Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms

Uria, Agustinus Robert; Zilda, Dewi Seswita

doi:10.1016/bs.afnr.2016.05.001

Cited by 12 publications

(10 citation statements)

References 86 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the programs to search for novel hydrolytic enzymes, we investigated the uncultured symbiotic microbiome of an Indonesian marine sponge collected in Kapoposang Island through functional metagenomic approach.This functional metagenomics was particularly directed on detection of the expressed amylases encoded on the microbiomes metagenome. Therefore the success of this approach depends on the compatibility of the cloned genes with the expression machinery of the heterologous host E. coli (Uria & Zilda, 2016).…”

Section: Resultsmentioning

confidence: 99%

“…The general approach of searching for microbial enzymes with desired activities is screening of natural diversity for hitherto unknown enzymes based on traditional cultivation-dependent microbiological methods that generally consist of isolation of pure cultures, screening of microbial isolates expressing desired enzymatic activity, characterization of the isolated enzymes of interest, and optimizing the enzyme production and recovery (Lämmle et al, 2007;Uria & Zilda, 2016). The fact that the vast majority of symbiotic bacterial consortia of marine sponges are amenable to cultivation (Amann et al, 1995;Hugenholtz et al, 1998;Webster and Hill, 2001) has encouraged us to employ cultivation-independent approach, called metagenomics, to gain access to hydrolytic enzymes produced by uncultured bacterial symbionts.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Metagenomics-Based Cloning of Amilase-Encoding Genes from the Uncultured Symbiotic Bacteria of a Marine Sponge Theonella swinhoei from Kapoposang Island, South Sulawesi

Priyono

Zilda²,

Kusnadi³

et al. 2017

Squalen Bull. Marine Fisheries Postharvest Biotech.

View full text Add to dashboard Cite

Marine sponges have recently been recognized as the source of enzymes, including members of hydrolases. Hydrolytic enzymes are extracellularly produced by sponge-associated bacteria to mediate the metabolism of complex organic matters, there by assisting the sponge hosts in nutrition and metabolic processes. Among hydrolytic enzymes, amilases has attracted increasing attention due to their potential industrial applications. This research work was aimed to utilize functional metagenomics approach for the discovery of amilases derived from the uncultured symbiotic bacteria of the Indonesian marine sponge Theonella swinhoei. W e initially constructed a small-insert metagenomic library in Escherichia coli by cloning of metagenome in the size range of 5-20 kb prepared from the sponge's microbiome. Further functional screening of the resulting metagenomic library led to the isolation of two recombinant E. coli clones potentially harboring amilase genes, as indicated by the presence of clearing zones surrounding the selective medium containing 1% amilum.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Metagenomics-Based Cloning of Amilase-Encoding Genes from the Uncultured Symbiotic Bacteria of a Marine Sponge Theonella swinhoei from Kapoposang Island, South Sulawesi

Priyono

Zilda²,

Kusnadi³

et al. 2017

Squalen Bull. Marine Fisheries Postharvest Biotech.

View full text Add to dashboard Cite

show abstract

“…In the microbial community, the numbers of uncultured microorganisms (99% or more) greatly exceeds that of culturable microorganisms (1% or less) [14,15]. Using the metagenomics technique microbial genes from diverse environments without cultivable technology can be directly obtained [16,17].…”

Section: Introductionmentioning

confidence: 99%

Simultaneous Enhancement of Thermostability and Catalytic Activity of a Metagenome-Derived β-Glucosidase Using Directed Evolution for the Biosynthesis of Butyl Glucoside

Yin

Hui

Kashif

et al. 2019

IJMS

View full text Add to dashboard Cite

Butyl glucoside synthesis using bioenzymatic methods at high temperatures has gained increasing interest. Protein engineering using directed evolution of a metagenome-derived β-glucosidase of Bgl1D was performed to identify enzymes with improved activity and thermostability. An interesting mutant Bgl1D187 protein containing five amino acid substitutions (S28T, Y37H, D44E, R91G, and L115N), showed catalytic efficiency (kcat/Km of 561.72 mM−1 s−1) toward ρ-nitrophenyl-β-d-glucopyranoside (ρNPG) that increased by 23-fold, half-life of inactivation by 10-fold, and further retained transglycosidation activity at 50 °C as compared with the wild-type Bgl1D protein. Site-directed mutagenesis also revealed that Asp44 residue was essential to β-glucosidase activity of Bgl1D. This study improved our understanding of the key amino acids of the novel β-glucosidases and presented a raw material with enhanced catalytic activity and thermostability for the synthesis of butyl glucosides.

show abstract

“…In the microbial community, only 1% or fewer microorganisms can be cultured in a medium [ 22 , 23 ], while the rest are uncultivable [ 24 ]. Metagenomics has been an advanced methodology, which involves successful extraction of whole genomic DNA from the environment, construction of metagenomic libraries, and screening for novel functional genes and/or biologically active compounds [ 25 , 26 ].…”

Section: Introductionmentioning

confidence: 99%

Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms

Gao

Zhao

et al. 2017

PLoS ONE

View full text Add to dashboard Cite

L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named ldc1E was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs. Multiple sequence alignment analysis revealed that Ldc1E contained a highly conserved motif Ser-X-His-Lys (Pxl), and molecular docking results showed that this motif was located in the active site and could combine with the cofactor pyridoxal 5′-phosphate. The ldc1E gene was subcloned into the pET-30a(+) vector and highly expressed in Escherichia coli BL21 (DE3) pLysS. The recombinant protein was purified to homogeneity. The maximum activity of Ldc1E occurred at pH 6.5 and 40°C using L-lysine monohydrochloride as the substrate. Recombinant Ldc1E had apparent Km, kcat, and kcat/Km values of 1.08±0.16 mM, 5.09±0.63 s−1, and 4.73×103 s−1 M−1, respectively. The specific activity of Ldc1E was 1.53±0.06 U mg−1 protein. Identifying a metagenome-derived LDC gene provided a rational reference for further gene modifications in industrial applications.

show abstract

Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms

Cited by 12 publications

References 86 publications

Metagenomics-Based Cloning of Amilase-Encoding Genes from the Uncultured Symbiotic Bacteria of a Marine Sponge Theonella swinhoei from Kapoposang Island, South Sulawesi

Metagenomics-Based Cloning of Amilase-Encoding Genes from the Uncultured Symbiotic Bacteria of a Marine Sponge Theonella swinhoei from Kapoposang Island, South Sulawesi

Simultaneous Enhancement of Thermostability and Catalytic Activity of a Metagenome-Derived β-Glucosidase Using Directed Evolution for the Biosynthesis of Butyl Glucoside

Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms

Contact Info

Product

Resources

About