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Li J, Xue C, Shen J, Liu G, Mei X, Sun M, Chang Y. Action Pattern of a Novel G-Specific Alginate Lyase: Determination of Subsite Specificity by HPAEC-PAD/MS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1170-1177. [PMID: 38111122 DOI: 10.1021/acs.jafc.3c06778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
G-specific alginate lyases are important tools for alginate fragment biodegradation and oligosaccharide production, which have great potential in alginate refining research. In this research, a novel G-specific alginate lyase Aly7Ce was cloned, expressed, and characterized, with the optimal reaction conditions at 30 °C and pH 8.0. By employing the UPSEC-VWD-MS method, Aly7Ce was confirmed as a random endoacting alginate lyase. Its minimum substrate was tetrasaccharide, and the final product majorly consisted of disaccharide to tetrasaccharide. HPAEC-PAD/MS method was employed to investigate the structurally different unsaturated alginate oligosaccharides. The substrate recognition and subsite specificity of Aly7Ce were revealed by detecting the oligosaccharide pattern in the enzymatic products with oligosaccharides or polysaccharides as substrates. Aly7Ce mainly attacked the second glycosidic linkage from the nonreducing end of oligosaccharide substrates. The subsite specificity of Aly7Ce was revealed as -2 (M/G), - 1 (G), + 1 (M/G), and +2 (M/G). The regular oligosaccharide products of Aly7Ce could be applied for the efficient preparation of ΔG, ΔGG, and ΔGGG with high purity. The G-specific alginate lyase Aly7Ce with a well-defined product composition and action pattern provided a novel tool for the modification and structural elucidation of alginate, as well as for the targeted preparation of oligosaccharides.
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Affiliation(s)
- Jiajing Li
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Jingjing Shen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guanchen Liu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Menghui Sun
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
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Du M, Li X, Qi W, Li Y, Wang L. Identification and characterization of a critical loop for the high activity of alginate lyase VaAly2 from the PL7_5 subfamily. Front Microbiol 2024; 14:1333597. [PMID: 38282736 PMCID: PMC10811132 DOI: 10.3389/fmicb.2023.1333597] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024] Open
Abstract
As the major component in the cell wall of brown algae, alginates are degradable by alginate lyases via β-elimination. Alginate lyases can be categorized into various polysaccharide lyase (PL) families, and PL7 family alginate lyases are the largest group and can be divided into six subfamilies. However, the major difference among different PL7 subfamilies is not fully understood. In this work, a marine alginate lyase, VaAly2, from Vibrio alginolyticus ATCC 17749 belonging to the PL7_5 subfamily was identified and characterized. It displayed comparatively high alginolytic activities toward different alginate substrates and functions as a bifunctional lyase. Molecular docking and biochemical analysis suggested that VaAly2 not only contains a key catalyzing motif (HQY) conserved in the PL7 family but also exhibits some specific characters limited in the PL7_5 subfamily members, such as the key residues and a long loop1 structure around the active center. Our work provides insight into a loop structure around the center site which plays an important role in the activity and substrate binding of alginate lyases belonging to the PL7_5 subfamily.
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Affiliation(s)
- Muxuan Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Life Sciences, Shandong University, Qingdao, China
| | - Xue Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Weipeng Qi
- Foshan Haitian (Gaoming) Flavoring & Food Co., Ltd., Foshan, China
| | - Yingjie Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Rønne ME, Tandrup T, Madsen M, Hunt CJ, Myers PN, Moll JM, Holck J, Brix S, Strube ML, Aachmann FL, Wilkens C, Svensson B. Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate. Appl Environ Microbiol 2023; 89:e0118523. [PMID: 37791757 PMCID: PMC10617595 DOI: 10.1128/aem.01185-23] [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: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 10/05/2023] Open
Abstract
Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an endo-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new Bacteroides ovatus strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The BoPL6 degraded polyG to oligosaccharides of DP 1-3, and BoPL17 released 4,5-unsaturated monouronate from polyM. BoPL38 degraded both alginates, polyM, polyG, and polyMG, in endo-mode; hence, it was assumed to deliver oligosaccharide substrates for BoPL6 and BoPL17, corresponding well with synergistic action on alginate. BoPL17 and BoPL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)6-barrel + anti-parallel β-sheet and (α/α)7-barrel folds, distinctive for these PL families. BoPL17 had a more open active site than the two homologous structures. BoPL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.IMPORTANCEHuman ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new Bacteroides ovatus strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster. BoPL6 and BoPL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids. BoPL38 produces oligosaccharides degraded by BoPL6 and BoPL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.
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Affiliation(s)
- Mette E. Rønne
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tobias Tandrup
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikkel Madsen
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Cameron J. Hunt
- Department of Biotechnology and Biomedicine, Enzyme Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pernille N. Myers
- Department of Biotechnology and Biomedicine, Disease Systems Immunology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Janne M. Moll
- Department of Biotechnology and Biomedicine, Disease Systems Immunology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Enzyme Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Disease Systems Immunology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikael L. Strube
- Department of Biotechnology and Biomedicine, Bacterial Ecophysiology and Biotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Finn L. Aachmann
- Department of Biotechnology and Food Science, Norwegian Biopolymer Laboratory (NOBIPOL), NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Casper Wilkens
- Department of Biotechnology and Biomedicine, Enzyme Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biotechnology and Biomedicine, Structural Enzymology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
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Gu Q, Lu Y, Zhou J, Yang W, Wang K, Liu X, Yu X. Enhancement of catalytic performance of alginate lyase through combinational site-directed mutagenesis. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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5
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Chen C, Cao S, Zhu B, Jiang L, Yao Z. Biochemical characterization and elucidation the degradation pattern of a new cold-adapted and Ca2+ activated alginate lyase for efficient preparation of alginate oligosaccharides. Enzyme Microb Technol 2023; 162:110146. [DOI: 10.1016/j.enzmictec.2022.110146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022]
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Dobruchowska JM, Bjornsdottir B, Fridjonsson OH, Altenbuchner J, Watzlawick H, Gerwig GJ, Dijkhuizen L, Kamerling JP, Hreggvidsson GO. Enzymatic depolymerization of alginate by two novel thermostable alginate lyases from Rhodothermus marinus. FRONTIERS IN PLANT SCIENCE 2022; 13:981602. [PMID: 36204061 PMCID: PMC9530828 DOI: 10.3389/fpls.2022.981602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
Alginate (alginic acid) is a linear polysaccharide, wherein (1→4)-linked β-D-mannuronic acid and its C5 epimer, α-L-guluronic acid, are arranged in varying sequences. Alginate lyases catalyze the depolymerization of alginate, thereby cleaving the (1→4) glycosidic linkages between the monomers by a β-elimination mechanism, to yield unsaturated 4-deoxy-L-erythro-hex-4-enopyranosyluronic acid (Δ) at the non-reducing end of resulting oligosaccharides (α-L-erythro configuration) or, depending on the enzyme, the unsaturated monosaccharide itself. In solution, the released free unsaturated monomer product is further hydrated in a spontaneous (keto-enol tautomerization) process to form two cyclic stereoisomers. In this study, two alginate lyase genes, designated alyRm3 and alyRm4, from the marine thermophilic bacterium Rhodothermus marinus (strain MAT378), were cloned and expressed in Escherichia coli. The recombinant enzymes were characterized, and their substrate specificity and product structures determined. AlyRm3 (PL39) and AlyRm4 (PL17) are among the most thermophilic and thermostable alginate lyases described to date with temperature optimum of activity at ∼75 and 81°C, respectively. The pH optimum of activity of AlyRm3 is ∼5.5 and AlyRm4 at pH 6.5. Detailed NMR analysis of the incubation products demonstrated that AlyRm3 is an endolytic lyase, while AlyRm4 is an exolytic lyase, cleaving monomers from the non-reducing end of oligo/poly-alginates.
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Affiliation(s)
- Justyna M. Dobruchowska
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | | | | | - Josef Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, Stuttgart, Germany
| | | | - Gerrit J. Gerwig
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | - Johannis P. Kamerling
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
| | - Gudmundur O. Hreggvidsson
- Matís Ltd., Reykjavík, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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Determination of oligosaccharide product distributions of PL7 alginate lyases by their structural elements. Commun Biol 2022; 5:782. [PMID: 35918517 PMCID: PMC9345997 DOI: 10.1038/s42003-022-03721-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022] Open
Abstract
Alginate lyases can be used to produce well-defined alginate oligosaccharides (AOSs) because of their specificities for AOS products. A large number of alginate lyases have been recorded in the CAZy database; however, the majority are annotated-only alginate lyases that include little information on their products, thus limiting their applications. Here, we establish a simple and experiment-saving approach to predict product distributions for PL7 alginate lyases through extensive structural biology, bioinformatics and biochemical studies. Structural study on several PL7 alginate lyases reveals that two loops around the substrate binding cleft determine product distribution. Furthermore, a database containing the loop information of all annotated-only single-domain PL7 alginate lyases is constructed, enabling systematic exploration of the association between loop and product distribution. Based on these results, a simplified loop/product distribution relationship is proposed, giving us information on product distribution directly from the amino acid sequence. Characterization of PL7 alginate lyase structure and products enables a bioinformatics approach to predict product distribution from the amino acid sequence.
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Ma LZ, Wang D, Liu Y, Zhang Z, Wozniak DJ. Regulation of Biofilm Exopolysaccharide Biosynthesis and Degradation in Pseudomonas aeruginosa. Annu Rev Microbiol 2022; 76:413-433. [DOI: 10.1146/annurev-micro-041320-111355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial communities enmeshed in a matrix of macromolecules, termed as biofilms, are the natural setting of bacteria. Exopolysaccharide is a critical matrix component of biofilms. Here, we focus on biofilm matrix exopolysaccharides in Pseudomonas aeruginosa. This opportunistic pathogen can adapt to a wide range of environments and can form biofilms or aggregates in a variety of surfaces or environments, such as the lungs of people with cystic fibrosis, catheters, wounds, and contact lenses. The ability to synthesize multiple exopolysaccharides is one of the advantages that facilitate bacterial survival in different environments. P. aeruginosa can produce several exopolysaccharides, including alginate, Psl, Pel, and lipopolysaccharide. In this review, we highlight the roles of each exopolysaccharide in P. aeruginosa biofilm development and how bacteria coordinate the biosynthesis of multiple exopolysaccharides and bacterial motility. In addition, we present advances in antibiofilm strategies targeting matrix exopolysaccharides, with a focus on glycoside hydrolases. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Luyan Z. Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yiwei Liu
- Department of Microbial Infection and Immunity and Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Zhenyu Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity and Department of Microbiology, Ohio State University, Columbus, Ohio, USA
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Barzkar N, Sheng R, Sohail M, Jahromi ST, Babich O, Sukhikh S, Nahavandi R. Alginate Lyases from Marine Bacteria: An Enzyme Ocean for Sustainable Future. Molecules 2022; 27:3375. [PMID: 35684316 PMCID: PMC9181867 DOI: 10.3390/molecules27113375] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 12/13/2022] Open
Abstract
The cell wall of brown algae contains alginate as a major constituent. This anionic polymer is a composite of β-d-mannuronate (M) and α-l-guluronate (G). Alginate can be degraded into oligosaccharides; both the polymer and its products exhibit antioxidative, antimicrobial, and immunomodulatory activities and, hence, find many commercial applications. Alginate is attacked by various enzymes, collectively termed alginate lyases, that degrade glycosidic bonds through β-elimination. Considering the abundance of brown algae in marine ecosystems, alginate is an important source of nutrients for marine organisms, and therefore, alginate lyases play a significant role in marine carbon recycling. Various marine microorganisms, particularly those that thrive in association with brown algae, have been reported as producers of alginate lyases. Conceivably, the marine-derived alginate lyases demonstrate salt tolerance, and many are activated in the presence of salts and, therefore, find applications in the food industry. Therefore, this review summarizes the structural and biochemical features of marine bacterial alginate lyases along with their applications. This comprehensive information can aid in the expansion of future prospects of alginate lyases.
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Affiliation(s)
- Noora Barzkar
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas 3995, Iran
| | - Ruilong Sheng
- CQM—Centro de Química da Madeira, Campus da Penteada, Universidade da Madeira, 9000-390 Funchal, Portugal;
- Department of Radiology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Muhammad Sohail
- Department of Microbiology, University of Karachi, Karachi 75270, Pakistan;
| | - Saeid Tamadoni Jahromi
- Persian Gulf and Oman Sea Ecology Research Center, Iranian Fisheries Sciences Research Institute, Agricultural Research Education and Extension Organization (AREEO), Bandar Abbas 9145, Iran;
| | - Olga Babich
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad 236016, Russia; (O.B.); (S.S.)
| | - Stanislav Sukhikh
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad 236016, Russia; (O.B.); (S.S.)
| | - Reza Nahavandi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj 8361, Iran;
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Gao SK, Yin R, Wang XC, Jiang HN, Liu XX, Lv W, Ma Y, Zhou YX. Structure Characteristics, Biochemical Properties, and Pharmaceutical Applications of Alginate Lyases. Mar Drugs 2021; 19:628. [PMID: 34822499 PMCID: PMC8618178 DOI: 10.3390/md19110628] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/27/2021] [Accepted: 11/06/2021] [Indexed: 02/07/2023] Open
Abstract
Alginate, the most abundant polysaccharides of brown algae, consists of various proportions of uronic acid epimers α-L-guluronic acid (G) and β-D-mannuronic acid (M). Alginate oligosaccharides (AOs), the degradation products of alginates, exhibit excellent bioactivities and a great potential for broad applications in pharmaceutical fields. Alginate lyases can degrade alginate to functional AOs with unsaturated bonds or monosaccharides, which can facilitate the biorefinery of brown algae. On account of the increasing applications of AOs and biorefinery of brown algae, there is a scientific need to explore the important aspects of alginate lyase, such as catalytic mechanism, structure, and property. This review covers fundamental aspects and recent developments in basic information, structural characteristics, the structure-substrate specificity or catalytic efficiency relationship, property, molecular modification, and applications. To meet the needs of biorefinery systems of a broad array of biochemical products, alginate lyases with special properties, such as salt-activated, wide pH adaptation range, and cold adaptation are outlined. Withal, various challenges in alginate lyase research are traced out, and future directions, specifically on the molecular biology part of alginate lyases, are delineated to further widen the horizon of these exceptional alginate lyases.
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Affiliation(s)
| | | | | | | | | | | | | | - Yan-Xia Zhou
- Marine College, Shandong University, Weihai 264209, China; (S.-K.G.); (R.Y.); (X.-C.W.); (H.-N.J.); (X.-X.L.); (W.L.); (Y.M.)
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11
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Violot S, Galisson F, Carrique L, Jugnarain V, Conchou L, Robert X, Thureau A, Helbert W, Aghajari N, Ballut L. Exploring molecular determinants of polysaccharide Lyase family 6-1 enzyme activity. Glycobiology 2021; 31:1557-1570. [PMID: 34245266 DOI: 10.1093/glycob/cwab073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 11/14/2022] Open
Abstract
The Polysaccharide Lyase Family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1-3. To decipher the mode of recognition and action of the enzymes belonging to subfamily PL6_1, we solved the crystal structures of Pedsa0632, Patl3640, Pedsa3628 and Pedsa3807, which all show different substrate specificities and mode of action (endo-/exo-lyase). Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirm that the conserved residues in subsites -1 to +3 of the catalytic site form a common platform which can accommodate various types of alginate in a very similar manner but with a series of original adaptations bringing them their specificities of action. From comparative studies with existing structures of PL6_1 alginate lyases, we observe that in the right-handed parallel β-helix fold shared by all these enzymes, the substrate binding site harbors the same overall conserved structures and organization. Despite this apparent similarity, it appears that members of the PL6_1 subfamily specifically accommodate and catalyze the degradation of different alginates suggesting that this common platform is actually a highly adaptable and specific tool.
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Affiliation(s)
- Sébastien Violot
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Frédéric Galisson
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Loïc Carrique
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Vinesh Jugnarain
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Léa Conchou
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Xavier Robert
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | | | - William Helbert
- Centre de Recherches sur les Macromolécules Végétales (CERMAV), Université Grenoble Alpes, CNRS, 38000 Grenoble, France
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
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12
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Li Q, Zheng L, Guo Z, Tang T, Zhu B. Alginate degrading enzymes: an updated comprehensive review of the structure, catalytic mechanism, modification method and applications of alginate lyases. Crit Rev Biotechnol 2021; 41:953-968. [PMID: 34015998 DOI: 10.1080/07388551.2021.1898330] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Alginate, a kind of linear acidic polysaccharide, consists of α-L-guluronate (G) and β-D-mannuronate (M). Both alginate and its degradation products (alginate oligosaccharides) possess abundant biological activities such as antioxidant activity, antitumor activity, and antimicrobial activity. Therefore, alginate and alginate oligosaccharides have great value in food, pharmaceutical, and agricultural fields. Alginate lyase can degrade alginate into alginate oligosaccharides via the β-elimination reaction. It plays an important role in marine carbon recycling and the deep utilization of brown algae. Elucidating the structural features of alginate lyase can improve our knowledge of its catalytic mechanisms. With the development of structural analysis techniques, increasing numbers of alginate lyases have been characterized at the structural level. Hence, it is essential and helpful to summarize and discuss the up-to-date findings. In this review, we have summarized progress on the structural features and the catalytic mechanisms of alginate lyases. Furthermore, the molecular modification strategies and the applications of alginate lyases have also been discussed. This comprehensive information should be helpful to expand the applications of alginate lyases.
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Affiliation(s)
- Qian Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ling Zheng
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Zilong Guo
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Tiancheng Tang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Benwei Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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Zhang K, Liu T, Liu W, Lyu Q. Structural insights into the substrate-binding cleft of AlyF reveal the first long-chain alginate-binding mode. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:336-346. [PMID: 33645537 DOI: 10.1107/s205979832100005x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/03/2021] [Indexed: 11/10/2022]
Abstract
The products of alginate degradation, alginate oligosaccharides (AOS), have potential applications in many areas, including functional foods and marine drugs. Enzyme-based approaches using alginate lyases have advantages in the preparation of well defined AOS and have attracted much attention in recent years. However, a lack of structural insight into the whole substrate-binding cleft for most known alginate lyases severely hampers their application in the industrial generation of well defined AOS. To solve this issue, AlyF was co-crystallized with the long alginate oligosaccharide G6 (L-hexaguluronic acid hexasodium salt), which is the longest bound substrate in all solved alginate lyase complex structures. AlyF formed interactions with G6 from subsites -3 to +3 without additional substrate-binding site interactions, suggesting that the substrate-binding cleft of AlyF was fully occupied by six sugars, which was further confirmed by isothermal titration calorimetry and differential scanning calorimetry analyses. More importantly, a combination of structural comparisons and mutagenetic analyses determined that three key loops (loop 1, Lys215-Glu236; loop 2, Gln402-Ile416; loop 3, Arg334-Gly348) mainly function in binding long substrates (degree of polymerization of >4). The potential flexibility of loop 1 and loop 2 might enable the substrate to continue to enter the cleft after binding to subsites +1 to +3; loop 3 stabilizes and orients the substrate at subsites -2 and -3. Taken together, these results provide the first possible alginate lyase-substrate binding profile for long-chain alginates, facilitating the rational design of new enzymes for industrial purposes.
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Affiliation(s)
- Keke Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Tao Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Weizhi Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Qianqian Lyu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
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14
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Mahajan S, Ramya TNC. Cellulophaga algicola alginate lyase inhibits biofilm formation of a clinical Pseudomonas aeruginosa strain MCC 2081. IUBMB Life 2020; 73:444-462. [PMID: 33350564 DOI: 10.1002/iub.2442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022]
Abstract
Alginate lyases are potential agents for disrupting alginate-rich Pseudomonas biofilms in the infected lungs of cystic fibrosis patients but there is as yet no clinically approved alginate lyase that can be used as a therapeutic. We report here the endolytic alginate lyase activity of a recombinant Cellulophaga algicola alginate lyase domain (CaAly) encoded by a gene that also codes for an N-terminal carbohydrate-binding module, CBM6, and a central F-type lectin domain (CaFLD). CaAly degraded both polyM and polyG alginates with optimal temperature and pH of 37°C and pH 7, respectively, with greater preference for polyG. Recombinant CaFLD bound to fucosylated glycans with a preference for H-type 2 glycan motif, and did not have any apparent effect on the enzyme activity of the co-associated alginate lyase domain in the recombinant protein construct, CaFLD_Aly. We assessed the potential of CaAly and other alginate lyases previously reported in published literature to inhibit biofilm formation by a clinical strain, Pseudomonas aeruginosa MCC 2081. Of all the alginate lyases tested, CaAly displayed most inhibition of in vitro biofilm formation on plastic surfaces. We also assessed its inhibitory ability against P. aeruginosa 2081 biofilms formed over a monolayer of A549 lung epithelial cells. Our study indicated that CaAly is efficacious in inhibition of biofilm formation even on A549 lung epithelial cell line monolayers.
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Affiliation(s)
- Sonal Mahajan
- Protein Science and Engineering Department, Institute of Microbial Technology, Chandigarh, India
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15
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Xu F, Chen XL, Sun XH, Dong F, Li CY, Li PY, Ding H, Chen Y, Zhang YZ, Wang P. Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the arctic. J Biol Chem 2020; 295:16380-16392. [PMID: 32967968 PMCID: PMC7705320 DOI: 10.1074/jbc.ra120.015106] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/13/2020] [Indexed: 11/06/2022] Open
Abstract
Alginate lyases play important roles in alginate degradation in the ocean. Although a large number of alginate lyases have been characterized, little is yet known about those in extremely cold polar environments, which may have unique mechanisms for environmental adaptation and for alginate degradation. Here, we report the characterization of a novel PL7 alginate lyase AlyC3 from Psychromonas sp. C-3 isolated from the Arctic brown alga Laminaria, including its phylogenetic classification, catalytic properties, and structure. We propose the establishment of a new PM-specific subfamily of PL7 (subfamily 6) represented by AlyC3 based on phylogenetic analysis and enzymatic properties. Structural and biochemical analyses showed that AlyC3 is a dimer, representing the first dimeric endo-alginate lyase structure. AlyC3 is activated by NaCl and adopts a novel salt-activated mechanism; that is, salinity adjusts the enzymatic activity by affecting its aggregation states. We further solved the structure of an inactive mutant H127A/Y244A in complex with a dimannuronate molecule and proposed the catalytic process of AlyC3 based on structural and biochemical analyses. We show that Arg82 and Tyr190 at the two ends of the catalytic canyon help the positioning of the repeated units of the substrate and that His127, Tyr244, Arg78, and Gln125 mediate the catalytic reaction. Our study uncovers, for the first time, the amino acid residues for alginate positioning in an alginate lyase and demonstrates that such residues involved in alginate positioning are conserved in other alginate lyases. This study provides a better understanding of the mechanisms of alginate degradation by alginate lyases.
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Affiliation(s)
- Fei Xu
- State Key Laboratory of Microbial Technology, and Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, and Marine Biotechnology Research Center, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao-Hui Sun
- State Key Laboratory of Microbial Technology, and Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Fang Dong
- State Key Laboratory of Microbial Technology, and Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Chun-Yang Li
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, and Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Haitao Ding
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Yin Chen
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China; School of Life Sciences, University of Warwick, Warwick, Coventry, United Kingdom
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, and Marine Biotechnology Research Center, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Peng Wang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
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16
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Blanco-Cabra N, Paetzold B, Ferrar T, Mazzolini R, Torrents E, Serrano L, LLuch-Senar M. Characterization of different alginate lyases for dissolving Pseudomonas aeruginosa biofilms. Sci Rep 2020; 10:9390. [PMID: 32523130 PMCID: PMC7287115 DOI: 10.1038/s41598-020-66293-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 05/15/2020] [Indexed: 12/16/2022] Open
Abstract
Aggregates of Pseudomonas aeruginosa form a protective barrier against antibiotics and the immune system. These barriers, known as biofilms, are associated with several infectious diseases. One of the main components of these biofilms is alginate, a homo- and hetero-polysaccharide that consists of β-D-mannuronate (M) and α-L-guluronate (G) units. Alginate lyases degrade this sugar and have been proposed as biotherapeutic agents to dissolve P. aeruginosa biofilms. However, there are contradictory reports in the literature regarding the efficacy of alginate lyases against biofilms and their synergistic effect with antibiotics. We found that most positive reports used a commercial crude extract from Flavobacterium multivorum as the alginate lyase source. By using anion exchange chromatography coupled to nano LC MS/MS, we identified two distinct enzymes in this extract, one has both polyM and polyG (polyM/G) degradation activities and it is similar in sequence to a broad-spectrum alginate lyase from Flavobacterium sp. S20 (Alg2A). The other enzyme has only polyG activity and it is similar in sequence to AlyA1 from Zobellia galactanivorans. By characterizing both of these enzymes together with three recombinant alginate lyases (a polyM, a polyG and a polyM/G), we showed that only enzymes with polyM/G activity such as Alg2A and A1-II' (alginate lyase from Sphingomonas sp.) are effective in dissolving biofilms. Furthermore, both activities are required to have a synergistic effect with antibiotics.
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Affiliation(s)
- Núria Blanco-Cabra
- Bacterial infections and antimicrobial therapies, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Tony Ferrar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
| | - Rocco Mazzolini
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
| | - Eduard Torrents
- Bacterial infections and antimicrobial therapies, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain.
| | - Maria LLuch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain.
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17
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Summers TJ, Daniel BP, Cheng Q, DeYonker NJ. Quantifying Inter-Residue Contacts through Interaction Energies. J Chem Inf Model 2019; 59:5034-5044. [DOI: 10.1021/acs.jcim.9b00804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Thomas J. Summers
- The Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152-3550, United States
| | - Baty P. Daniel
- The Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152-3550, United States
| | - Qianyi Cheng
- The Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152-3550, United States
| | - Nathan J. DeYonker
- The Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152-3550, United States
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18
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Huang G, Wen S, Liao S, Wang Q, Pan S, Zhang R, Lei F, Liao W, Feng J, Huang S. Characterization of a bifunctional alginate lyase as a new member of the polysaccharide lyase family 17 from a marine strain BP-2. Biotechnol Lett 2019; 41:1187-1200. [PMID: 31418101 PMCID: PMC6742608 DOI: 10.1007/s10529-019-02722-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/08/2019] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Bifunctional alginate lyase can efficiently saccharify alginate biomass and prepare functional oligosaccharides of alginate. RESULTS A new BP-2 strain that produces alginate lyase was screened and identified from rotted Sargassum. A new alginate lyase, Alg17B, belonging to the polysaccharide lyase family 17, was isolated and purified from BP-2 fermentation broth by freeze-drying, dialysis, and ion exchange chromatography. The enzymatic properties of the purified lyase were investigated. The molecular weight of Alg17B was approximately 77 kDa, its optimum reaction temperature was 40-45 °C, and its optimum reaction pH was 7.5-8.0. The enzyme was relatively stable at pH 7.0-8.0, with a temperature range of 25-35 °C, and the specific activity of the purified enzyme reached 4036 U/mg. A low Na+ concentration stimulated Alg17B enzyme activity, but Ca2+, Zn2+, and other metal ions inhibited it. Substrate specificity analysis, thin-layer chromatography, and mass spectrometry showed that Alg17B is an alginate lyase that catalyses the hydrolysis of sodium alginate, polymannuronic acid (polyM) and polyguluronic acid to produce monosaccharides and low molecular weight oligosaccharides. Alg17B is also bifunctional, exhibiting both endolytic and exolytic activities toward alginate, and has a wide substrate utilization range with a preference for polyM. CONCLUSIONS Alg17B can be used to saccharify the main carbohydrate, alginate, in the ethanolic production of brown algae fuel as well as in preparing and researching oligosaccharides.
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Affiliation(s)
- Guiyuan Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Shunhua Wen
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
- Research and Development Department, Xiamen Innodx Biotech Co. Ltd, Xiamen, China
| | - Siming Liao
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, Nanning, China
| | - Qiaozhen Wang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Shihan Pan
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Rongcan Zhang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Fu Lei
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Wei Liao
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
- The Food and Biotechnology, Guangxi Vocational and Technical College, Nanning, China
| | - Jie Feng
- School of Pharmaceutical Science, Guangxi Medical University, Nanning, 530021, China
| | - Shushi Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China.
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19
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Liu J, Yang S, Li X, Yan Q, Reaney MJT, Jiang Z. Alginate Oligosaccharides: Production, Biological Activities, and Potential Applications. Compr Rev Food Sci Food Saf 2019; 18:1859-1881. [DOI: 10.1111/1541-4337.12494] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/09/2019] [Accepted: 07/29/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Jun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural Univ. Beijing 100083 China
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology and Business Univ. Beijing 100048 China
| | - Shaoqing Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural Univ. Beijing 100083 China
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology and Business Univ. Beijing 100048 China
| | - Qiaojuan Yan
- Bioresource Utilization LaboratoryCollege of EngineeringChina Agricultural Univ. Beijing 100083 China
| | - Martin J. T. Reaney
- Dept. of Plant SciencesUniv. of Saskatchewan Saskatoon SK S7N 5A8 Canada
- Guangdong Saskatchewan Oilseed Joint Laboratory (GUSTO)Dept. of Food Science and EngineeringJinan Univ. Guangzhou 510632 China
| | - Zhengqiang Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural Univ. Beijing 100083 China
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20
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Pei X, Chang Y, Shen J. Cloning, expression and characterization of an endo-acting bifunctional alginate lyase of marine bacterium Wenyingzhuangia fucanilytica. Protein Expr Purif 2018; 154:44-51. [PMID: 30248453 DOI: 10.1016/j.pep.2018.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 11/15/2022]
Abstract
Alginate is the major constituent of brown algae and a commercially important polysaccharide with wide applications. Alginate lyases are desired tools for degrading alginate. Based on the genome mining of marine bacterium Wenyingzhuangia funcanilytica, an alginate lyase Aly7B_Wf was discovered, cloned and expressed in Escherichia coli. Aly7B_Wf belonged to subfamily 6 of PL7 family. Its biochemical properties, kinetic constants, substrate specificity and degradation pattern were clarified. The enzyme is an endo-acting bifunctional alginate lyase, and preferably cleaved polymannuronate (polyM). The Km (0.0237 ± 0.0004 μM, 0.0105 ± 0.0002 mg/mL) and kcat/Km (1180.65 ± 19.81 μM-1 s-1, 2654.34 ± 44.54 mg-1 ml s-1) indicated relatively high substrate-binding affinity and catalysis efficiency of Aly7B_Wf. By using mass spectrometry, final products of alginate degraded by Aly7B_Wf were identified as alginate hexasaccharide to disaccharide, and final products of polyguluronate (polyG) and polyM were confirmed as tetrasaccharide to disaccharide. The most predominant oligosaccharide in the final products of polyG and polyM was trisaccharide and disaccharide respectively. The broad substrate specificity, endo-acting degradation pattern and high catalysis efficiency suggested that Aly7B_Wf could be utilizied as a potential tool for tailoring the size of alginate and preparing alginate oligosaccharides.
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Affiliation(s)
- Xiaojie Pei
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
| | - Jingjing Shen
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
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21
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Zhuang J, Zhang K, Liu X, Liu W, Lyu Q, Ji A. Characterization of a Novel PolyM-Preferred Alginate Lyase from Marine Vibrio splendidus OU02. Mar Drugs 2018; 16:md16090295. [PMID: 30135412 PMCID: PMC6165035 DOI: 10.3390/md16090295] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 08/09/2018] [Accepted: 08/21/2018] [Indexed: 01/02/2023] Open
Abstract
Alginate lyases are enzymes that degrade alginate into oligosaccharides which possess a variety of biological activities. Discovering and characterizing novel alginate lyases has great significance for industrial and medical applications. In this study, we reported a novel alginate lyase, AlyA-OU02, derived from the marine Vibrio splendidus OU02. The BLASTP searches showed that AlyA-OU02 belonged to polysaccharide lyase family 7 (PL7) and contained two consecutive PL7 domains, which was rare among the alginate lyases in PL7 family. Both the two domains, AlyAa and AlyAb, had lyase activities, while AlyAa exhibited polyM preference, and AlyAb was polyG-preferred. In addition, the enzyme activity of AlyAa was much higher than AlyAb at 25 °C. The full-length enzyme of AlyA-OU02 showed polyM preference, which was the same as AlyAa. AlyAa degraded alginate into di-, tri-, and tetra-alginate oligosaccharides, while AlyAb degraded alginate into tri-, tetra-, and penta-alginate oligosaccharides. The degraded products of AlyA-OU02 were similar to AlyAa. Our work provided a potential candidate in the application of alginate oligosaccharide production and the characterization of the two domains might provide insights into the use of alginate of this organism.
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Affiliation(s)
| | - Keke Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Xiaohua Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Weizhi Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Qianqian Lyu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Aiguo Ji
- Marine College, Shandong University, Weihai 264209, China.
- School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
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22
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Zhu B, Ning L, Jiang Y, Ge L. Biochemical Characterization and Degradation Pattern of a Novel Endo-Type Bifunctional Alginate Lyase AlyA from Marine Bacterium Isoptericola halotolerans. Mar Drugs 2018; 16:E258. [PMID: 30065151 PMCID: PMC6117692 DOI: 10.3390/md16080258] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/21/2018] [Accepted: 07/27/2018] [Indexed: 01/13/2023] Open
Abstract
Alginate lyases are important tools to prepare oligosaccharides with various physiological activities by degrading alginate. Particularly, the bifunctional alginate lyase can efficiently hydrolyze the polysaccharide into oligosaccharides. Herein, we cloned and identified a novel bifunctional alginate lyase, AlyA, with a high activity and broad substrate specificity from bacterium Isoptericola halotolerans NJ-05 for oligosaccharides preparation. For further applications in industry, the enzyme has been characterized and its action mode has been also elucidated. It exhibited the highest activity (7984.82 U/mg) at pH 7.5 and 55 °C. Additionally, it possessed a broad substrate specificity, showing high activities towards not only polyM (polyβ-d-mannuronate) (7658.63 U/mg), but also polyG (poly α-l-guluronate) (8643.29 U/mg). Furthermore, the Km value of AlyA towards polyG (3.2 mM) was lower than that towards sodium alginate (5.6 mM) and polyM (6.7 mM). TLC (Thin Layer Chromatography) and ESI-MS (Electrospray Ionization Mass Spectrometry) were used to study the action mode of the enzyme, showing that it can hydrolyze the substrates in an endolytic manner to release a series of oligosaccharides such as disaccharide, trisaccharide, and tetrasaccharide. This study provided extended insights into the substrate recognition and degrading pattern of the alginate lyases, with a broad substrate specificity.
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Affiliation(s)
- Benwei Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, Jiangsu, China.
| | - Limin Ning
- College of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China.
| | - Yucui Jiang
- College of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China.
| | - Lin Ge
- Technology Transfer Center, Nanjing Forest University, Nanjing 210037, Jiangsu, China.
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23
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Yagi H, Fujise A, Itabashi N, Ohshiro T. Characterization of a novel endo-type alginate lyase derived from Shewanella sp. YH1. J Biochem 2018; 163:341-350. [PMID: 29319800 DOI: 10.1093/jb/mvy001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/24/2017] [Indexed: 12/18/2022] Open
Abstract
Alginate, which is an anionic polysaccharide, is widely distributed in the cell wall of brown algae. Alginate and the products of its degradation (oligosaccharides) are used in stabilizers, thickeners and gelling agents, especially in the food industry. The degradation of alginate generally involves a combination of several alginate lyases (exo-type, endo-type and oligoalginate lyase). Enhancing the efficiency of the production of alginate degradation products may require the identification of novel alginate lyases with unique characteristics. In this study, we isolated an alginate-utilizing bacterium, Shewanella sp. YH1, from seawater collected off the coast of Tottori prefecture, Japan. The detected novel alginate lyase was named AlgSI-PL7, and was classified in polysaccharide lyase family 7. The enzyme was purified from Shewanella sp. YH1 and a recombinant AlgSI-PL7 was produced in Escherichia coli. The optimal temperature and pH for enzyme activity were around 45°C and 8, respectively. Interestingly, we observed that AlgSI-PL7 was not thermotolerant, but could refold to its active form following an almost complete denaturation at approximately 60°C. Moreover, the degradation of alginate by AlgSI-PL7 produced two to five oligosaccharides, implying this enzyme was an endo-type lyase. Our findings suggest that AlgSI-PL7 may be useful as an industrial enzyme.
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Affiliation(s)
- Hisashi Yagi
- Center for Research on Green Sustainable Chemistry
| | - Asako Fujise
- Department of Chemistry and Biotechnology, Graduate School of Engineering
| | - Narumi Itabashi
- Department of Biotechnology, Faculty of Engineering, Tottori University, Tottori, Japan
| | - Takashi Ohshiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering
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24
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Inoue A. Characterization of PL-7 Family Alginate Lyases From Marine Organisms and Their Applications. Methods Enzymol 2018; 605:499-524. [PMID: 29909836 DOI: 10.1016/bs.mie.2018.01.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Alginate, an anionic heteropolysaccharide extracted from natural brown algae, has useful properties for the food, chemical, medical, and agricultural industries. Degradation of alginate by alginate lyase is a key process to produce unsaturated oligoalginate and unsaturated monosaccharide 4-deoxy-l-erythro-5-hexoseulose uronic acid. Alginate lyases belonging to the polysaccharide lyase family 7 have been found in, and isolated from, organisms thriving in various environments. Furthermore, research on their function and structure has also progressed well. Here, the preparation of native and recombinant PL-7 alginate lyases and the methods for evaluation of enzymatic activity are summarized. Examples of PL-7 alginate lyase applications are also described.
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Xu F, Wang P, Zhang YZ, Chen XL. Diversity of Three-Dimensional Structures and Catalytic Mechanisms of Alginate Lyases. Appl Environ Microbiol 2018; 84:e02040-17. [PMID: 29150496 PMCID: PMC5772247 DOI: 10.1128/aem.02040-17] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alginate is a linear polysaccharide produced mainly by brown algae in marine environments. Alginate consists of a linear block copolymer made up of two monomeric units, β-d-mannuronate (M) and its C-5 epimer α-l-guluronate (G). Alginate lyases are polysaccharide lyases (PL) that degrade alginate via a β-elimination reaction. These enzymes play an important role in marine carbon recycling and also have widespread industrial applications. So far, more than 1,774 alginate lyase sequences have been identified and are distributed into 7 PL families. In this review, the folds, conformational changes during catalysis, and catalytic mechanisms of alginate lyases are described. Thus far, structures for 15 alginate lyases have been solved and are divided into 3 fold classes: the β-jelly roll class (PL7, -14, and -18), the (α/α)n toroid class (PL5, -15, and -17), and the β-helix fold (PL6). These enzymes adopt two different mechanisms for catalysis, and three kinds of conformational changes occur during this process. Moreover, common features in the structures, conformational changes, and catalytic mechanisms are summarized, providing a comprehensive understanding on alginate lyases.
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Affiliation(s)
- Fei Xu
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Peng Wang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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Sim PF, Furusawa G, Teh AH. Functional and Structural Studies of a Multidomain Alginate Lyase from Persicobacter sp. CCB-QB2. Sci Rep 2017; 7:13656. [PMID: 29057942 PMCID: PMC5651945 DOI: 10.1038/s41598-017-13288-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/19/2017] [Indexed: 11/30/2022] Open
Abstract
AlyQ from Persicobacter sp. CCB-QB2 is an alginate lyase with three domains — a carbohydrate-binding domain modestly resembling family 16 carbohydrate-binding module (CBM16), a family 32 CBM (CBM32) domain, and an alginate lyase domain belonging to polysaccharide lyase family 7 (PL7). Although AlyQ can also act on polyguluronate (poly-G) and polymannuronate (poly-M), it is most active on alginate. Studies with truncated AlyQ showed that the CBM32 domain did not contribute to enhancing AlyQ’s activity under the assayed conditions. Nevertheless, it could bind to cleaved but not intact alginate, indicating that the CBM32 domain recognises alginate termini. The crystal structure containing both CBM32 and catalytic domains show that they do not interact with one another. The CBM32 domain contains a conserved Arg that may bind to the carboxyl group of alginate. The catalytic domain, meanwhile, shares a conserved substrate-binding groove, and the presence of two negatively charged Asp residues may dictate substrate specificity especially at subsite +1. As Persicobacter sp. CCB-QB2 was unable to utilise alginate, AlyQ may function to help the bacterium degrade cell walls more efficiently.
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Affiliation(s)
- Pei-Fang Sim
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900, Bayan Lepas, Penang, Malaysia
| | - Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900, Bayan Lepas, Penang, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900, Bayan Lepas, Penang, Malaysia.
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Yagi H, Fujise A, Itabashi N, Ohshiro T. Purification and characterization of a novel alginate lyase from the marine bacterium Cobetia sp. NAP1 isolated from brown algae. Biosci Biotechnol Biochem 2016; 80:2338-2346. [PMID: 27648685 DOI: 10.1080/09168451.2016.1232154] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/23/2016] [Indexed: 01/28/2023]
Abstract
The application of marine resources, instead of fossil fuels, for biomass production is important for building a sustainable society. Seaweed is valuable as a source of marine biomass for producing biofuels such as ethanol, and can be used in various fields. Alginate is an anionic polysaccharide that forms the main component of brown algae. Various alginate lyases (e.g. exo- and endo-types and oligoalginate lyase) are generally used to degrade alginate. We herein describe a novel alginate lyase, AlgC-PL7, which belongs to the polysaccharide lyase 7 family. AlgC-PL7 was isolated from the halophilic Gram-negative bacterium Cobetia sp. NAP1 collected from the brown algae Padina arborescens Holmes. The optimal temperature and pH for AlgC-PL7 activity were 45 °C and 8, respectively. Additionally, AlgC-PL7 was thermostable and salt-tolerant, exhibited broad substrate specificity, and degraded alginate into monosaccharides. Therefore, AlgC-PL7 is a promising enzyme for the production of biofuels.
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Affiliation(s)
- Hisashi Yagi
- a Center for Research on Green Sustainable Chemistry , Tottori University , Tottori , Japan
| | - Asako Fujise
- b Department of Chemistry and Biotechnology , Graduate School of Engineering, Tottori University , Tottori , Japan
| | - Narumi Itabashi
- c Faculty of Engineering, Department of Biotechnology , Tottori University , Tottori , Japan
| | - Takashi Ohshiro
- b Department of Chemistry and Biotechnology , Graduate School of Engineering, Tottori University , Tottori , Japan
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Marine Microbiological Enzymes: Studies with Multiple Strategies and Prospects. Mar Drugs 2016; 14:md14100171. [PMID: 27669268 PMCID: PMC5082319 DOI: 10.3390/md14100171] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/04/2016] [Accepted: 09/14/2016] [Indexed: 11/16/2022] Open
Abstract
Marine microorganisms produce a series of promising enzymes that have been widely used or are potentially valuable for our daily life. Both classic and newly developed biochemistry technologies have been broadly used to study marine and terrestrial microbiological enzymes. In this brief review, we provide a research update and prospects regarding regulatory mechanisms and related strategies of acyl-homoserine lactones (AHL) lactonase, which is an important but largely unexplored enzyme. We also detail the status and catalytic mechanism of the main types of polysaccharide-degrading enzymes that broadly exist among marine microorganisms but have been poorly explored. In order to facilitate understanding, the regulatory and synthetic biology strategies of terrestrial microorganisms are also mentioned in comparison. We anticipate that this review will provide an outline of multiple strategies for promising marine microbial enzymes and open new avenues for the exploration, engineering and application of various enzymes.
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Takeshita S, Oda T. Usefulness of Alginate Lyases Derived from Marine Organisms for the Preparation of Alginate Oligomers with Various Bioactivities. ADVANCES IN FOOD AND NUTRITION RESEARCH 2016; 79:137-160. [PMID: 27770859 DOI: 10.1016/bs.afnr.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Alginate-degrading enzyme, alginate lyase, catalyzes the cleavage of glycosidic 1-4 O-linkages between uronic acid residues of alginate by a β-elimination reaction leaving a 4-deoxy-l-erythro-hex-4-ene pyranosyluronate as nonreducing terminal end. The enzymes from a wide variety of sources such as marine molluscs, seaweeds, and marine bacteria have been discovered and studied not only from a point of view of enzymological interest of enzyme itself but also for elucidation of fine chemical structure of alginate, structure-activity relationship of alginate, and biological activities and physicochemical features of the enzymatic digestion products. Based on the substrate specificities, alginate lyases are classified into three groups: poly(β-d-mannuronate) lyase, poly(α-l-guluronate) lyase, and bifunctional alginate lyase, which are specific to mannuronate, guluronate, and both uronic acid residues, respectively. We have studied enzymological aspects of these three types of alginate lyases, and bioactivities of enzymatically digested alginate oligomers. In this chapter, we described the purification and characterization of three types of alginate lyases from different marine origins and overviewed the bioactivities of alginate oligomers.
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Affiliation(s)
- S Takeshita
- Center for Industry, University and Government Cooperation, Nagasaki University, Nagasaki, Japan.
| | - T Oda
- Graduate School of Fisheries Science & Environmental Studies, Nagasaki University, Nagasaki, Japan
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Mathieu S, Henrissat B, Labre F, Skjåk-Bræk G, Helbert W. Functional Exploration of the Polysaccharide Lyase Family PL6. PLoS One 2016; 11:e0159415. [PMID: 27438604 PMCID: PMC4954714 DOI: 10.1371/journal.pone.0159415] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/03/2016] [Indexed: 11/19/2022] Open
Abstract
Alginate, the main cell-wall polysaccharide of brown algae, is composed of two residues: mannuronic acid (M-residues) and, its C5-epimer, guluronic acid (G-residues). Alginate lyases define a class of enzymes that cleave the glycosidic bond of alginate by β-elimination. They are classified according to their ability to recognize the distribution of M- and G-residues and are named M-, G- or MG-lyases. In the CAZy database, alginate lyases have been grouped by sequence similarity into seven distinct polysaccharide lyase families. The polysaccharide lyase family PL6 is subdivided into three subfamilies. Subfamily PL6_1 includes three biochemically characterized enzymes (two alginate lyases and one dermatan sulfatase lyase). No characterized enzymes have been described in the two other subfamilies (PL6_2 and PL6_3). To improve the prediction of polysaccharide-lyase activity in the PL6 family, we re-examined the classification of the PL6 family and biochemically characterized a set of enzymes reflecting the diversity of the protein sequences. Our results show that subfamily PL6_1 includes two dermatan sulfates lyases and several alginate lyases that have various substrate specificities and modes of action. In contrast, subfamilies PL6_2 and PL6_3 were found to contain only endo-poly-MG-lyases.
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Affiliation(s)
- Sophie Mathieu
- CERMAV, CNRS and Grenoble Alpes Université, BP53, 38000, Grenoble, Cedex 9, France
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 13288, Marseille, France
- INRA, USC 1408 AFMB, 13288, Marseille, France
| | - Flavien Labre
- CERMAV, CNRS and Grenoble Alpes Université, BP53, 38000, Grenoble, Cedex 9, France
| | - Gudmund Skjåk-Bræk
- Department of Biotechnology, Norwegian University of Science and Technology, NTNU Sem Sælands vei 6–8, 7491, Trondheim, Norway
| | - William Helbert
- CERMAV, CNRS and Grenoble Alpes Université, BP53, 38000, Grenoble, Cedex 9, France
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Chen XL, Dong S, Xu F, Dong F, Li PY, Zhang XY, Zhou BC, Zhang YZ, Xie BB. Characterization of a New Cold-Adapted and Salt-Activated Polysaccharide Lyase Family 7 Alginate Lyase from Pseudoalteromonas sp. SM0524. Front Microbiol 2016; 7:1120. [PMID: 27486451 PMCID: PMC4949377 DOI: 10.3389/fmicb.2016.01120] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/06/2016] [Indexed: 11/23/2022] Open
Abstract
Marine bacterial alginate lyases play a role in marine alginate degradation and carbon cycling. Although a large number of alginate lyases have been characterized, reports on alginate lyases with special characteristics are still rather less. Here, a gene alyPM encoding an alginate lyase of polysaccharide lyase family 7 (PL7) was cloned from marine Pseudoalteromonas sp. SM0524 and expressed in Escherichia coli. AlyPM shows 41% sequence identity to characterized alginate lyases, indicating that AlyPM is a new PL7 enzyme. The optimal pH for AlyPM activity was 8.5. AlyPM showed the highest activity at 30°C and remained 19% of the highest activity at 5°C. AlyPM was unstable at temperatures above 30°C and had a low Tm of 37°C. These data indicate that AlyPM is a cold-adapted enzyme. Moreover, AlyPM is a salt-activated enzyme. AlyPM activity in 0.5–1.2 M NaCl was sixfolds higher than that in 0 M NaCl, probably caused by a significant increase in substrate affinity, because the Km of AlyPM in 0.5 M NaCl decreased more than 20-folds than that in 0 M NaCl. AlyPM preferably degraded polymannuronate and mainly released dimers and trimers. These data indicate that AlyPM is a new PL7 endo-alginate lyase with special characteristics.
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Affiliation(s)
- Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research Center, Shandong UniversityJinan, China
| | - Sheng Dong
- State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research Center, Shandong UniversityJinan, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research Center, Shandong UniversityJinan, China
| | - Fang Dong
- State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research Center, Shandong UniversityJinan, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research Center, Shandong UniversityJinan, China; Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research Center, Shandong UniversityJinan, China
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center, Shandong University Jinan, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research Center, Shandong UniversityJinan, China; Institute of Marine Science and Technology, Shandong UniversityJinan, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research Center, Shandong UniversityJinan, China
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Inoue A, Anraku M, Nakagawa S, Ojima T. Discovery of a Novel Alginate Lyase from Nitratiruptor sp. SB155-2 Thriving at Deep-sea Hydrothermal Vents and Identification of the Residues Responsible for Its Heat Stability. J Biol Chem 2016; 291:15551-63. [PMID: 27231344 DOI: 10.1074/jbc.m115.713230] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Indexed: 11/06/2022] Open
Abstract
Extremophiles are expected to represent a source of enzymes having unique functional properties. The hypothetical protein NIS_0185, termed NitAly in this study, was identified as an alginate lyase-homolog protein in the genomic database of ϵ-Proteobacteria Nitratiruptor sp. SB155-2, which was isolated from deep-sea hydrothermal vents at a water depth of 1,000 m. Among the characterized alginate lyases in the polysaccharide lyase family 7 (PL-7), the amino acid sequence of NitAly showed the highest identity (39%) with that of red alga Pyropia yezoensis alginate lyase PyAly. Recombinant NitAly (rNitAly) was successfully expressed in Escherichia coli Purified rNitAly degraded alginate in an endolytic manner. Among alginate block types, polyM was preferable to polyG and polyMG as a substrate, and its end degradation products were mainly tri-, tetra-, and penta-saccharides. The optimum temperature and pH values were 70 °C and around 6, respectively. A high concentration of NaCl (0.8-1.4 m) was required for maximum activity. In addition, a 50% loss of activity was observed after incubation at 67 °C for 30 min. Heat stability was decreased in the presence of 5 mm DTT, and Cys-80 and Cys-232 were identified as the residues responsible for heat stability but not lyase activity. Introducing two cysteines into PyAly based on homology modeling using Pseudomonas aeruginosa alginate lyase PA1167 as the template enhanced its heat stability. Thus, NitAly is a functional alginate lyase, with its unique optimum conditions adapted to its environment. These insights into the heat stability of NitAly could be applied to improve that of other PL-7 alginate lyases.
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Affiliation(s)
- Akira Inoue
- From the Laboratory of Marine Biotechnology and Microbiology, Division of Applied Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan
| | - Moe Anraku
- From the Laboratory of Marine Biotechnology and Microbiology, Division of Applied Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan
| | - Satoshi Nakagawa
- From the Laboratory of Marine Biotechnology and Microbiology, Division of Applied Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan
| | - Takao Ojima
- From the Laboratory of Marine Biotechnology and Microbiology, Division of Applied Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan
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Ji SQ, Wang B, Lu M, Li FL. Defluviitalea phaphyphila sp. nov., a Novel Thermophilic Bacterium That Degrades Brown Algae. Appl Environ Microbiol 2016; 82:868-77. [PMID: 26590273 PMCID: PMC4725288 DOI: 10.1128/aem.03297-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/15/2015] [Indexed: 11/20/2022] Open
Abstract
Brown algae are one of the largest groups of oceanic primary producers for CO2 removal and carbon sinks for coastal regions. However, the mechanism for brown alga assimilation remains largely unknown in thermophilic microorganisms. In this work, a thermophilic alginolytic community was enriched from coastal sediment, from which an obligate anaerobic and thermophilic bacterial strain, designated Alg1, was isolated. Alg1 shared a 16S rRNA gene identity of 94.6% with Defluviitalea saccharophila LIND6LT2(T). Phenotypic, chemotaxonomic, and phylogenetic studies suggested strain Alg1 represented a novel species of the genus Defluviitalea, for which the name Defluviitalea phaphyphila sp. nov. is proposed. Alg1 exhibited an intriguing ability to convert carbohydrates of brown algae, including alginate, laminarin, and mannitol, to ethanol and acetic acid. Three gene clusters participating in this process were predicted to be in the genome, and candidate enzymes were successfully expressed, purified, and characterized. Six alginate lyases were demonstrated to synergistically deconstruct alginate into unsaturated monosaccharide, followed by one uronic acid reductase and two 2-keto-3-deoxy-d-gluconate (KDG) kinases to produce pyruvate. A nonclassical mannitol 1-phosphate dehydrogenase, catalyzing D-mannitol 1-phosphate to fructose 1-phosphate in the presence of NAD(+), and one laminarase also were disclosed. This work revealed that a thermophilic brown alga-decomposing system containing numerous novel thermophilic alginate lyases and a unique mannitol 1-phosphate dehydrogenase was adopted by the natural ethanologenic strain Alg1 during the process of evolution in hostile habitats.
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Affiliation(s)
- Shi-Qi Ji
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Bing Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Ming Lu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People's Republic of China
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Inoue A, Mashino C, Uji T, Saga N, Mikami K, Ojima T. Characterization of an Eukaryotic PL-7 Alginate Lyase in the Marine Red Alga Pyropia yezoensis. ACTA ACUST UNITED AC 2015; 4:240-248. [PMID: 28553576 PMCID: PMC5436490 DOI: 10.2174/2211550104666150915210434] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 11/22/2022]
Abstract
BACKGROUND Alginate lyases belonging to polysaccharide lyase family-7 (PL-7) are the most well studied on their structures and functions among whole alginate lyases. However, all characterized PL-7 alginate lyases are from prokaryotic bacteria cells. Here we report the first identification of eukaryotic PL-7 alginate lyase from marine red alga Pyropia yezoensis. METHODS The cDNA encoding an alginate lyase PyAly was cloned and was used for the construction of recombinant PyAly (rPyAly) expression system in Escherichia coli. Purified rPyAly was assayed to identify its enzymatic properties. Its expression pattern in P. yessoensis was also investigated. RESULTS PyAly is likely a secreted protein consisting of an N-terminal signal peptide of 25 residues and a catalytic domain of 216 residues. The amino-acid sequence of the catalytic domain showed 19-29% identities to those of bacterial characterized alginate lyases classified into family PL-7. Recombinant PyAly protein, rPyAly, which was produced with E. coli BL21(DE3) by cold-inducible expression system, drastically decreased the viscosity of alginate solution in the early stage of reaction. The most preferable substrate for rPyAly was the poly(M) of alginate with an optimal temperature and pH at 35oC and 8.0, respectively. After reaction, unsaturated tri- and tetra-saccharides were produced from poly(M) as major end products. These enzymatic properties indicated that PyAly is an endolytic alginate lyase belonging to PL-7. Moreover, we found that the PyAly gene is split into 4 exons with 3 introns. PyAly was also specifically expressed in the gametophytic haplopid stage. CONCLUSION This study demonstrates that PyAly in marine red alga P. yezoensis is a novel PL-7 alginate lyase with an endolytic manner. PyAly is a gametophyte-specifically expressed protein and its structural gene is composed of four exons and three introns. Thus, PyAly is the first enzymatically characterized eukaryotic PL-7 alginate lyase.
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Affiliation(s)
- Akira Inoue
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Chieco Mashino
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Toshiki Uji
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Naotsune Saga
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Koji Mikami
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Takao Ojima
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
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Zhu B, Yin H. Alginate lyase: Review of major sources and classification, properties, structure-function analysis and applications. Bioengineered 2015; 6:125-31. [PMID: 25831216 PMCID: PMC4601208 DOI: 10.1080/21655979.2015.1030543] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022] Open
Abstract
Alginate lyases catalyze the degradation of alginate, a complex copolymer of α-L-guluronate and its C5 epimer β-D-mannuronate. The enzymes have been isolated from various kinds of organisms with different substrate specificities, including algae, marine mollusks, marine and terrestrial bacteria, and some viruses and fungi. With the progress of structural biology, many kinds of alginate lyases of different polysaccharide lyases families have been characterized by obtaining crystal structures, and the catalytic mechanism has also been elucidated. Combined with various studies, we summarized the source, classification and properties of the alginate lyases from different polysaccharide lyases families. The relationship between substrate specificity and protein sequence was also investigated.
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Affiliation(s)
- Benwei Zhu
- Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian, PR China
- University of Chinese Academy of Sciences; Beijing, PR China
| | - Heng Yin
- Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian, PR China
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36
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Dong S, Wei TD, Chen XL, Li CY, Wang P, Xie BB, Qin QL, Zhang XY, Pang XH, Zhou BC, Zhang YZ. Molecular insight into the role of the N-terminal extension in the maturation, substrate recognition, and catalysis of a bacterial alginate lyase from polysaccharide lyase family 18. J Biol Chem 2014; 289:29558-69. [PMID: 25210041 DOI: 10.1074/jbc.m114.584573] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial alginate lyases, which are members of several polysaccharide lyase (PL) families, have important biological roles and biotechnological applications. The mechanisms for maturation, substrate recognition, and catalysis of PL18 alginate lyases are still largely unknown. A PL18 alginate lyase, aly-SJ02, from Pseudoalteromonas sp. 0524 displays a β-jelly roll scaffold. Structural and biochemical analyses indicated that the N-terminal extension in the aly-SJ02 precursor may act as an intramolecular chaperone to mediate the correct folding of the catalytic domain. Molecular dynamics simulations and mutational assays suggested that the lid loops over the aly-SJ02 active center serve as a gate for substrate entry. Molecular docking and site-directed mutations revealed that certain conserved residues at the active center, especially those at subsites +1 and +2, are crucial for substrate recognition. Tyr(353) may function as both a catalytic base and acid. Based on our results, a model for the catalysis of aly-SJ02 in alginate depolymerization is proposed. Moreover, although bacterial alginate lyases from families PL5, 7, 15, and 18 adopt distinct scaffolds, they share the same conformation of catalytic residues, reflecting their convergent evolution. Our results provide the foremost insight into the mechanisms of maturation, substrate recognition, and catalysis of a PL18 alginate lyase.
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Affiliation(s)
- Sheng Dong
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Tian-Di Wei
- From the State Key Laboratory of Microbial Technology and
| | - Xiu-Lan Chen
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Chun-Yang Li
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Peng Wang
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Bin-Bin Xie
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Qi-Long Qin
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Xi-Ying Zhang
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Xiu-Hua Pang
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Bai-Cheng Zhou
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Yu-Zhong Zhang
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
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Yan J, Mao J, Xie J. Bacteriophage Polysaccharide Depolymerases and Biomedical Applications. BioDrugs 2013; 28:265-74. [DOI: 10.1007/s40259-013-0081-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Thomas F, Lundqvist LCE, Jam M, Jeudy A, Barbeyron T, Sandström C, Michel G, Czjzek M. Comparative characterization of two marine alginate lyases from Zobellia galactanivorans reveals distinct modes of action and exquisite adaptation to their natural substrate. J Biol Chem 2013; 288:23021-37. [PMID: 23782694 DOI: 10.1074/jbc.m113.467217] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cell walls of brown algae are complex supramolecular assemblies containing various original, sulfated, and carboxylated polysaccharides. Among these, the major marine polysaccharide component, alginate, represents an important biomass that is successfully turned over by the heterotrophic marine bacteria. In the marine flavobacterium Zobellia galactanivorans, the catabolism and uptake of alginate are encoded by operon structures that resemble the typical Bacteroidetes polysaccharide utilization locus. The genome of Z. galactanivorans contains seven putative alginate lyase genes, five of which are localized within two clusters comprising additional carbohydrate-related genes. This study reports on the detailed biochemical and structural characterization of two of these. We demonstrate here that AlyA1PL7 is an endolytic guluronate lyase, and AlyA5 cleaves unsaturated units, α-L-guluronate or β-D-manuronate residues, at the nonreducing end of oligo-alginates in an exolytic fashion. Despite a common jelly roll-fold, these striking differences of the mode of action are explained by a distinct active site topology, an open cleft in AlyA1(PL7), whereas AlyA5 displays a pocket topology due to the presence of additional loops partially obstructing the catalytic groove. Finally, in contrast to PL7 alginate lyases from terrestrial bacteria, both enzymes proceed according to a calcium-dependent mechanism suggesting an exquisite adaptation to their natural substrate in the context of brown algal cell walls.
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Affiliation(s)
- François Thomas
- University of Marie and Pierre Curie Paris 6, UMR 7139, Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Brittany, France
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Crystal structure of the N-terminal domain of a glycoside hydrolase family 131 protein from Coprinopsis cinerea. FEBS Lett 2013; 587:2193-8. [DOI: 10.1016/j.febslet.2013.05.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 11/22/2022]
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Hu T, Li C, Zhao X, Li G, Yu G, Guan H. Preparation and characterization of guluronic acid oligosaccharides degraded by a rapid microwave irradiation method. Carbohydr Res 2013; 373:53-8. [PMID: 23584235 DOI: 10.1016/j.carres.2013.03.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 10/27/2022]
Abstract
Guluronic acid oligosaccharides (GOS) with degree of polymerization (DP) ranging from 1 to 10 were prepared by a rapid microwave degradation method. Polyguluronic acid, fractionated from alginate hydrolysate, was dissolved in dilute ammonia water at a concentration of 20 mg/mL (pH 5) and then hydrolyzed under microwave irradiation (1600 W) at 130°C for 15 min to produce GOS mixture. The GOS mixture was separated by a Bio-Gel P6 column and ten fractions were obtained. Each GOS fraction was further characterized by electrospray ionization mass spectrometry, (1)H NMR, (13)C NMR, and 2D NMR spectroscopy techniques. The data showed that the GOS fractions were saturated oligoguluronates with general molecular formula C(6n)H(8n+2)O(6n+1) (n=1-10). This microwave degradation method was not only convenient, less time consuming, and environment-friendly, but also produced GOS with high yield (71%) and eliminating a desalting procedure compared to conventional acid hydrolysis method.
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Affiliation(s)
- Ting Hu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
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Dong S, Yang J, Zhang XY, Shi M, Song XY, Chen XL, Zhang YZ. Cultivable alginate lyase-excreting bacteria associated with the Arctic brown alga Laminaria. Mar Drugs 2012; 10:2481-91. [PMID: 23203272 PMCID: PMC3509530 DOI: 10.3390/md10112481] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/24/2012] [Accepted: 10/26/2012] [Indexed: 11/17/2022] Open
Abstract
Although some alginate lyases have been isolated from marine bacteria, alginate lyases-excreting bacteria from the Arctic alga have not yet been investigated. Here, the diversity of the bacteria associated with the brown alga Laminaria from the Arctic Ocean was investigated for the first time. Sixty five strains belonging to nine genera were recovered from six Laminaria samples, in which Psychrobacter (33/65), Psychromonas (10/65) and Polaribacter (8/65) were the predominant groups. Moreover, 21 alginate lyase-excreting strains were further screened from these Laminaria-associated bacteria. These alginate lyase-excreting strains belong to five genera. Psychromonas (8/21), Psedoalteromonas (6/21) and Polaribacter (4/21) are the predominant genera, and Psychrobacter, Winogradskyella, Psychromonas and Polaribacter were first found to produce alginate lyases. The optimal temperatures for the growth and algiante lyase production of many strains were as low as 10–20 °C, indicating that they are psychrophilic bacteria. The alginate lyases produced by 11 strains showed the highest activity at 20–30 °C, indicating that these enzymes are cold-adapted enzymes. Some strians showed high levels of extracellular alginate lyase activity around 200 U/mL. These results suggest that these algiante lyase-excreting bacteria from the Arctic alga are good materials for studying bacterial cold-adapted alginate lyases.
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Affiliation(s)
| | | | | | | | | | - Xiu-Lan Chen
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China; (S.D.); (J.Y.); (X.-Y.Z.); (M.S.); (X.-Y.S.); (Y.-Z.Z.)
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42
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Sakatoku A, Wakabayashi M, Tanaka Y, Tanaka D, Nakamura S. Isolation of a novel Saccharophagus species (Myt-1) capable of degrading a variety of seaweeds and polysaccharides. Microbiologyopen 2012; 1:2-12. [PMID: 22950007 PMCID: PMC3426404 DOI: 10.1002/mbo3.10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 12/29/2011] [Accepted: 12/30/2011] [Indexed: 11/06/2022] Open
Abstract
A bacterial strain, Myt-1, was isolated in Toyama Bay in Toyama Prefecture, Japan. Myt-1 was capable of reducing the thalli of various seaweed species to single cell detritus particles. A 16S rDNA homology search revealed that the closest relative of Myt-1 was Saccharophagus degradans 2-40 (CP000282; 100% similarity), which was first isolated in Chesapeake Bay in Virginia, USA. The Myt-1 strain was capable of degrading more than 10 polysaccharides, almost all of which were also degraded by S. degradans 2-40. Analyses of alginase gene DNA sequence homology, DNA-DNA homology, and zymogram analysis of obtained polysaccharidases suggested that Myt-1 was a new species of Saccharophagus. Thus, Myt-1 is only the second species in this genus, which has contained only one strain and species since 1988, and was tentatively designated Saccharophagus sp. Myt-1. Myt-1 has considerable potential for reducing the volume of seaweed wastes, and for producing functional materials from seaweed substrate.
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Affiliation(s)
- A Sakatoku
- Graduate School of Science and Engineering, University of Toyama Toyama 930-8555, Japan
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Mikami B, Ban M, Suzuki S, Yoon HJ, Miyake O, Yamasaki M, Ogura K, Maruyama Y, Hashimoto W, Murata K. Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1207-16. [PMID: 22948922 DOI: 10.1107/s090744491202495x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 05/31/2012] [Indexed: 11/11/2022]
Abstract
The structures of two mutants (H192A and Y246F) of a mannuronate-specific alginate lyase, A1-III, from Sphingomonas species A1 complexed with a tetrasaccharide substrate [4-deoxy-L-erythro-hex-4-ene-pyranosyluronate-(mannuronate)(2)-mannuronic acid] were determined by X-ray crystallography at around 2.2 Å resolution together with the apo form of the H192A mutant. The final models of the complex forms, which comprised two monomers (of 353 amino-acid residues each), 268-287 water molecules and two tetrasaccharide substrates, had R factors of around 0.17. A large conformational change occurred in the position of the lid loop (residues 64-85) in holo H192A and Y246F compared with that in apo H192A. The lid loop migrated about 14 Å from an open form to a closed form to interact with the bound tetrasaccharide and a catalytic residue. The tetrasaccharide was bound in the active cleft at subsites -3 to +1 as a substrate form in which the glycosidic linkage to be cleaved existed between subsites -1 and +1. In particular, the O(η) atom of Tyr68 in the closed lid loop forms a hydrogen bond to the side chain of a presumed catalytic residue, O(η) of Tyr246, which acts both as an acid and a base catalyst in a syn mechanism.
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Affiliation(s)
- Bunzo Mikami
- Department of Applied Life Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan.
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Lundqvist LC, Jam M, Barbeyron T, Czjzek M, Sandström C. Substrate specificity of the recombinant alginate lyase from the marine bacteria Pseudomonas alginovora. Carbohydr Res 2012; 352:44-50. [DOI: 10.1016/j.carres.2012.02.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/07/2012] [Accepted: 02/10/2012] [Indexed: 11/17/2022]
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Wakabayashi M, Sakatoku A, Noda F, Noda M, Tanaka D, Nakamura S. Isolation and characterization of Microbulbifer species 6532A degrading seaweed thalli to single cell detritus particles. Biodegradation 2012; 23:93-105. [PMID: 21681519 DOI: 10.1007/s10532-011-9489-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 06/04/2011] [Indexed: 10/18/2022]
Abstract
To reduce the volume of seaweed wastes and extract polysaccharides, seaweed-degrading bacteria were isolated from drifting macroalgae harvested along the coast of Toyama Bay, Japan. Sixty-four bacterial isolates were capable of degrading "Wakame" (Undaria pinnatifida) thallus fragments into single cell detritus (SCD) particles. Amongst these, strain 6532A was the most active degrader of thallus fragments, and was capable of degrading thallus fragments to SCD particles within a day. Although the sequence similarity of the 16S rRNA gene of strain 6532A was 100% similar to that of Microbulbifer elongatus JAMB-A7, several distinct differences were observed between strains, including motility, morphology, and utilization of D: -arabinose and gelatin. Consequently, strain 6532A was classified as a new Microbulbifer strain, and was designated Microbulbifer sp. 6532A. Strain 6532A was capable of degrading both alginate and cellulose in the culture medium, zymogram analysis of which revealed the presence of multiple alginate lyases and cellulases. To the best of our knowledge, this is the first study to directly demonstrate the existence of these enzymes in Microbulbifer species. Shotgun cloning and sequencing of the alginate lyase gene in 6532A revealed a 1,074-bp open reading frame, which was designated algMsp. The reading frame encoded a PL family seven enzyme composed of 358 amino acids (38,181 Da). With a similarity of 74.2%, the deduced amino acid sequence was most similar to a Saccharophagus enzyme (alg 7C). These findings suggest that algMsp in strain 6532A is a novel alginate lyase gene.
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Jain A, Sankararamakrishnan R. Dynamics of Noncovalent Interactions in All-α and All-β Class Proteins: Implications for the Stability of Amyloid Aggregates. J Chem Inf Model 2011; 51:3208-16. [DOI: 10.1021/ci200302q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Alok Jain
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur −208016, India
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Li JW, Dong S, Song J, Li CB, Chen XL, Xie BB, Zhang YZ. Purification and characterization of a bifunctional alginate lyase from Pseudoalteromonas sp. SM0524. Mar Drugs 2011; 9:109-23. [PMID: 21339950 PMCID: PMC3039154 DOI: 10.3390/md9010109] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Revised: 01/15/2011] [Accepted: 01/19/2011] [Indexed: 11/16/2022] Open
Abstract
An alginate lyase-producing bacterial strain, Pseudoalteromonas sp. SM0524, was screened from marine rotten kelp. In an optimized condition, the production of alginate lyase from Pseudoalteromonas sp. SM0524 reached 62.6 U/mL, suggesting that strain SM0524 is a good producer of alginate lyases. The bifunctional alginate lyase aly-SJ02 secreted by strain SM0524 was purified. Aly-SJ02 had an apparent molecular mass of 32 kDa. The optimal temperature and pH of aly-SJ02 toward sodium alginate was 50 °C and 8.5, respectively. The half life period of aly-SJ02 was 41 min at 40 °C and 20 min at 50 °C. Aly-SJ02 was most stable at pH 8.0. N-terminal sequence analysis suggested that aly-SJ02 may be an alginate lyase of polysaccharide lyase family 18. Aly-SJ02 showed activities toward both polyG (α-l-guluronic acid) and polyM (β-D-mannuronic acid), indicating that it is a bifunctional alginate lyase. Aly-SJ02 had lower K(m) toward polyG than toward polyM and sodium alginate. Thin layer chromatography and ESI-MS analyses showed that aly-SJ02 mainly released dimers and trimers from polyM and alginate, and trimers and tetramers from polyG, which suggests that aly-SJ02 may be a good tool to produce dimers and trimers from alginate.
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Affiliation(s)
- Jian-Wei Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China; E-Mails: (J.-W.L.); (S.D.); (J.S.); (B.-B.X.); (Y.-Z.Z.)
| | - Sheng Dong
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China; E-Mails: (J.-W.L.); (S.D.); (J.S.); (B.-B.X.); (Y.-Z.Z.)
| | - Jie Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China; E-Mails: (J.-W.L.); (S.D.); (J.S.); (B.-B.X.); (Y.-Z.Z.)
| | - Chun-Bo Li
- Biomedical Analysis Center, Tsinghua University, Beijing 100084, China; E-Mail: (C.-B.L.)
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China; E-Mails: (J.-W.L.); (S.D.); (J.S.); (B.-B.X.); (Y.-Z.Z.)
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China; E-Mails: (J.-W.L.); (S.D.); (J.S.); (B.-B.X.); (Y.-Z.Z.)
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China; E-Mails: (J.-W.L.); (S.D.); (J.S.); (B.-B.X.); (Y.-Z.Z.)
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Tøndervik A, Klinkenberg G, Aarstad OA, Drabløs F, Ertesvåg H, Ellingsen TE, Skjåk-Bræk G, Valla S, Sletta H. Isolation of mutant alginate lyases with cleavage specificity for di-guluronic acid linkages. J Biol Chem 2010; 285:35284-92. [PMID: 20826807 PMCID: PMC2975152 DOI: 10.1074/jbc.m110.162800] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 09/01/2010] [Indexed: 11/06/2022] Open
Abstract
Alginates are commercially valuable and complex polysaccharides composed of varying amounts and distribution patterns of 1-4-linked β-D-mannuronic acid (M) and α-L-guluronic acid (G). This structural variability strongly affects polymer physicochemical properties and thereby both commercial applications and biological functions. One promising approach to alginate fine structure elucidation involves the use of alginate lyases, which degrade the polysaccharide by cleaving the glycosidic linkages through a β-elimination reaction. For such studies one would ideally like to have different lyases, each of which cleaves only one of the four possible linkages in alginates: G-G, G-M, M-G, and M-M. So far no lyase specific for only G-G linkages has been described, and here we report the construction of such an enzyme by mutating the gene encoding Klebsiella pneumoniae lyase AlyA (a polysaccharide lyase family 7 lyase), which cleaves both G-G and G-M linkages. After error-prone PCR mutagenesis and high throughput screening of ∼7000 lyase mutants, enzyme variants with a strongly improved G-G specificity were identified. Furthermore, in the absence of Ca(2+), one of these lyases (AlyA5) was found to display no detectable activity against G-M linkages. G-G linkages were cleaved with ∼10% of the optimal activity under the same conditions. The substitutions conferring altered specificity to the mutant enzymes are located in conserved regions in the polysaccharide lyase family 7 alginate lyases. Structure-function analyses by comparison with the known three-dimensional structure of Sphingomonas sp. A1 lyase A1-II' suggests that the improved G-G specificity might be caused by increased affinity for nonproductive binding of the alternating G-M structure.
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Affiliation(s)
- Anne Tøndervik
- From the Department of Biotechnology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway and
- the Departments of Biotechnology and
| | - Geir Klinkenberg
- From the Department of Biotechnology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway and
| | | | - Finn Drabløs
- Cancer Research and Molecular Medicine, The Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | | | - Trond E. Ellingsen
- From the Department of Biotechnology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway and
| | | | | | - Håvard Sletta
- From the Department of Biotechnology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway and
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Uchimura K, Miyazaki M, Nogi Y, Kobayashi T, Horikoshi K. Cloning and sequencing of alginate lyase genes from deep-sea strains of Vibrio and Agarivorans and characterization of a new Vibrio enzyme. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:526-533. [PMID: 19941025 DOI: 10.1007/s10126-009-9237-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 09/20/2009] [Indexed: 05/27/2023]
Abstract
Four alginate lyase genes were cloned and sequenced from the genomic DNAs of deep-sea bacteria, namely members of Vibrio and Agarivorans. Three of them were from Vibrio sp. JAM-A9m, which encoded alginate lyases, A9mT, A9mC, and A9mL. A9mT was composed of 286 amino acids and 57% homologous to AlxM of Photobacterium sp. A9mC (221 amino acids) and A9mL (522 amino acids) had the highest degree of similarity to two individual alginate lyases of Vibrio splendidus with 74% and 84% identity, respectively. The other gene for alginate lyase, A1mU, was shotgun cloned from Agarivorans sp. JAM-A1m. A1mU (286 amino acids) showed the highest homology to AlyVOA of Vibrio sp. with 76% identity. All alginate lyases belong to polysaccharide lyase family 7, although, they do not show significant similarity to one another with 14% to 58% identity. Among the above lyases, the recombinant A9mT was purified to homogeneity and characterized. The molecular mass of A9mT was around 28 kDa. The enzyme was remarkably salt activated and showed the highest thermal stability in the presence of NaCl. A9mT favorably degraded mannuronate polymer in alginate. We discussed substrate specificities of family 7 alginate lyases based on their conserved amino acid sequences.
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Affiliation(s)
- Kohsuke Uchimura
- Institute of Biogeoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Japan
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