Characterization of Alginate Lyase Gene Using a Metagenomic Library Constructed from the Gut Microflora of Abalone

Overview

Journal J Ind Microbiol Biotechnol

Publisher Oxford University Press

Specialty Biotechnology

Date 2011 Nov 11

PMID 22072436

Citations 13

Authors

Su-Jung Sim

Keun Sik Baik

Seong Chan Park

Han Na Choe

Chi Nam Seong

Tai-Sun Shin

Hee Chul Woo

Jeong-Yong Cho

Duwoon Kim

Affiliations

Soon will be listed here.

Abstract

A metagenomic fosmid library was constructed using a genomic DNA mixture extracted from the gut microflora of abalone. The library gave an alginate lyase positive clone (AlyDW) harboring a 31.7-kbp insert. The AlyDW insert consisted of 22 open reading frames (ORFs). The deduced amino acid sequences of ORFs 11-13 were similar to those of known alginate lyase genes, which are found adjacent in the genome of Klebsiella pneumoniae subsp. aerogenes, Vibrio splendidus, and Vibrio sp. belonging to the phylum Gammaproteobacteria. Among the three recombinant proteins expressed from the three ORFs, alginate lyase activity was only observed in the recombinant protein (AlyDW11) coded by ORF 11. The expressed protein (AlyDW11) had the highest alginate lyase activity at pH 7.0 and 45°C in the presence of 1 mM AgNO(3). The alginate lyase activity of ORF 11 was confirmed to be endolytic by thin-layer chromatography. AlyDW11 preferred poly(β-D: -mannuronate) as a substrate over poly(α-L: -guluronate). AlyDW11 contained three highly conserved regions, RSEL, QIH, and YFKAGVYNQ, which may act to stabilize the three-dimensional conformation and function of the alginate lyase.

Citing Articles

Determination of oligosaccharide product distributions of PL7 alginate lyases by their structural elements.

Zhang K, Li Z, Zhu Q, Cao H, He X, Zhang X Commun Biol. 2022; 5(1):782.

PMID: 35918517 PMC: 9345997. DOI: 10.1038/s42003-022-03721-1.

Exploring the Intestinal Microbiota and Metabolome Profiles Associated With Feed Efficiency in Pacific Abalone ().

Yu W, Lu Y, Shen Y, Liu J, Gong S, Yu F Front Microbiol. 2022; 13:852460.

PMID: 35369429 PMC: 8969561. DOI: 10.3389/fmicb.2022.852460.

Characterization of a New Biofunctional, Exolytic Alginate Lyase from sp. s12 with High Catalytic Activity and Cold-Adapted Features.

Yin R, Yi Y, Chen Z, Wang B, Li X, Zhou Y Mar Drugs. 2021; 19(4).

PMID: 33800691 PMC: 8065536. DOI: 10.3390/md19040191.

Characterization of a New Bifunctional and Cold-Adapted Polysaccharide Lyase (PL) Family 7 Alginate Lyase from sp.

Zhou H, Xu S, Yin X, Wang F, Li Y Mar Drugs. 2020; 18(8).

PMID: 32722647 PMC: 7460543. DOI: 10.3390/md18080388.

Microbial community and functions associated with digestion of algal polysaccharides in the visceral tract of Haliotis discus hannai: Insights from metagenome and metatranscriptome analysis.

Nam B, Jang J, Caetano-Anolles K, Kim Y, Park J, Sohn H PLoS One. 2018; 13(10):e0205594.

PMID: 30308038 PMC: 6181387. DOI: 10.1371/journal.pone.0205594.

References

Shimizu E, Ojima T, Nishita K . cDNA cloning of an alginate lyase from abalone, Haliotis discus hannai. Carbohydr Res. 2003; 338(24):2841-52. DOI: 10.1016/j.carres.2003.08.009. View

Kim S, Lee C, Kim M, Yeo Y, Yoon S, Kang H . Screening and characterization of an enzyme with beta-glucosidase activity from environmental DNA. J Microbiol Biotechnol. 2007; 17(6):905-12. View

Laemmli U . Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970; 227(5259):680-5. DOI: 10.1038/227680a0. View

Ammiraju J, Yu Y, Luo M, Kudrna D, Kim H, Goicoechea J . Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome. Theor Appl Genet. 2005; 111(8):1596-607. DOI: 10.1007/s00122-005-0091-3. View

Voget S, Steele H, Streit W . Characterization of a metagenome-derived halotolerant cellulase. J Biotechnol. 2006; 126(1):26-36. DOI: 10.1016/j.jbiotec.2006.02.011. View

NAKADA H, Sweeny P . Alginic acid degradation by eliminases from abalone hepatopancreas. J Biol Chem. 1967; 242(5):845-51. View

Li J, Dong S, Song J, Li C, Chen X, Xie B . Purification and characterization of a bifunctional alginate lyase from Pseudoalteromonas sp. SM0524. Mar Drugs. 2011; 9(1):109-23. PMC: 3039154. DOI: 10.3390/md9010109. View

Suenaga H, Ohnuki T, Miyazaki K . Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Environ Microbiol. 2007; 9(9):2289-97. DOI: 10.1111/j.1462-2920.2007.01342.x. View

Baron A, Wong T, Hicks S, Gacesa P, Willcock D, McPherson M . Alginate lyase from Klebsiella pneumoniae, subsp. aerogenes: gene cloning, sequence analysis and high-level production in Escherichia coli. Gene. 1994; 143(1):61-6. DOI: 10.1016/0378-1119(94)90605-x. View

10.

Treusch A, Kletzin A, Raddatz G, Ochsenreiter T, Quaiser A, Meurer G . Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea. Environ Microbiol. 2004; 6(9):970-80. DOI: 10.1111/j.1462-2920.2004.00663.x. View

11.

Lopez-Garcia P, Brochier C, Moreira D, Rodriguez-Valera F . Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ Microbiol. 2003; 6(1):19-34. DOI: 10.1046/j.1462-2920.2003.00533.x. View

12.

Green 3rd F, Clausen C, Highley T . Adaptation of the Nelson-Somogyi reducing-sugar assay to a microassay using microtiter plates. Anal Biochem. 1989; 182(2):197-9. DOI: 10.1016/0003-2697(89)90578-2. View

13.

Miyake O, Ochiai A, Hashimoto W, Murata K . Origin and diversity of alginate lyases of families PL-5 and -7 in Sphingomonas sp. strain A1. J Bacteriol. 2004; 186(9):2891-6. PMC: 387801. DOI: 10.1128/JB.186.9.2891-2896.2004. View

14.

Quaiser A, Ochsenreiter T, Klenk H, Kletzin A, Treusch A, Meurer G . First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol. 2002; 4(10):603-11. DOI: 10.1046/j.1462-2920.2002.00345.x. View

15.

Malissard M, Duez C, GUINAND M, Vacheron M, Michel G, Marty N . Sequence of a gene encoding a (poly ManA) alginate lyase active on Pseudomonas aeruginosa alginate. FEMS Microbiol Lett. 1993; 110(1):101-6. DOI: 10.1111/j.1574-6968.1993.tb06302.x. View

16.

Shimokawa T, Yoshida S, Kusakabe I, Takeuchi T, Murata K, Kobayashi H . Some properties and action mode of (1-->4)-alpha-L-guluronan lyase from Enterobacter cloacae M-1. Carbohydr Res. 1998; 304(2):125-32. DOI: 10.1016/s0008-6215(97)00230-9. View

17.

Gordon D, Abajian C, Green P . Consed: a graphical tool for sequence finishing. Genome Res. 1998; 8(3):195-202. DOI: 10.1101/gr.8.3.195. View

18.

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. Mar Biotechnol (NY). 2009; 12(5):526-33. DOI: 10.1007/s10126-009-9237-7. View

19.

Maki H, Mori A, Fujiyama K, Kinoshita S, Yoshida T . Cloning, sequence analysis and expression in Escherichia coli of a gene encoding an alginate lyase from Pseudomonas sp. OS-ALG-9. J Gen Microbiol. 1993; 139(5):987-93. DOI: 10.1099/00221287-139-5-987. View

20.

Iwamoto M, Kurachi M, Nakashima T, Kim D, Yamaguchi K, Oda T . Structure-activity relationship of alginate oligosaccharides in the induction of cytokine production from RAW264.7 cells. FEBS Lett. 2005; 579(20):4423-9. DOI: 10.1016/j.febslet.2005.07.007. View