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. 2015 Jun 30;6:672. doi: 10.3389/fmicb.2015.00672

Table 1.

Some novel enzymes of industrial interest discovered through functional metagenomics.

Enzyme Closest known homolog Method/Host Environment References
Four lipolytic enzymes Moderate identity (<50%) to lipolytic proteins from Streptomyces, Moraxella, Acinetobacter, and Sulfolobus sp. Activity based screening of E. coli plasmid library Soil from a meadow, a sugar beet field and the Nieme River valley, Germany Henne et al., 2000
Low pH, thermostable α-amylase High sequence similarity to α-amylase of Pyrococcus sp. KOD1 Function-based screening of E. coli plasmid library followed by expression of gene of interest in Pseudomonas fluorescens for functional evaluation Deep sea and acid soil Richardson et al., 2002
12 esterases, 9 endo-β-1,4-glucanases, and 1 cyclodextrinase Various putative source organisms Functional screening of lambda phage library transformed into E. coli Rumen of dairy cow Ferrer et al., 2005b
Three ß-glucanases Low sequence identities to known ß-glucanases. Other sequences present in one of the inserts showed identity to Bacteroides sp. Function-based screening of E. coli BAC library Large bowel of mouse Walter et al., 2005
β-agarase 77% identity to corresponding protein in Pseudoalteromonas atlantica Activity based screening of E. coli plasmid library Soil Voget et al., 2003
Two esterases One esterase showed 83% identity to metagenome-derived EstA3 (AAZ48934) and 59% identity to a betalactamase (YP_003266771) of Haliangium ochraceum DSM 14365. The other esterase showed 37% identity to a hypothetical protein from Neisseria elongata Activity based screening of two separate libraries: (plasmid and fosmid) transformed into E. coli Soil Water Ouyang et al., 2013
Two esterases One esterase showed 51% identity to a class C ß-lactamase from Burkholderia pseudomallei and was also 61% similar and 45% identical to a functional esterase (AAF59826) from Burkholderia gladioli. Second esterase showed 59% identity to a ß-lactamase from Sphingopyxis alaskensis Activity based screening of two E. coli cosmid libraries Soil Drinking water Elend et al., 2006
Esterase Unidentified mesophilic soil microbe Activity based screening of E. coli plasmid library Environmental soil samples: mudflats, beaches, forests Kim et al., 2006
Thermostable esterase 64% similarity to an enzyme from Pyrobaculum calidifontis Activity based screening of E. coli fosmid library Mud Sediment-rich water Rhee et al., 2005
Two esterases One esterase showed highest identity (64.9%) to a putative esterase (YP_220901) from Brucella abortus biovar 1. The other esterase showed highest identity (40.4%) to a putative esterase (ZP_01658665) from Parvibaculum lavamentivorans Activity based screening of E. coli BAC library Surface seawater, South China Sea Chu et al., 2008
Six lipolytic clones The six clones individually showed highest identity to the following proteins: (i) Esterase/lipase (ZP_00034241), Burkholderia fungorum, (ii) Thermophilic carboxylesterase (1EVQA), Alicyclobacillus acidocaldarius (iii) Thermophilic carboxylesterase (1EVQA), A. acidocaldarius (iv) Esterase/lipase (ZP_00034303), B. fungorum (v) Esterase/lipase (ZP_00034303), B. fungorum (vi) Esterase HDE (BAA82510), petroleum-degrading bacterium HD-1 Activity based screening of E. coli fosmid library Forest topsoil Lee et al., 2004
Cellulase (β-glucosidase activity) Low sequence identity to Plasmodium and Borrelia species Function-based screening of E. coli library Soil Jiang et al., 2009
Glycosyl hydrolase >60% identity to β-1-4-endoglucanase from Prevotella bryantii B14 (AAC97596) and β-1-4-xylanase from Prevotella ruminicola 23 (AAC36862). 100% identity to a partial sequence (AAB20175) of the N terminus B14 enzyme from P. bryantii. Functional screening of lambda phage library transformed into E. coli Cow rumen fluid Palackal et al., 2007
137 nitrilase genes (Relevant in fine chemical synthesis in drug manufacture) Varying degrees of amino acid sequence similarity to proteins from several sequence clades within the nitrilase subfamily A phagemid library expressed in E. coli screened by selection for the ability to grow on a nitrile substrate Soil Water Robertson et al., 2004
Halotolerant and moderately thermostable tannase New member of tannase superfamily Activity-based screening of E. coli plasmid library Cotton field soil Yao et al., 2011
Three carboxylic ester hydrolases 77% amino acid identity to lipolytic enzyme (AEM45126) from German forest soil-derived metagenomic library Activity-based screening of E. coli plasmid library Forest soil Biver and Vandenbol, 2013
Alkaline serine protease Most closely related to an alkaline protease isolated from Bacillus sp. Activity-based screening of IPTG-inducible vector library expressed in E. coli Forest soil Biver et al., 2013a
Fibrinolytic metalloprotease (zinc-dependent) Amino acid sequence showed 46% identity to metallopeptidase from Dechloromonas aromatica (AAZ45577) Activity-based screening of E. coli fosmid library Mud, Korean west coast Lee et al., 2007
Two serine proteases First novel protease: 52% amino acid identity to a thermophilic alkaline protease from Geobacillus stearothermophillus (AAK29176). Second novel protease: 51% sequence identity with a putative protease of Bacillus sphaericus (CAB46075) Activity-based screening of E. coli plasmid and fosmid libraries Surface sand from Gobi and Death Valley deserts Neveu et al., 2011
Alkaline serine protease 98% sequence similarity with uncharacterized proteases of various Shewanella sp. Activity-based screening of E. coli plasmid library Goat skin surface Pushpam et al., 2011
Cold-active lipase 91% identity to a known lipase from Pseudomonas fluorescens B68 (AY694785) Activity based screening of E. coli cosmid library Oil-contaminated soil, Northern Germany Elend et al., 2007
Moderately thermostable (and thermally activated) lipase Acidobacteria phylum Activity based screening of E. coli fosmid library Soil, Brazilian Atlantic Forest Faoro et al., 2012
Five esterases Two did not show significant sequence identity to known esterases, the remaining genes showed low to moderate identity to known esterases Activity based screening of E. coli phagemid vector library Brine: seawater interface, Uranian hypersaline basin Ferrer et al., 2005a
Thermostable family VII esterase with high stability in organic solvents 45% identity to Haliangium ochraceum DSM 14365 (ACY17267) Activity based screening of E. coli fosmid library Compost Kang et al., 2011
Alkaline-stable family IV lipase 83% identity with a cold-active esterase from a deep-sea metagenomic library (ADA70028). 59% identity with an esterase from Vibrio splendidus LGP32 (YP_002394831) Activity based screening of E. coli plasmid library Marine sediment, South China Sea Peng et al., 2014
Protease-insensitive feruloyl esterase 56% identity to predicted esterase from Eubacterium siraeum V10Sc8a (CBL34630). 55% identity to predicted esterase from E. siraeum (CBK96609) Function-based screening of E. coli fosmid library China Holstein cow rumen Cheng et al., 2012a
Xylanase 44% identity to glycoside hydrolase family protein from Clostridium thermocellum ATCC 27405 (YP001038252) Function-based screening of E. coli fosmid library China Holstein cow rumen Cheng et al., 2012b
Two UDP glycotransferase (UGT) genes. One is a novel macroside glycotransferase (MGT) The first one is weakly similar (71% similarity) to hypothetical UGT from Fibrisoma limi. The second one is highly similar to a hypothetical MGT from Bacillus thuringiensis Thin layer chromatography (TLC)-based functional screening of E. coli fosmid library Elephant feces, Hagenbeck Zoo, Germany. Tidal flat sediment, Elbe river, Germany. Rabausch et al., 2013
Cold-adapted ß-galactosidase Highest percentage identities to β-galactosidases from Planococcus sp. “SOS Orange” (39%), Planococcus sp. L4 (39%), and Bacillus halodurans C-125 (39%) Function-based screening of E. coli plasmid library followed by expression of gene of interest in Pichia pastoris for analysis and characterization Topsoil samples, Daqing oil field, Heilongjiang Province in China Wang et al., 2010
Cold-active ß-galactosidase 53% identity to β-galactosidases from Clostridium hathewayi Function-based screening of E. coli plasmid library. Ikaite columns SW Greenland Vester et al., 2014
ß-galactosidase Not available Function-based screening of E. coli plasmid library followed by expression of gene of interest in Pichia pastoris for functional evaluation Not available Wang et al., 2012
11 amidase genes (Three novel) Three novel amidases: the first showed highest identity (54%) to putative isochorismatase hydrolase from Streptomyces sp. strain AA4; the second showed 45% primary amino acid sequence identity with a hypothetical protein (further information not available); the third showed 57% primary amino acid sequence identity with a protein that contains a transmembrane ABC transporter signature motif and possibly encodes a polypeptide with amidase activity PIGEX-based screening of benzoate-responsive sensor plasmid library transformed into E. coli Activated sludge from aeration tank of a coke plant; wastewater treatment plant, Japan Uchiyama and Miyazaki, 2010
Periplasmic α-amylase 100% similarity with malS gene in E. coli (X58994.1) PIGEX-based screening of maltose-induced plasmid library transformed into E. coli Cow dung, India Pooja et al., 2015
37 genes with lipolytic activity 29–90% sequence identity to known and putative proteins from numerous different species, including uncultured bacteria Activity based screening of E. coli plasmid and fosmid libraries Forest soil, Germany Nacke et al., 2011