PMID: 38582482 DOI: 10.1016/j.ijbiomac.2024.131413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
β-1,3-Galactanases selectively degrade β-1,3-galactan, thus it is an attractive enzyme technique to map high-galactan structure and prepare galactooligosaccharides. In this work, a gene encoding exo-β-1,3-galactanase (PxGal43) was screened form Paenibacillus xylanexedens, consisting of a GH43 domain, a CBM32 domain and α-L-arabinofuranosidase B (AbfB) domain. Using β-1,3-galactan (AG-II-P) as substrate, the recombined enzyme expressed in Escherichia coli BL21 (DE3) exhibited an optimal activity at pH 7.0 and 30 °C. The enzyme was thermostable, retaining >70 % activity after incubating at 50 °C for 2 h. In addition, it showed high tolerance to various metal ions, denaturants and detergents. Substrate specificity indicated that PxGal43 hydrolysis only β-1,3-linked galactosyl oligosaccharides and polysaccharides, releasing galactose as an exo-acting manner. The function of the CBM32 and AbfB domain was revealed by their sequential deletion and suggested that their connection to the catalytic domain was crucial for the oligomerization, catalytic activity, substrate binding and thermal stability of PxGal43. The substrate docking and site-directed mutagenesis proposed that Glu191, Gln244, Asp138 and Glu81 served as the catalytic acid, catalytic base, pKa modulator, and substrate identifier in PxGal43, respectively. These results provide a better understanding and optimization of multi-domain bacterial GH43 β-1,3-galactanase for the degradation of arabinogalactan.
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Affiliation(s)
- Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Min Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Shuxin Wei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiaowen Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yaqin Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhengyang Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yanling Ji
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
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Ashy RA, Jalal RS, Sonbol HS, Alqahtani MD, Sefrji FO, Alshareef SA, Alshehrei FM, Abuauf HW, Baz L, Tashkandi MA, Hakeem IJ, Refai MY, Abulfaraj AA. Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera. Front Microbiol 2023; 14:1166148. [PMID: 37260683 PMCID: PMC10227523 DOI: 10.3389/fmicb.2023.1166148] [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: 02/15/2023] [Accepted: 04/10/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes. Methods Genes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil. Results Abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H2O2 and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include "antibiotic efflux pump" for ARGs soxR, OleC, and MuxB, "antibiotic target alteration" for parY mutant, and "antibiotic inactivation" for arr-1. Discussion These ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.
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Affiliation(s)
- Ruba A. Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rewaa S. Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Hana S. Sonbol
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mashael D. Alqahtani
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatmah O. Sefrji
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatimah M. Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Haneen W. Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Manal A. Tashkandi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Aala A. Abulfaraj
- Biological Sciences Department, College of Science & Arts, King AbdulAziz University, Rabigh, Saudi Arabia
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3
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Cloning, Expression, Purification and Characterization of the β-galactosidase PoβGal35A from Penicillium oxalicum. Mol Biotechnol 2022:10.1007/s12033-022-00620-y. [DOI: 10.1007/s12033-022-00620-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022]
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4
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Long C, Qi XL, Venema K. Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review. Front Nutr 2022; 9:948302. [PMID: 36245487 PMCID: PMC9554435 DOI: 10.3389/fnut.2022.948302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Approximately 35% of rapeseed meal (RSM) dry matter (DM) are carbohydrates, half of which are water-soluble carbohydrates. The cell wall of rapeseed meal contains arabinan, galactomannan, homogalacturonan, rhamnogalacturonan I, type II arabinogalactan, glucuronoxylan, XXGG-type and XXXG-type xyloglucan, and cellulose. Glycoside hydrolases including in the degradation of RSM carbohydrates are α-L-Arabinofuranosidases (EC 3.2.1.55), endo-α-1,5-L-arabinanases (EC 3.2.1.99), Endo-1,4-β-mannanase (EC 3.2.1.78), β-mannosidase (EC 3.2.1.25), α-galactosidase (EC 3.2.1.22), reducing-end-disaccharide-lyase (pectate disaccharide-lyase) (EC 4.2.2.9), (1 → 4)-6-O-methyl-α-D-galacturonan lyase (pectin lyase) (EC 4.2.2.10), (1 → 4)-α-D-galacturonan reducing-end-trisaccharide-lyase (pectate trisaccharide-lyase) (EC 4.2.2.22), α-1,4-D-galacturonan lyase (pectate lyase) (EC 4.2.2.2), (1 → 4)-α-D-galacturonan glycanohydrolase (endo-polygalacturonase) (EC 3.2.1.15), Rhamnogalacturonan hydrolase, Rhamnogalacturonan lyase (EC 4.2.2.23), Exo-β-1,3-galactanase (EC 3.2.1.145), endo-β-1,6-galactanase (EC 3.2.1.164), Endo-β-1,4-glucanase (EC 3.2.1.4), α-xylosidase (EC 3.2.1.177), β-glucosidase (EC 3.2.1.21) endo-β-1,4-glucanase (EC 3.2.1.4), exo-β-1,4-glucanase (EC 3.2.1.91), and β-glucosidase (EC 3.2.1.21). In conclusion, this review summarizes the chemical and nutritional compositions of RSM, and the microbial degradation of RSM cell wall carbohydrates which are important to allow to develop strategies to improve recalcitrant RSM carbohydrate degradation by the gut microbiota, and eventually to improve animal feed digestibility, feed efficiency, and animal performance.
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Affiliation(s)
- Cheng Long
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
- Faculty of Science and Engineering, Centre for Healthy Eating and Food Innovation, Maastricht University - Campus Venlo, Venlo, Netherlands
| | - Xiao-Long Qi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Koen Venema
- Faculty of Science and Engineering, Centre for Healthy Eating and Food Innovation, Maastricht University - Campus Venlo, Venlo, Netherlands
- *Correspondence: Koen Venema
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Villa-Rivera MG, Cano-Camacho H, López-Romero E, Zavala-Páramo MG. The Role of Arabinogalactan Type II Degradation in Plant-Microbe Interactions. Front Microbiol 2021; 12:730543. [PMID: 34512607 PMCID: PMC8424115 DOI: 10.3389/fmicb.2021.730543] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Arabinogalactans (AGs) are structural polysaccharides of the plant cell wall. A small proportion of the AGs are associated with hemicellulose and pectin. Furthermore, AGs are associated with proteins forming the so-called arabinogalactan proteins (AGPs), which can be found in the plant cell wall or attached through a glycosylphosphatidylinositol (GPI) anchor to the plasma membrane. AGPs are a family of highly glycosylated proteins grouped with cell wall proteins rich in hydroxyproline. These glycoproteins have important and diverse functions in plants, such as growth, cellular differentiation, signaling, and microbe-plant interactions, and several reports suggest that carbohydrate components are crucial for AGP functions. In beneficial plant-microbe interactions, AGPs attract symbiotic species of fungi or bacteria, promote the development of infectious structures and the colonization of root tips, and furthermore, these interactions can activate plant defense mechanisms. On the other hand, plants secrete and accumulate AGPs at infection sites, creating cross-links with pectin. As part of the plant cell wall degradation machinery, beneficial and pathogenic fungi and bacteria can produce the enzymes necessary for the complete depolymerization of AGs including endo-β-(1,3), β-(1,4) and β-(1,6)-galactanases, β-(1,3/1,6) galactanases, α-L-arabinofuranosidases, β-L-arabinopyranosidases, and β-D-glucuronidases. These hydrolytic enzymes are secreted during plant-pathogen interactions and could have implications for the function of AGPs. It has been proposed that AGPs could prevent infection by pathogenic microorganisms because their degradation products generated by hydrolytic enzymes of pathogens function as damage-associated molecular patterns (DAMPs) eliciting the plant defense response. In this review, we describe the structure and function of AGs and AGPs as components of the plant cell wall. Additionally, we describe the set of enzymes secreted by microorganisms to degrade AGs from AGPs and its possible implication for plant-microbe interactions.
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Affiliation(s)
- Maria Guadalupe Villa-Rivera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Mexico
| | - Everardo López-Romero
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Mexico
| | - María Guadalupe Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Mexico
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6
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Kondo T, Kichijo M, Maruta A, Nakaya M, Takenaka S, Arakawa T, Fushinobu S, Sakamoto T. Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. J Biol Chem 2021; 297:101001. [PMID: 34303708 PMCID: PMC8377490 DOI: 10.1016/j.jbc.2021.101001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/24/2022] Open
Abstract
Gum arabic (GA) is widely used as an emulsion stabilizer and coating in several industrial applications, such as foods and pharmaceuticals. GA contains a complex carbohydrate moiety, and the nonreducing ends of the side chains are often capped with l-rhamnose; thus, enzymes that can remove these caps are promising tools for the structural analysis of the carbohydrates comprising GA. In this study, GA-specific l-rhamnose-α-1,4-d-glucuronate lyase from the fungus Fusarium oxysporum 12S (FoRham1) was cloned and characterized. FoRham1 showed the highest amino acid sequence similarity with enzymes belonging to the glycoside hydrolase family 145; however, the catalytic residue on the posterior pocket of the β-propeller fold protein was not conserved. The catalytic residues of FoRham1 were instead conserved with ulvan lyases belonging to polysaccharide lyase family 24. Kinetic analysis showed that FoRham1 has the highest catalytic efficiency for the substrate α-l-rhamnose-(1→4)-d-glucuronic acid. The crystal structures of ligand-free and α-l-rhamnose-(1→4)-d-glucuronic acid –bound FoRham1 were determined, and the active site was identified on the anterior side of the β-propeller. The three-dimensional structure of the active site and mutagenesis analysis revealed the detailed catalytic mechanism of FoRham1. Our findings offer a new enzymatic tool for the further analysis of the GA carbohydrate structure and for elucidating its physiological functions in plants. Based on these results, we renamed glycoside hydrolase family 145 as a new polysaccharide lyase family 42, in which FoRham1 is included.
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Affiliation(s)
- Tatsuya Kondo
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Miyu Kichijo
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Akiho Maruta
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Makoto Nakaya
- Center for Research and Development of Bioresources, Organization for Research Promotion, Osaka Prefecture University, Osaka, Japan
- Department of Nutrition, Otemae College of Nutrition and Confectionery, Osaka, Japan
| | - Shigeo Takenaka
- Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University, Osaka, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Tatsuji Sakamoto
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
- For correspondence: Tatsuji Sakamoto
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Kondo T, Kichijo M, Nakaya M, Takenaka S, Arakawa T, Kotake T, Fushinobu S, Sakamoto T. Biochemical and structural characterization of a novel 4‐
O
‐α‐
l
‐rhamnosyl‐β‐
d
‐glucuronidase from
Fusarium oxysporum. FEBS J 2021; 288:4918-4938. [DOI: 10.1111/febs.15795] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 01/27/2023]
Affiliation(s)
- Tatsuya Kondo
- Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Miyu Kichijo
- Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Makoto Nakaya
- Center for Research and Development of Bioresources, Organization for Research Promotion Osaka Prefecture University Sakai Japan
- Department of Nutrition Otemae College of Nutrition and Confectionery Osaka Japan
| | - Shigeo Takenaka
- Graduate School of Comprehensive Rehabilitation Osaka Prefecture University Habikino Japan
| | - Takatoshi Arakawa
- Department of Biotechnology The University of Tokyo Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Tokyo Japan
| | - Toshihisa Kotake
- Graduate School of Science and Engineering Saitama University Saitama Japan
| | - Shinya Fushinobu
- Department of Biotechnology The University of Tokyo Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Tokyo Japan
| | - Tatsuji Sakamoto
- Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
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Arabinogalactan Utilization by Bifidobacterium longum subsp. longum NCC 2705 and Bacteroides caccae ATCC 43185 in Monoculture and Coculture. Microorganisms 2020; 8:microorganisms8111703. [PMID: 33142707 PMCID: PMC7693162 DOI: 10.3390/microorganisms8111703] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
Arabinogalactan (AG) has been studied as a potential prebiotic in view of stimulating bifidobacteria presence in the gut microbiota. However, bifidobacteria prefer fermentation of oligosaccharides to that of polysaccharides. The contribution of other gut bacteria may allow better growth of bifidobacteria on AG. β-galactanases and β-galactosidases are the main enzymes for the degradation of AG. Additional enzymes such as α-L-arabinofuranosidase and β-L-arabinopyranosidase are required to remove the arabinose side chains. All of these predicted functions are encoded by the genomes of both Bifidobacterium longum subsp. longum NCC 2705 and Bacteroides caccae ATCC 43185. However, neither strain was able to grow significantly on AG, with 25% (B. longum subsp. longum NCC 2705) and 39% (Bac. caccae ATCC 43185) of AG degraded after 48-h fermentation, respectively. In this study, the β-galactanase, β-galactosidase, α-L-arabinofuranosidase, and β-L-arabinopyranosidase from both strains were investigated. The extracellular β-galactosidases of both B. longum subsp. longum NCC 2705 and Bac. caccae ATCC 43185 were able to cleave the β-1,3; 1,4 and 1,6 linkages. However, the β-galactosidase activity of B. longum subsp. longum NCC 2705 was weaker for the β-1,4 linkage, compared with the β-1,3 and 1,6 linkages. The arabinose side chains of AG inhibited the cleavage of β-1,3 and 1,6 linkages by the endo-β-galactanase from both strains, and partially inhibited the cleavage of β-1,4 linkages by the endo-β-1,4 galactanase from Bac. caccae ATCC 43185. The α-L-arabinofuranosidase and β-L-arabinopyranosidase from both strains were unable to cleave arabinose from AG under the conditions used. These results show limited breakdown of AG by these two strains in monoculture. When cocultured with Bac. caccae ATCC 43185, B. longum subsp. longum NCC 2705 grew significantly better than in monoculture on AG after 6 h of fermentation (p < 0.05). The coculture showed 48% AG degradation after 48 h of fermentation, along with reduced pH. Furthermore, compared to monoculture of Bac. caccae ATCC 43185, the concentration of succinate significantly increased from 0.01 ± 0.01 to 4.41 ± 0.61 mM, whereas propionate significantly decreased from 13.07 ± 0.37 to 9.75 ± 2.01 mM in the coculture (p < 0.05). These results suggest that the growth and metabolic activities of Bac. caccae ATCC 43185 were restrained in the coculture, as the pH decreased due to the metabolism of B. longum subsp. longum NCC 2705.
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9
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Kondo T, Nishimura Y, Matsuyama K, Ishimaru M, Nakazawa M, Ueda M, Sakamoto T. Characterization of three GH35 β-galactosidases, enzymes able to shave galactosyl residues linked to rhamnogalacturonan in pectin, from Penicillium chrysogenum 31B. Appl Microbiol Biotechnol 2019; 104:1135-1148. [DOI: 10.1007/s00253-019-10299-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/24/2019] [Accepted: 12/03/2019] [Indexed: 11/29/2022]
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10
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Fujita K, Sasaki Y, Kitahara K. Degradation of plant arabinogalactan proteins by intestinal bacteria: characteristics and functions of the enzymes involved. Appl Microbiol Biotechnol 2019; 103:7451-7457. [PMID: 31384991 DOI: 10.1007/s00253-019-10049-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 10/26/2022]
Abstract
Arabinogalactan proteins (AGPs) are complex plant proteoglycans that function as dietary fiber utilized by human intestinal bacteria such as Bifidobacterium and Bacteroides species. However, the degradative mechanism is unknown because of the complexity of sugar chains of AGPs as well as variation among plant species and organs. Recently, AGP degradative enzymes have been characterized in Bifidobacterium and Bacteroides species. In this review, we summarize the characteristics and functions of AGP degradative enzymes in human intestinal bacteria.
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Affiliation(s)
- Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan. .,The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.
| | - Yuki Sasaki
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kanefumi Kitahara
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
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11
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Munoz-Munoz J, Cartmell A, Terrapon N, Baslé A, Henrissat B, Gilbert HJ. An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins. J Biol Chem 2017. [PMID: 28637865 DOI: 10.1074/jbc.m117.794578] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represents a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis we screened the potential enzymatic functions of hypothetical proteins encoded by genes of Bacteroides thetaiotaomicron that were up-regulated by arabinogalactan proteins or AGPs. Although AGPs are ubiquitous in plants, there is a paucity of information on their detailed structure, the function of these glycans in planta, and the mechanisms by which they are depolymerized in microbial ecosystems. Here we have discovered a new polysaccharide lyase family that is specific for the l-rhamnose-α1,4-d-glucuronic acid linkage that caps the side chains of complex AGPs. The reaction product generated by the lyase, Δ4,5-unsaturated uronic acid, is removed from AGP by a glycoside hydrolase located in family GH105, producing the final product 4-deoxy-β-l-threo-hex-4-enepyranosyl-uronic acid. The crystal structure of a member of the novel lyase family revealed a catalytic domain that displays an (α/α)6 barrel-fold. In the center of the barrel is a deep pocket, which, based on mutagenesis data and amino acid conservation, comprises the active site of the lyase. A tyrosine is the proposed catalytic base in the β-elimination reaction. This study illustrates how highly complex glycans can be used as a scaffold to discover new enzyme families within microbial ecosystems where carbohydrate metabolism is a major evolutionary driver.
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Affiliation(s)
- José Munoz-Munoz
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Alan Cartmell
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicolas Terrapon
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Arnaud Baslé
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France.,the USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France, and.,the Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,
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Bifidobacterium longum subsp. longum Exo-β-1,3-Galactanase, an enzyme for the degradation of type II arabinogalactan. Appl Environ Microbiol 2015; 80:4577-84. [PMID: 24837371 DOI: 10.1128/aem.00802-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Type II arabinogalactan (AG-II) is a suitable carbohydrate source for Bifidobacterium longum subsp. longum, but the degradative enzymes have never been characterized. In this study, we characterized an exo-β-1,3-galactanase, BLLJ_1840, belonging to glycoside hydrolase family 43 from B. longum subsp. longum JCM1217. The recombinant BLLJ_1840 expressed in Escherichia coli hydrolyzed β-1,3-linked galactooligosaccharides but not β-1,4- and β-1,6-linked galactooligosaccharides. The enzyme also hydrolyzed larch wood arabinogalactan (LWAG), which comprises a β-1,3-linked galactan backbone with β-1,6-linked galactan side chains. The kcat/Km ratio of dearabinosylated LWAG was 24-fold higher than that of β-1,3-galactan. BLLJ_1840 is a novel type of exo-β-1,3-galactanase with a higher affinity for the β-1,6-substituted β-1,3-galactan than for nonsubstituted β-1,3-galactan. BLLJ_1840 has 27% to 28% identities with other characterized exo--1,3-galactanases from bacteria and fungi. The homologous genes are conserved in several strains of B. longum subsp. longum and B. longum subsp. infantis but not in other bifidobacteria. Transcriptional analysis revealed that BLLJ_1840 is intensively induced with BLLJ_1841, an endo-β-1,6-galactanase candidate, in the presence of LWAG. This is the first report of exo-β-1,3-galactanase in bifidobacteria, which is an enzyme used for the acquisition of AG-II in B. longum subsp. longum.
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Sakamoto T, Ishimaru M. Peculiarities and applications of galactanolytic enzymes that act on type I and II arabinogalactans. Appl Microbiol Biotechnol 2013; 97:5201-13. [PMID: 23666442 DOI: 10.1007/s00253-013-4946-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/20/2013] [Accepted: 04/22/2013] [Indexed: 10/26/2022]
Abstract
Arabinogalactans (AGs) are branched galactans to which arabinose residues are bound as side chains and are widely distributed in plant cell walls. They can be grouped into two types based on the structures of their backbones. Type I AGs have β-1,4-galactan backbones and are often covalently linked to the rhamnogalacturonan-I region of pectins. Type II AGs have β-1,3-galactan backbones and are often covalently linked to proteins. The main enzymes involved in the degradation of AGs are endo-β-galactanases, exo-β-galactanases, and β-galactosidases, although other enzymes such as α-L-arabinofuranosidases, β-L-arabinopyranosidases, and β-D-glucuronidases are required to remove the side chains for efficient degradation of the polysaccharides. Galactanolytic enzymes have a wide variety of potential uses, including the bioconversion of AGs to fermentable sugars for production of commodity chemicals like ethanol, biobleaching of cellulose pulp, modulation of pectin properties, improving animal feed, and determining the chemical structure of AGs. This review summarizes our current knowledge about the biochemical properties and potential applications of AG-degrading enzymes.
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Affiliation(s)
- Tatsuji Sakamoto
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.
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Okawa M, Fukamachi K, Tanaka H, Sakamoto T. Identification of an exo-ß-1,3-D-galactanase from Fusarium oxysporum and the synergistic effect with related enzymes on degradation of type II arabinogalactan. Appl Microbiol Biotechnol 2013; 97:9685-94. [PMID: 23429923 DOI: 10.1007/s00253-013-4759-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 02/04/2013] [Accepted: 02/06/2013] [Indexed: 11/28/2022]
Abstract
An exo-ß-1,3-D-galactanase (Fo/1,3Gal) was purified from the culture filtrate of Fusarium oxysporum 12S. A cDNA encoding Fo/1,3Gal was isolated by in vitro cloning. Module sequence analysis revealed a "GH43_6" domain and a "CBM35_galactosidase-like" domain in Fo/1,3Gal. The recombinant enzyme (rFo/1,3Gal) expressed in Pichia pastoris degraded ß-1,3-galactan and ß-1,3-galactobiose (Gal2), and released only galactose (Gal). In contrast, the enzyme did not hydrolyze p-nitrophenyl ß-D-galactopyranoside, ß-1,4-Gal2, or ß-1,6-Gal2. The enzyme also showed low activity towards native type II arabinogalactans such as larchwood arabinogalactan (LWAG) and gum arabic. Using LWAG as substrate, rFo/1,3Gal released Gal, ß-1,6-Gal2, ß-1,6-galactotriose (Gal3), and ß-1,6-Gal3 substituted with a single arabinofuranose residue accompanied with unidentified oligosaccharides, indicating that the enzyme can by-pass the branching points of ß-1,3-galactan backbones. A time course analysis of products released by rFo/1,3Gal on LWAG revealed that ß-1,6-Gal2 is the main side chain in LWAG and that the activity of rFo/1,3Gal was decreased when degrees of polymerization of side chains increase. rFo/1,3Gal worked synergistically with three other recombinant F. oxysporum enzymes (ß-1,6-galactanase, ß-L-arabinopyranosidase, and α-L-arabinofuranosidase) that degrade side chains, on the degradation of LWAG. However, the synergism was much lower than anticipated, probably because LWAG have longer side chains than the three enzymes used are able to remove or ß-1,3-galactan main chain is interrupted with glycosidic linkages that are different from the ß-1,3-galactosyl linkage. Affinity gel electrophoresis revealed that rFo/1,3Gal specifically bound to ß-1,3-galactan.
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Affiliation(s)
- Mizuho Okawa
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, 599-8531, Osaka, Japan
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Sakamoto T, Nishimura Y, Makino Y, Sunagawa Y, Harada N. Biochemical characterization of a GH53 endo-β-1,4-galactanase and a GH35 exo-β-1,4-galactanase from Penicillium chrysogenum. Appl Microbiol Biotechnol 2012; 97:2895-906. [DOI: 10.1007/s00253-012-4154-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 05/03/2012] [Accepted: 05/03/2012] [Indexed: 11/27/2022]
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