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Covington JK, Torosian N, Cook AM, Palmer M, Bryan SG, Nou NO, Mewalal R, Harmon-Smith M, Blaby IK, Cheng JF, Hess M, Brumm PJ, Singh NK, Venkateswaran K, Hedlund BP. Biochemical characterization of Fsa16295Glu from "Fervidibacter sacchari," the first hyperthermophilic GH50 with β-1,3-endoglucanase activity and founding member of the subfamily GH50_3. Front Microbiol 2024; 15:1355444. [PMID: 38725686 PMCID: PMC11079163 DOI: 10.3389/fmicb.2024.1355444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
The aerobic hyperthermophile "Fervidibacter sacchari" catabolizes diverse polysaccharides and is the only cultivated member of the class "Fervidibacteria" within the phylum Armatimonadota. It encodes 117 putative glycoside hydrolases (GHs), including two from GH family 50 (GH50). In this study, we expressed, purified, and functionally characterized one of these GH50 enzymes, Fsa16295Glu. We show that Fsa16295Glu is a β-1,3-endoglucanase with optimal activity on carboxymethyl curdlan (CM-curdlan) and only weak agarase activity, despite most GH50 enzymes being described as β-agarases. The purified enzyme has a wide temperature range of 4-95°C (optimal 80°C), making it the first characterized hyperthermophilic representative of GH50. The enzyme is also active at a broad pH range of at least 5.5-11 (optimal 6.5-10). Fsa16295Glu possesses a relatively high kcat/KM of 1.82 × 107 s-1 M-1 with CM-curdlan and degrades CM-curdlan nearly completely to sugar monomers, indicating preferential hydrolysis of glucans containing β-1,3 linkages. Finally, a phylogenetic analysis of Fsa16295Glu and all other GH50 enzymes revealed that Fsa16295Glu is distant from other characterized enzymes but phylogenetically related to enzymes from thermophilic archaea that were likely acquired horizontally from "Fervidibacteria." Given its functional and phylogenetic novelty, we propose that Fsa16295Glu represents a new enzyme subfamily, GH50_3.
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Affiliation(s)
| | - Nicole Torosian
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Allison M. Cook
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Scott G. Bryan
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Nancy O. Nou
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Ritesh Mewalal
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Miranda Harmon-Smith
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ian K. Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Matthias Hess
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | | | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
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Zhang M, Wang J, Zeng R, Wang D, Wang W, Tong X, Qu W. Agarose-Degrading Characteristics of a Deep-Sea Bacterium Vibrio Natriegens WPAGA4 and Its Cold-Adapted GH50 Agarase Aga3420. Mar Drugs 2022; 20:692. [PMID: 36355015 PMCID: PMC9698624 DOI: 10.3390/md20110692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 11/23/2023] Open
Abstract
Up until now, the characterizations of GH50 agarases from Vibrio species have rarely been reported compared to GH16 agarases. In this study, a deep-sea strain, WPAGA4, was isolated and identified as Vibrio natriegens due to the maximum similarity of its 16S rRNA gene sequence, the values of its average nucleotide identity, and through digital DNA-DNA hybridization. Two circular chromosomes in V. natriegens WPAGA4 were assembled. A total of 4561 coding genes, 37 rRNA, 131 tRNA, and 59 other non-coding RNA genes were predicted in the genome of V. natriegens WPAGA4. An agarase gene belonging to the GH50 family was annotated in the genome sequence and expressed in E. coli cells. The optimum temperature and pH of the recombinant Aga3420 (rAga3420) were 40 °C and 7.0, respectively. Neoagarobiose (NA2) was the only product during the degradation process of agarose by rAga3420. rAga3420 had a favorable stability following incubation at 10-30 °C for 50 min. The Km, Vmax, and kcat values of rAga3420 were 2.8 mg/mL, 78.1 U/mg, and 376.9 s-1, respectively. rAga3420 displayed cold-adapted properties as 59.7% and 41.2% of the relative activity remained at 10 3 °C and 0 °C, respectively. This property ensured V. natriegens WPAGA4 could degrade and metabolize the agarose in cold deep-sea environments and enables rAga3420 to be an appropriate industrial enzyme for NA2 production, with industrial potential in medical and cosmetic fields.
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Affiliation(s)
- Mengyuan Zhang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Runying Zeng
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China
| | - Dingquan Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Wenxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Xiufang Tong
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
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Jiang C, Zhang T, Xu Y, Mao X. Characterization of a GH50 β-Agarase: A Biotechnological Tool for Preparing Oligosaccharides from Agarose and Porphyran. J Agric Food Chem 2022; 70:9931-9940. [PMID: 35866448 DOI: 10.1021/acs.jafc.2c02107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Agarase is of vital significance for functional agaro-oligosaccharides production from algal dived agarose. Especially, the exolytic agarases have the advantage of obtaining agaro-oligosaccharides with a specific degree of polymerization. Herein, we cloned and expressed a novel glycoside hydrolase (GH) 50 family β-agarase OUC-PgJC50 from Photobacterium gaetbulicola. The degradation pattern analysis indicated that OUC-PgJC50 not only showed an exolytic activity with main products of neoagarotetraose from hydrolyzing agarose but also show a hydrolytic activity to transform neoagarotetraose into neoagarobiose. This is the first time that the discovery of a neoagarotetraose-producing exolytic GH50 β-agarase possesses the activity to transform neoagarotetraose into neoagarobiose, which provided new insight into the recognition of the degradation mode of agarases. Molecular docking and sequence alignment analysis further revealed the His654 residue in OUC-PgJC50 may play a vital role in forming a strong force with l-AHG residue at -4 subsite that helps to produce neoagarotetraose from catalyzing agarose. Moreover, the catalytic ability of OUC-PgJC50 toward another agar polysaccharide porphyran was also described that could hydrolyze porphyran into sulfated oligosaccharides, in which the LA6S-d-Gal was the main products. This study is of vital significance for developing the application range of GH50 β-agarases.
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Affiliation(s)
- Chengcheng Jiang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Tianyu Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yuxian Xu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Dong C, Lin B, Song Y, Peng T, Zhong M, Li J, Hu Z. Characterization and activity enhancement of a novel exo-type agarase Aga575 from Aquimarina agarilytica ZC1. Appl Microbiol Biotechnol 2021; 105:8287-8296. [PMID: 34605970 DOI: 10.1007/s00253-021-11553-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/22/2021] [Accepted: 08/25/2021] [Indexed: 01/14/2023]
Abstract
The novel β-agarase gene aga575 from the agarolytic bacterium Aquimarina agarilytica ZC1 is composed of 2142 bp, and the encoded protein Aga575 has the highest amino acid sequence homology of only 65.2% with known agarases. Though carrying a domain of glycoside hydrolase family 42 in the C-terminal, Aga575 should belong to glycoside hydrolase family 50 according to the phylogenetic analysis. Gene aga575 was successfully cloned and overexpressed in Escherichia coli Rosetta (DE3) cells. The recombinant protein had the maximal agarase activity at pH 8.0 and 37 °C. The values Km and Vmax toward agarose were 8.4 mg/mL and 52.2 U/mg, respectively. Aga575 hydrolyzed agarose and neoagarooligosaccharides to yield neoagarobiose as the sole product. The agarose hydrolysis pattern of Aga575 indicated that it was an exo-type β-agarase. Random mutagenesis was carried out to obtain two beneficial mutants M1 (R534G) and M2 (S4R-R424G) with higher activities. The results showed that the agarase activity of mutant M1 and M2 reached 162% and 192% of the wild-type agarase Aga575, respectively. Moreover, the activity of the mixed mutant M1/M2 (S4R-R424G-R534G) increased to 227%. KEY POINTS: • Aga575 is a novel exo-type β-agarase degrading agarose to yield neoagarobiose as the sole product. • Though owning a domain of glycoside hydrolase family GH42, Aga575 should belong to family GH50. • The agarase activity of one mutant increased to 227% of the wild-type Aga575.
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Affiliation(s)
- Chaonan Dong
- Department of Biology, Shantou University, Shantou, 515063, China
| | - Bokun Lin
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, China.
| | - Yan Song
- Department of Biology, Shantou University, Shantou, 515063, China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, 515063, China
| | - Mingqi Zhong
- Department of Biology, Shantou University, Shantou, 515063, China
| | - Jin Li
- Department of Biology, Shantou University, Shantou, 515063, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, 515063, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China.
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