Martinez-Martinez M

References (8)

Title : Metagenomic Mining for Esterases in the Microbial Community of Los Rueldos Acid Mine Drainage Formation - Vidal_2022_Front.Microbiol_13_868839
Author(s) : Vidal P , Martinez-Martinez M , Fernandez-Lopez L , Roda S , Mendez-Garcia C , Golyshina OV , Guallar V , Pelaez AI , Ferrer M
Ref : Front Microbiol , 13 :868839 , 2022
Abstract : Acid mine drainage (AMD) systems are extremely acidic and are metal-rich formations inhabited by relatively low-complexity communities of acidophiles whose enzymes remain mostly uncharacterized. Indeed, enzymes from only a few AMD sites have been studied. The low number of available cultured representatives and genome sequences of acidophiles inhabiting AMDs makes it difficult to assess the potential of these environments for enzyme bioprospecting. In this study, using naive and in silico metagenomic approaches, we retrieved 16 esterases from the alpha/beta-hydrolase fold superfamily with the closest match from uncultured acidophilic Acidobacteria, Actinobacteria (Acidithrix, Acidimicrobium, and Ferrimicrobium), Acidiphilium, and other Proteobacteria inhabiting the Los Rueldos site, which is a unique AMD formation in northwestern Spain with a pH of -2. Within this set, only two polypeptides showed high homology (99.4%), while for the rest, the pairwise identities ranged between 4 and 44.9%, suggesting that the diversity of active polypeptides was dominated not by a particular type of protein or highly similar clusters of proteins, but by diverse non-redundant sequences. The enzymes exhibited amino acid sequence identities ranging from 39 to 99% relative to homologous proteins in public databases, including those from other AMDs, thus indicating the potential novelty of proteins associated with a specialized acidophilic community. Ten of the 16 hydrolases were successfully expressed in Escherichia coli. The pH for optimal activity ranged from 7.0 to 9.0, with the enzymes retaining 33-68% of their activities at pH 5.5, which was consistent with the relative frequencies of acid residues (from 54 to 67%). The enzymes were the most active at 30-65 degreesC, retaining 20-61% of their activity under the thermal conditions characterizing Los Rueldos (13.8 +/- 0.6 degreesC). The analysis of the substrate specificity revealed the capacity of six hydrolases to efficiently degrade (up to 1,652 +/- 75 U/g at pH 8.0 and 30 degreesC) acrylic- and terephthalic-like [including bis(2-hydroxyethyl)-terephthalate, BHET] esters, and these enzymes could potentially be of use for developing plastic degradation strategies yet to be explored. Our assessment uncovers the novelty and potential biotechnological interest of enzymes present in the microbial populations that inhibit the Los Rueldos AMD system.
ESTHER : Vidal_2022_Front.Microbiol_13_868839
PubMedSearch : Vidal_2022_Front.Microbiol_13_868839
PubMedID: 35663881
Gene_locus related to this paper: 9zzzz-t1a3k4 , 9zzzz-t1ci96 , 9zzzz-t1b379 , 9zzzz-t1be47 , 9zzzz-t1d4I7 , 9actn-KY010298 , 9bact-KY010297

Title : Genetically engineered proteins with two active sites for enhanced biocatalysis and synergistic chemo- and biocatalysis - Alonso_2020_Nat.Catal_3_319
Author(s) : Alonso S , Santiago G , Cea-Rama I , Fernandez-Lopez L , Coscolin C , Modregger J , Ressmann A , Martinez-Martinez M , Marrero H , Bargiela R , Pita M , Gonzalez-Alfonso JL , Briand M , Rojo D , Barbas C , Plou FJ , Golyshin PN , Shahgaldian P , Sanz-Aparicio J , Guallar V , Ferrer M
Ref : Nature Catalysis , 3 :319 , 2019
Abstract : Enzyme engineering has allowed not only the de novo creation of active sites catalysing known biological reactions with rates close to diffusion limits, but also the generation of abiological sites performing new-to-nature reactions. However, the catalytic advantages of engineering multiple active sites into a single protein scaffold are yet to be established. Here, we report on pro-teins with two active sites of biological and/or abiological origin, for improved natural and non-natural catalysis. The approach increased the catalytic properties, such as enzyme efficiency, substrate scope, stereoselectivity and optimal temperature window, of an esterase containing two biological sites. Then, one of the active sites was metamorphosed into a metal-complex chemocatalytic site for oxidation and Friedel-Crafts alkylation reactions, facilitating synergistic chemo- and biocatalysis in a single protein. The transformations of 1-naphthyl acetate into 1,4-naphthoquinone (conversion approx. 100%) and vinyl crotonate and benzene into 3-phenylbutyric acid (>=83%; e.e. >99.9%) were achieved in one pot with this artificial multifunc-tional metalloenzyme.
ESTHER : Alonso_2020_Nat.Catal_3_319
PubMedSearch : Alonso_2020_Nat.Catal_3_319
PubMedID:
Gene_locus related to this paper: 9bact-LAE6

Title : Determinants and prediction of esterase substrate promiscuity patterns - Martinez-Martinez_2018_ACS.Chem.Biol_13_225
Author(s) : Martinez-Martinez M , Coscolin C , Santiago G , Chow J , Stogios PJ , Bargiela R , Gertler C , Navarro-Fernandez J , Bollinger A , Thies S , Mendez-Garcia C , Popovic A , Brown G , Chernikova TN , Garcia-Moyano A , Bjergah GE , Perez-Garcia P , Hai T , Del Pozo MV , Stokke R , Steen IH , Cui H , Xu X , Nocek BP , Alcaide M , Distaso M , Mesa V , Pelaez AI , Sanchez J , Buchholz PCF , Pleiss J , Fernandez-Guerra A , Glockner FO , Golyshina OV , Yakimov MM , Savchenko A , Jaeger KE , Yakunin AF , Streit WR , Golyshin PN , Guallar V , Ferrer M
Ref : ACS Chemical Biology , 13 :225 , 2018
Abstract : Esterases receive special attention because their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others, remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps ranking (classifying) promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence datasets.
ESTHER : Martinez-Martinez_2018_ACS.Chem.Biol_13_225
PubMedSearch : Martinez-Martinez_2018_ACS.Chem.Biol_13_225
PubMedID: 29182315
Gene_locus related to this paper: 9zzzz-a0a2k8jn75 , 9zzzz-a0a2k8jt94 , 9zzzz-a0a0g3fj44 , 9zzzz-a0a0g3fh10 , 9zzzz-a0a0g3fh03 , 9bact-a0a1s5qkj8 , 9zzzz-a0a0g3feh5 , 9zzzz-a0a0g3fkz4 , 9zzzz-a0a0g3fh07 , 9zzzz-a0a0g3fh34 , 9zzzz-a0a0g3fh31 , 9bact-KY458167 , alcbs-q0vqa3 , 9bact-a0a1s5qki8 , 9zzzz-a0a0g3feq8 , 9zzzz-a0a0g3feh8 , 9zzzz-a0a0g3fh19 , 9bact-KY203037 , 9bact-a0a1s5ql22 , 9bact-a0a1s5qm34 , 9bact-KY203034 , 9bact-r9qzg0 , 9bact-a0a1s5qly8 , 9zzzz-a0a0g3fkz8 , 9zzzz-a0a0g3feg9 , 9zzzz-KY203033 , 9zzzz-a0a0g3fes4 , 9zzzz-a0a0g3fh42 , 9bact-a0a1s5qlx2 , 9zzzz-KY483651 , 9bact-a0a1s5qmh4 , 9zzzz-KY203032 , 9zzzz-EH87 , 9zzzz-a0a0g3fei1 , 9zzzz-a0a0g3fet2 , 9zzzz-KY483647 , 9zzzz-EH82 , 9zzzz-a0a0g3fe15 , 9bact-KY203031 , 9bact-t1w006 , 9zzzz-a0a0g3fet6 , 9bact-KY458164 , geoth-g8myf3 , 9bact-a0a1s5ql04 , 9gamm-a0a1y0ihk7 , 9bact-a0a1s5qly6 , 9bact-a0a1s5qkg4 , 9bact-a0a1s5qkm4 , 9gamm-s5tv80 , 9gamm-a0a0c4zhg2 , 9zzzz-t1b379 , 9gamm-KY483646 , 9bact-KY458160 , 9zzzz-a0a0g3fj57 , 9gamm-s5t8349 , 9arch-KY203036 , 9bact-KY458168 , 9zzzz-a0a0g3fes0 , 9zzzz-t1be47 , 9bact-KY458159 , 9zzzz-a0a0g3fh39 , 9bact-t1vzd5 , 9prot-EH41 , 9bact-Lip114 , alcbs-q0vt77 , 9bact-a0a1s5qke6 , 9bact-a0a1s5qkf3 , 9prot-SRP030024 , 9gamm-s5t532 , 9bact-a0a1s5qkl2 , 9bact-a0a1s5qkk8 , 9zzzz-KY203030 , 9zzzz-t1d4I7 , 9prot-KY019260 , 9bact-a0a1s5qm38 , 9arch-KY458161 , 9prot-KY010302 , 9zzzz-a0a0g3fl25 , 9actn-KY010298 , 9gamm-s5u059 , 9bact-a0a1s5qmi7 , 9bact-KY010297 , 9bact-KY483642 , 9bact-a0a1s5qkj1 , 9bact-KY010299 , 9bact-KY483648 , alcbs-q0vtl7 , 9bact-a0a1s5qf1 , 9bact-a0a1s5qkg0 , 9bact-a0a0h4tgu6 , 9bact-MilE3 , 9bact-LAE6 , 9alte-MGS-MT1 , 9bact-r9qzf7 , 9gamm-k0c6t6 , alcbs-q0vl36 , alcbs-q0vlq1 , alcbs-q0vq49 , bacsu-pnbae , canar-LipB , canan-lipasA , geost-lipas , marav-a1u5n0 , pseps-i7k8x5 , staep-GEHD , symth-q67mr3 , altma-s5cfn7 , cycsp-k0c2b8 , alcbs-q0vlk5 , 9bact-k7qe48 , 9bact-MGS-M1 , 9bact-MGS-M2 , 9bact-a0a0b5kns5 , 9zzzz-a0a0g3fej4 , 9zzzz-a0a0g3fj60 , 9zzzz-a0a0g3fej0 , 9zzzz-a0a0g3fj64 , 9bact-a0a0b5kc16 , 9zzzz-a0a0g3feg6 , 9zzzz-a0a0g3feu6

Title : Rational Engineering of Multiple Active Sites in an Ester Hydrolase - Santiago_2018_Biochemistry_57_2245
Author(s) : Santiago G , Martinez-Martinez M , Alonso S , Bargiela R , Coscolin C , Golyshin PN , Guallar V , Ferrer M
Ref : Biochemistry , 57 :2245 , 2018
Abstract : Effects of altering the properties of an active site in an enzymatic homogeneous catalyst have been extensively reported. However, the possibility of increasing the number of such sites, as commonly done in heterogeneous catalytic materials, remains unexplored, particularly because those have to accommodate appropriate residues in specific configurations. This possibility was investigated by using a serine ester hydrolase as the target enzyme. By using the Protein Energy Landscape Exploration software, which maps ligand diffusion and binding, we found a potential binding pocket capable of holding an extra catalytic triad and oxyanion hole contacts. By introducing two mutations, this binding pocket became a catalytic site. Its substrate specificity, substrate preference, and catalytic activity were different from those of the native site of the wild type ester hydrolase and other hydrolases, due to the differences in the active site architecture. Converting the binding pocket into an extra catalytic active site was proven to be a successful approach to create a serine ester hydrolase with two functional reactive groups. Our results illustrate the accuracy and predictive nature of modern modeling techniques, opening novel catalytic opportunities coming from the presence of different catalytic environments in single enzymes.
ESTHER : Santiago_2018_Biochemistry_57_2245
PubMedSearch : Santiago_2018_Biochemistry_57_2245
PubMedID: 29600855
Gene_locus related to this paper: 9bact-LAE6

Title : Functional-Based Screening Methods for Detecting Esterase and Lipase Activity Against Multiple Substrates - Reyes-Duarte_2018_Methods.Mol.Biol_1835_109
Author(s) : Reyes-Duarte D , Coscolin C , Martinez-Martinez M , Ferrer M , Garcia-Arellano H
Ref : Methods Mol Biol , 1835 :109 , 2018
Abstract : Functional screens have been extensively used for searching native enzymes or mutant variants in clone libraries. Esterases and lipases are the most retrieved enzymes, because they are within the more demanded industrial enzymes and because a number of simple and generic screening methods can be applied for their screen. Here, we describe the use of a generic pH indicator assay protocol which unambiguously allows detecting in high-throughput manner esterase and lipase activity and quantifying specific activities using an ester concentration above 0.5 mM. The described method is simple and generic to allow the selection of esterases and lipases targeting desired esters.
ESTHER : Reyes-Duarte_2018_Methods.Mol.Biol_1835_109
PubMedSearch : Reyes-Duarte_2018_Methods.Mol.Biol_1835_109
PubMedID: 30109647

Title : High Throughput Screening of Esterases, Lipases and Phospholipases in Mutant and Metagenomic Libraries: A Review - Pena-Garcia_2016_Comb.Chem.High.Throughput.Screen_19_605
Author(s) : Pena-Garcia C , Martinez-Martinez M , Reyes-Duarte D , Ferrer M
Ref : Comb Chem High Throughput Screen , 19 :605 , 2016
Abstract : Nowadays, enzymes can be efficiently identified and screened from metagenomic resources or mutant libraries. A set of a few hundred new enzymes can be found using a simple substrate within few months. Hence, the establishment of collections of enzymes is no longer a big hurdle. However, a key problem is the relatively low rate of positive hits and that a timeline of several years from the identification of a gene to the development of a process is the reality rather than the exception. Major problems are related to the time-consuming and cost-intensive screening process that only very few enzymes finally pass. Accessing to the highest possible enzyme and mutant diversity by different, but complementary approaches is increasingly important. The aim of this review is to deliver state-of-art status of traditional and novel screening protocols for targeting lipases, esterases and phospholipases of industrial relevance, and that can be applied at high throughput scale (HTS) for at least 200 distinct substrates, at a speed of more than 105 - 108 clones/day. We also review fine-tuning sequence analysis pipelines and in silico tools, which can further improve enzyme selection by an unprecedent speed (up to 1030 enzymes). If the hit rate in an enzyme collection could be increased by HTS approaches, it can be expected that also the very further expensive and time-consuming enzyme optimization phase could be significantly shortened, as the processes of enzyme-candidate selection by such methods can be adapted to conditions most likely similar to the ones needed at industrial scale.
ESTHER : Pena-Garcia_2016_Comb.Chem.High.Throughput.Screen_19_605
PubMedSearch : Pena-Garcia_2016_Comb.Chem.High.Throughput.Screen_19_605
PubMedID: 26552433

Title : Biochemical studies on a versatile esterase that is most catalytically active with polyaromatic esters - Martinez-Martinez_2014_Microb.Biotechnol_7_184
Author(s) : Martinez-Martinez M , Lores I , Pena-Garcia C , Bargiela R , Reyes-Duarte D , Guazzaroni ME , Pelaez AI , Sanchez J , Ferrer M
Ref : Microb Biotechnol , : , 2014
Abstract : Herein, we applied a community genomic approach using a naphthalene-enriched community (CN1) to isolate a versatile esterase (CN1E1) from the alpha/beta-hydrolase family. The protein shares low-to-medium identity (</= 57%) with known esterase/lipase-like proteins. The enzyme is most active at 25-30 degrees C and pH 8.5; it retains approximately 55% of its activity at 4 degrees C and less than 8% at >/= 55 degrees C, which indicates that it is a cold-adapted enzyme. CN1E1 has a distinct substrate preference compared with other alpha/beta-hydrolases because it is catalytically most active for hydrolysing polyaromatic hydrocarbon (phenanthrene, anthracene, naphthalene, benzoyl, protocatechuate and phthalate) esters (7200-21 000 units g-1 protein at 40 degrees C and pH 8.0). The enzyme also accepts 44 structurally different common esters with different levels of enantio-selectivity (1.0-55 000 units g-1 protein), including (+/-)-menthyl-acetate, (+/-)-neomenthyl acetate, (+/-)-pantolactone, (+/-)-methyl-mandelate, (+/-)-methyl-lactate and (+/-)-glycidyl 4-nitrobenzoate (in that order). The results provide the first biochemical evidence suggesting that such broad-spectrum esterases may be an ecological advantage for bacteria that mineralize recalcitrant pollutants (including oil refinery products, plasticizers and pesticides) as carbon sources under pollution pressure. They also offer a new tool for the stereo-assembly (i.e. through ester bonds) of multi-aromatic molecules with benzene rings that are useful for biology, chemistry and materials sciences for cases in which enzyme methods are not yet available.
ESTHER : Martinez-Martinez_2014_Microb.Biotechnol_7_184
PubMedSearch : Martinez-Martinez_2014_Microb.Biotechnol_7_184
PubMedID: 24418210
Gene_locus related to this paper: 9bacl-h6nd87

Title : Biochemical diversity of carboxyl esterases and lipases from lake arreo (Spain): a metagenomic approach - Martinez-Martinez_2013_Appl.Environ.Microbiol_79_3553
Author(s) : Martinez-Martinez M , Alcaide M , Tchigvintsev A , Reva O , Polaina J , Bargiela R , Guazzaroni ME , Chicote A , Canet A , Valero F , Rico Eguizabal E , Guerrero Mdel C , Yakunin AF , Ferrer M
Ref : Applied Environmental Microbiology , 79 :3553 , 2013
Abstract : The esterases and lipases from the alpha/beta hydrolase superfamily exhibit an enormous sequence diversity, fold plasticity, and activities. Here, we present the comprehensive sequence and biochemical analyses of seven distinct esterases and lipases from the metagenome of Lake Arreo, an evaporite karstic lake in Spain (42 degrees 46'N, 2 degrees 59'W; altitude, 655 m). Together with oligonucleotide usage patterns and BLASTP analysis, our study of esterases/lipases mined from Lake Arreo suggests that its sediment contains moderately halophilic and cold-adapted proteobacteria containing DNA fragments of distantly related plasmids or chromosomal genomic islands of plasmid and phage origins. This metagenome encodes esterases/lipases with broad substrate profiles (tested over a set of 101 structurally diverse esters) and habitat-specific characteristics, as they exhibit maximal activity at alkaline pH (8.0 to 8.5) and temperature of 16 to 40 degrees C, and they are stimulated (1.5 to 2.2 times) by chloride ions (0.1 to 1.2 M), reflecting an adaptation to environmental conditions. Our work provides further insights into the potential significance of the Lake Arreo esterases/lipases for biotechnology processes (i.e., production of enantiomers and sugar esters), because these enzymes are salt tolerant and are active at low temperatures and against a broad range of substrates. As an example, the ability of a single protein to hydrolyze triacylglycerols, (non)halogenated alkyl and aryl esters, cinnamoyl and carbohydrate esters, lactones, and chiral epoxides to a similar extent was demonstrated.
ESTHER : Martinez-Martinez_2013_Appl.Environ.Microbiol_79_3553
PubMedSearch : Martinez-Martinez_2013_Appl.Environ.Microbiol_79_3553
PubMedID: 23542620
Gene_locus related to this paper: 9bact-LAE6