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 |