Bacterial lipolytic enzymes: classification and properties

ARPIGNY, Jean Louis; Jaeger, Karl‐Erich

doi:10.1042/0264-6021:3430177

Cited by 540 publications

(575 citation statements)

References 51 publications

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“…Lip5.1_5, Lip5.3_3, Lip5.5_4, Lip5.13_3, Lip5.14_3, and Lip5.19_3 belong to family IV, Lip5.13_1 to family V, and Lip5.11_3 and Lip5.15_3 to family VIII. The products of the Lip5.7_2 and Lip5.12_2 loci could not be assigned to any esterase family described by Arpigny and Jaeger (37) or to either of the novel families EstA (39) and LipG (16). However, these locus products could be assigned to the Pfam alpha/beta-hydrolase family (subfamilies 6 and 5, respectively), which contains numerous esterases.…”

Section: Resultsmentioning

confidence: 84%

“…Putative esterase loci were assigned to four carboxylesterase families by amino acid sequence alignment (data not shown). Lip5.8_1 shows sequence similarity to members of bacterial esterase family II (37,38). Lip5.1_5, Lip5.3_3, Lip5.5_4, Lip5.13_3, Lip5.14_3, and Lip5.19_3 belong to family IV, Lip5.13_1 to family V, and Lip5.11_3 and Lip5.15_3 to family VIII.…”

Section: Resultsmentioning

confidence: 99%

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Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Martin

Biver

Steels

et al. 2014

Appl Environ Microbiol

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A metagenomic library was constructed from microorganisms associated with the brown alga Ascophyllum nodosum. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci. Sequence and gene cluster analysis showed the wide diversity of the identified enzymes and gave an idea of the microbial populations present during the sample collection period. Lastly, an endo-␤-1,4-glucanase having less than 50% identity to sequences of known cellulases was purified and partially characterized, showing activity at low temperature and after prolonged incubation in concentrated salt solutions. Previous surveys have revealed that less than 1% of existing microorganisms can be studied by traditional culturing methods. This leaves most microorganisms and their by-products unknown and unexploited (1, 2) and explains why metagenomics, a culture-independent approach using total microbial genomes from environmental samples, has met with great success over the past decade (3, 4). Sequence-based metagenomics has already provided information about the composition, organization, function, and hierarchy of microbial communities in particular habitats (5). On the other hand, functional genomics applied to metagenomic libraries from diverse environments has led to the discovery of many new enzymes and bioactive compounds and to substantial enrichment of genome databases. To date, most of the enzymes brought to light through metagenomics have been derived from soil (6-9) and gut (10-13) samples.Marine microorganisms represent promising candidate sources of original biocatalysts, as they are exposed to extreme conditions of temperature, pressure, salinity, nutrient availability, etc. Hence, functional screening of marine microbial populations should yield new enzymes with specific and unique physiological and biochemical properties, produced by organisms far different from those usually described in terrestrial environments (14). New enzymes have already been identified in marine metagenomic libraries from seawater samples (15, 16) and from microorganisms in symbiosis with marine organisms such as sponges and corals (17). To our knowledge, however, nobody has yet performed functional screening of metagenomic libraries from algal microbial communities. As algal microbial biofilms are in constant interaction with algal biomass, they represent an interesting source of enzymes and other active compounds (18). Sequence-based studies have already revealed the importance and functions of microbial communities living on the surfaces of algae, showing tight interdependence between algae and their biofilms (19-21). Furthermore, many genes coding for enzymes involved in hydrolyzing algal biomass, such as cellulases, xylanases, ␣-amylases, and specific algal polysaccharidases (e.g., agarases, carrageenases, and alginate lyases), have been identified from cultivable marine bacteria (22,23). Only a few such enzymes have been found in marine metagenomes by functional screening. For example, no cellulase gene...

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Section: Resultsmentioning

confidence: 84%

Section: Resultsmentioning

confidence: 99%

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Martin

Biver

Steels

et al. 2014

Appl Environ Microbiol

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“…H55-G56-G57-G58-Y59 Possibly IV a Consensus GXSXG-lipase motifs are given for families (46)(47)(48). Family IV, GDSAGG; family VI, NGGPG.…”

Section: Metagenome Library Construction and Screening For Carboxyl Ementioning

confidence: 99%

“…The selected ␣/␤ hydrolases contain a classical Ser-Asp-His catalytic triad, but the catalytic elbow and oxyanion hole [i.e., the GXSXGG and H/N-GGG(A)/P-X motifs] often diverged from the consensus, as revealed by sequence analysis (Table 1). Nonetheless, the degree of sequence conservation among these catalytic motifs and in the overall enzyme sequence was sufficient to categorize the enzymes into the following two esterase/lipase subfamilies (46)(47)(48): family VI (MGS-RG1 and MGS-RG2) and family IV (MGS-RG3) (see Fig. S2 in the supplemental material).…”

Section: Metagenome Library Construction and Screening For Carboxyl Ementioning

confidence: 99%

Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics

Alcaide

Tchigvintsev

Martínez-Martínez

et al. 2015

Appl Environ Microbiol

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iThe shrimp Rimicaris exoculata dominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting the R. exoculata gill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (<52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera of Proteobacteria related to Thiothrix/Leucothrix (MGS-RG1/RG2) and to the Rhodobacteraceae group (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with ester substrates (<356 U mg ؊1 ) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low optimal temperature (30°C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50°C and were salt activated and barotolerant. They also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities. Metagenomics provides a means for the discovery of entirely new enzymes in microorganisms and their communities without the need to culture these microorganisms as individual species, which is technically very difficult (1-5). Although the discovery of new enzyme activities has progressed considerably (6), it has not managed to go beyond the effective identification of enzymatic activities at a rather limited number of environmental sites. While an extensive search in the specialized literature and public databases indicated that microbial communities from approximately 1,800 different sites worldwide have been examined for their genomic content, only in approximately 200 of those locations (11% of the total) have new active clones or enzymes been identified and/or partially characterized. Thus, only a tiny fraction of the Earth's biosphere has been explored for the purpose of enzyme discovery, despite the fact that natural microbial diversity has been recognized to be the major source of new microbes (7). Such diversity also contains novel genes and functions (8) whose activities remain mostly unknown but whose potential to contribute to an innovation-based economy is recognized (9, 10).One of the habitats less explored to date in terms of examining enzyme repertoires is the deep-sea realm, where...

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“…3). 41,42 This group contains the Class C b-lactamases and a number of b-lactamase like proteins, though the exact function of many of these proteins has yet to be biochemically determined.…”

Section: Analysis Of the Abgt Genementioning

confidence: 99%

Inhibition of the growth ofBacillus subtilisDSM10 by a newly discovered antibacterial protein from the soil metagenome

et al. 2015

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(2015) Inhibition of the growth of Bacillussubtilis DSM10 by a newly discovered antibacterial protein from the soil metagenome, Bioengineered, 6:2, 89-98, DOI: 10.1080/21655979.2015 A functional metagenomics based approach exploiting the microbiota of suppressive soils from an organic field site has succeeded in the identification of a clone with the ability to inhibit the growth of Bacillus subtilis DSM10. Sequencing of the fosmid identified a putative b-lactamase-like gene abgT. Transposon mutagenesis of the abgT gene resulted in a loss in ability to inhibit the growth of B. subtilis DSM10. Further analysis of the deduced amino acid sequence of AbgT revealed moderate homology to esterases, suggesting that the protein may possess hydrolytic activity. Weak lipolytic activity was detected; however the clone did not appear to produce any b-lactamase activity. Phylogenetic analysis revealed the protein is a member of the family VIII group of lipase/esterases and clusters with a number of proteins of metagenomic origin. The abgT gene was sub-cloned into a protein expression vector and when introduced into the abgT transposon mutant clones restored the ability of the clones to inhibit the growth of B. subtilis DSM10, clearly indicating that the abgT gene is involved in the antibacterial activity. While the precise role of this protein has yet to fully elucidated, it may be involved in the generation of free fatty acid with antibacterial properties. Thus functional metagenomic approaches continue to provide a significant resource for the discovery of novel functional proteins and it is clear that hydrolytic enzymes, such as AbgT, may be a potential source for the development of future antimicrobial therapies.

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Bacterial lipolytic enzymes: classification and properties

Cited by 540 publications

References 51 publications

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics

Inhibition of the growth ofBacillus subtilisDSM10 by a newly discovered antibacterial protein from the soil metagenome

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