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The Mobility of the Cap Domain Is Essential for the Substrate Promiscuity of a Family IV Esterase from Sorghum Rhizosphere Microbiome. Appl Environ Microbiol 2023; 89:e0180722. [PMID: 36602332 PMCID: PMC9888213 DOI: 10.1128/aem.01807-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Metagenomics offers the possibility to screen for versatile biocatalysts. In this study, the microbial community of the Sorghum bicolor rhizosphere was spiked with technical cashew nut shell liquid, and after incubation, the environmental DNA (eDNA) was extracted and subsequently used to build a metagenomic library. We report the biochemical features and crystal structure of a novel esterase from the family IV, EH0, retrieved from an uncultured sphingomonad after a functional screen in tributyrin agar plates. EH0 (optimum temperature [Topt], 50°C; melting temperature [Tm], 55.7°C; optimum pH [pHopt], 9.5) was stable in the presence of 10 to 20% (vol/vol) organic solvents and exhibited hydrolytic activity against p-nitrophenyl esters from acetate to palmitate, preferably butyrate (496 U mg-1), and a large battery of 69 structurally different esters (up to 30.2 U mg-1), including bis(2-hydroxyethyl)-terephthalate (0.16 ± 0.06 U mg-1). This broad substrate specificity contrasts with the fact that EH0 showed a long and narrow catalytic tunnel, whose access appears to be hindered by a tight folding of its cap domain. We propose that this cap domain is a highly flexible structure whose opening is mediated by unique structural elements, one of which is the presence of two contiguous proline residues likely acting as possible hinges, which together allow for the entrance of the substrates. Therefore, this work provides a new role for the cap domain, which until now was thought to be an immobile element that contained hydrophobic patches involved in substrate prerecognition and in turn substrate specificity within family IV esterases. IMPORTANCE A better understanding of structure-function relationships of enzymes allows revelation of key structural motifs or elements. Here, we studied the structural basis of the substrate promiscuity of EH0, a family IV esterase, isolated from a sample of the Sorghum bicolor rhizosphere microbiome exposed to technical cashew nut shell liquid. The analysis of EH0 revealed the potential of the sorghum rhizosphere microbiome as a source of enzymes with interesting properties, such as pH and solvent tolerance and remarkably broad substrate promiscuity. Its structure resembled those of homologous proteins from mesophilic Parvibaculum and Erythrobacter spp. and hyperthermophilic Pyrobaculum and Sulfolobus spp. and had a very narrow, single-entry access tunnel to the active site, with access controlled by a capping domain that includes a number of nonconserved proline residues. These structural markers, distinct from those of other substrate-promiscuous esterases, can help in tuning substrate profiles beyond tunnel and active site engineering.
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Tang L, Xia Y, Wu X, Chen X, Zhang X, Li H. Screening and characterization of a novel thermostable lipase with detergent-additive potential from the metagenomic library of a mangrove soil. Gene 2017; 625:64-71. [DOI: 10.1016/j.gene.2017.04.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/26/2017] [Indexed: 10/19/2022]
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Coyotzi S, Pratscher J, Murrell JC, Neufeld JD. Targeted metagenomics of active microbial populations with stable-isotope probing. Curr Opin Biotechnol 2016; 41:1-8. [DOI: 10.1016/j.copbio.2016.02.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/09/2016] [Accepted: 02/13/2016] [Indexed: 02/02/2023]
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Bandeira PT, Alnoch RC, de Oliveira AR, de Souza EM, de O. Pedrosa F, Krieger N, Piovan L. Enzymatic kinetic resolution of aliphatic sec -alcohols by LipG9, a metagenomic lipase. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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López-López O, Cerdán ME, González Siso MI. New extremophilic lipases and esterases from metagenomics. Curr Protein Pept Sci 2015; 15:445-55. [PMID: 24588890 PMCID: PMC4093774 DOI: 10.2174/1389203715666140228153801] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 01/21/2014] [Accepted: 02/25/2014] [Indexed: 11/22/2022]
Abstract
Lipolytic enzymes catalyze the hydrolysis of ester bonds in the presence of water. In media with low water content or in organic solvents, they can catalyze synthetic reactions such as esterification and transesterification. Lipases and esterases, in particular those from extremophilic origin, are robust enzymes, functional under the harsh conditions of industrial processes owing to their inherent thermostability and resistance towards organic solvents, which combined with their high chemo-, regio- and enantioselectivity make them very attractive biocatalysts for a variety of industrial applications. Likewise, enzymes from extremophile sources can provide additional features such as activity at extreme temperatures, extreme pH values or high salinity levels, which could be interesting for certain purposes. New lipases and esterases have traditionally been discovered by the isolation of microbial strains producing lipolytic activity. The Genome Projects Era allowed genome mining, exploiting homology with known lipases and esterases, to be used in the search for new enzymes. The Metagenomic Era meant a step forward in this field with the study of the metagenome, the pool of genomes in an environmental microbial community. Current molecular biology techniques make it possible to construct total environmental DNA libraries, including the genomes of unculturable organisms, opening a new window to a vast field of unknown enzymes with new and unique properties. Here, we review the latest advances and findings from research into new extremophilic lipases and esterases, using metagenomic approaches, and their potential industrial and biotechnological applications.
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Affiliation(s)
| | | | - Maria I González Siso
- University of A Coruna, Faculty of Sciences, Department of Cellular and Molecular Biology, Biochemistry and Molecular Biology Area. Campus A Zapateira s/n, 15071, A Coruna, Spain.
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Rodríguez MC, Loaces I, Amarelle V, Senatore D, Iriarte A, Fabiano E, Noya F. Est10: A Novel Alkaline Esterase Isolated from Bovine Rumen Belonging to the New Family XV of Lipolytic Enzymes. PLoS One 2015; 10:e0126651. [PMID: 25973851 PMCID: PMC4431682 DOI: 10.1371/journal.pone.0126651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 04/04/2015] [Indexed: 11/18/2022] Open
Abstract
A metagenomic fosmid library from bovine rumen was used to identify clones with lipolytic activity. One positive clone was isolated. The gene responsible for the observed phenotype was identified by in vitro transposon mutagenesis and sequencing and was named est10. The 367 amino acids sequence harbors a signal peptide, the conserved secondary structure arrangement of alpha/beta hydrolases, and a GHSQG pentapeptide which is characteristic of esterases and lipases. Homology based 3D-modelling confirmed the conserved spatial orientation of the serine in a nucleophilic elbow. By sequence comparison, Est10 is related to hydrolases that are grouped into the non-specific Pfam family DUF3089 and to other characterized esterases that were recently classified into the new family XV of lipolytic enzymes. Est10 was heterologously expressed in Escherichia coli as a His-tagged fusion protein, purified and biochemically characterized. Est10 showed maximum activity towards C4 aliphatic chains and undetectable activity towards C10 and longer chains which prompted its classification as an esterase. However, it was able to efficiently catalyze the hydrolysis of aryl esters such as methyl phenylacetate and phenyl acetate. The optimum pH of this enzyme is 9.0, which is uncommon for esterases, and it exhibits an optimal temperature at 40°C. The activity of Est10 was inhibited by metal ions, detergents, chelating agents and additives. We have characterized an alkaline esterase produced by a still unidentified bacterium belonging to a recently proposed new family of esterases.
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Affiliation(s)
- María Cecilia Rodríguez
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Inés Loaces
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Vanesa Amarelle
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Daniella Senatore
- Laboratorio de Ecología Microbiana, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Andrés Iriarte
- Departamento de Genómica, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Elena Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
| | - Francisco Noya
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas "Clemente Estable", Montevideo, Uruguay
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Alnoch RC, Martini VP, Glogauer A, Costa ACDS, Piovan L, Muller-Santos M, de Souza EM, de Oliveira Pedrosa F, Mitchell DA, Krieger N. Immobilization and characterization of a new regioselective and enantioselective lipase obtained from a metagenomic library. PLoS One 2015; 10:e0114945. [PMID: 25706996 PMCID: PMC4338019 DOI: 10.1371/journal.pone.0114945] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/16/2014] [Indexed: 11/19/2022] Open
Abstract
In previous work, a new lipase and its cognate foldase were identified and isolated from a metagenomic library constructed from soil samples contaminated with fat. This new lipase, called LipG9, is a true lipase that shows specific activities that are comparable to those of well-known industrially-used lipases with high activity against long-chain triglycerides. In the present work, LipG9 was co-expressed and co-immobilized with its foldase, on an inert hydrophobic support (Accurel MP1000). We studied the performance of this immobilized LipG9 (Im-LipG9) in organic media, in order to evaluate its potential for use in biocatalysis. Im-LipG9 showed good stability, maintaining a residual activity of more than 70% at 50 °C after incubation in n-heptane (log P 4.0) for 8 h. It was also stable in polar organic solvents such as ethanol (log P -0.23) and acetone (log P -0.31), maintaining more than 80% of its original activity after 8 h incubation at 30 °C. The synthesis of ethyl esters was tested with fatty acids of different chain lengths in n-heptane at 30 °C. The best conversions (90% in 3 h) were obtained for medium and long chain saturated fatty acids (C8, C14 and C16), with the maximum specific activity, 29 U per gram of immobilized preparation, being obtained with palmitic acid (C16). Im-LipG9 was sn-1,3-specific. In the transesterification of the alcohol (R,S)-1-phenylethanol with vinyl acetate and the hydrolysis of the analogous ester, (R,S)-1-phenylethyl acetate, Im-LipG9 showed excellent enantioselectivity for the R-isomer of both substrates (E> 200), giving an enantiomeric excess (ee) of higher than 95% for the products at 49% conversion. The results obtained in this work provide the basis for the development of applications of LipG9 in biocatalysis.
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Affiliation(s)
- Robson Carlos Alnoch
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx. P. 19046 Centro Politécnico, Curitiba 81531–980, Paraná, Brazil
| | | | - Arnaldo Glogauer
- Agência Tecpar de Inovação, Instituto de Tecnologia do Paraná—Tecpar, Curitiba 81350–010, Paraná, Brazil
| | - Allen Carolina dos Santos Costa
- Departamento de Química, Universidade Federal do Paraná, Cx. P. 19081 Centro Politécnico, Curitiba 81531–980, Paraná, Brazil
| | - Leandro Piovan
- Departamento de Química, Universidade Federal do Paraná, Cx. P. 19081 Centro Politécnico, Curitiba 81531–980, Paraná, Brazil
| | - Marcelo Muller-Santos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx. P. 19046 Centro Politécnico, Curitiba 81531–980, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx. P. 19046 Centro Politécnico, Curitiba 81531–980, Paraná, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx. P. 19046 Centro Politécnico, Curitiba 81531–980, Paraná, Brazil
| | - David Alexander Mitchell
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx. P. 19046 Centro Politécnico, Curitiba 81531–980, Paraná, Brazil
| | - Nadia Krieger
- Departamento de Química, Universidade Federal do Paraná, Cx. P. 19081 Centro Politécnico, Curitiba 81531–980, Paraná, Brazil
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Martini VP, Glogauer A, Müller-Santos M, Iulek J, de Souza EM, Mitchell DA, Pedrosa FO, Krieger N. First co-expression of a lipase and its specific foldase obtained by metagenomics. Microb Cell Fact 2014; 13:171. [PMID: 25510188 PMCID: PMC4305245 DOI: 10.1186/s12934-014-0171-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 11/20/2014] [Indexed: 11/10/2022] Open
Abstract
Background Metagenomics is a useful tool in the search for new lipases that might have characteristics that make them suitable for application in biocatalysis. This paper reports the cloning, co-expression, purification and characterization of a new lipase, denominated LipG9, and its specific foldase, LifG9, from a metagenomic library derived from a fat-contaminated soil. Results Within the metagenomic library, the gene lipg9 was cloned jointly with the gene of the foldase, lifg9. LipG9 and LifG9 have 96% and 84% identity, respectively, with the corresponding proteins of Aeromonas veronii B565. LipG9 and LifG9 were co-expressed, both in N-truncated form, in Escherichia coli BL21(DE3), using the vectors pET28a(+) and pT7-7, respectively, and then purified by affinity chromatography using a Ni2+ column (HiTrap Chelating HP). The purified enzyme eluted from the column complexed with its foldase. The molecular masses of the N-truncated proteins were 32 kDa for LipG9, including the N-terminal His-tag with 6 residues, and 23 kDa for LifG9, which did not have a His-tag. The biochemical and kinetic characteristics of the purified lipase-foldase preparation were investigated. This preparation was active and stable over a wide range of pH values (6.5-9.5) and temperatures (10-40°C), with the highest specific activity, of 1500 U mg−1, being obtained at pH 7.5 at 30°C. It also had high specific activities against tributyrin, tricaprylin and triolein, with values of 1852, 1566 and 817 U mg−1, respectively. A phylogenetic analysis placed LipG9 in the lipase subfamily I.1. A comparison of the sequence of LipG9 with those of other bacterial lipases in the Protein Data Bank showed that LipG9 contains not only the classic catalytic triad (Ser103, Asp250, His272), with the catalytic Ser occurring within a conserved pentapeptide, Gly-His-Ser-His-Gly, but also a conserved disulfide bridge and a conserved calcium binding site. The homology-modeled structure presents a canonical α/β hydrolase folding type I. Conclusions This paper is the first to report the successful co-expression of a lipase and its associated foldase from a metagenomic library. The high activity and stability of Lip-LifG9 suggest that it has a good potential for use in biocatalysis. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0171-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Viviane Paula Martini
- Departamento de Química, Universidade Federal do Paraná, Cx. P. 19081 Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil. .,Instituto Federal do Paraná - Campus Irati, Rua Pedro Koppe, 100, Irati, 84500-000, Paraná, Brazil.
| | - Arnaldo Glogauer
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx. P. 19046, Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil. .,Agência Tecpar de Inovação, Instituto de Tecnologia do Paraná - Tecpar, Curitiba, 81350-010, Paraná, Brazil.
| | - Marcelo Müller-Santos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx. P. 19046, Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil.
| | - Jorge Iulek
- Departamento de Química, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, Ponta Grossa, 84070-900, Paraná, Brazil.
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx. P. 19046, Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil.
| | - David Alexander Mitchell
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx. P. 19046, Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil.
| | - Fabio Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx. P. 19046, Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil.
| | - Nadia Krieger
- Departamento de Química, Universidade Federal do Paraná, Cx. P. 19081 Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil.
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Dellagnezze BM, de Sousa GV, Martins LL, Domingos DF, Limache EEG, de Vasconcellos SP, da Cruz GF, de Oliveira VM. Bioremediation potential of microorganisms derived from petroleum reservoirs. MARINE POLLUTION BULLETIN 2014; 89:191-200. [PMID: 25457810 DOI: 10.1016/j.marpolbul.2014.10.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 10/03/2014] [Accepted: 10/04/2014] [Indexed: 06/04/2023]
Abstract
Bacterial strains and metagenomic clones, both obtained from petroleum reservoirs, were evaluated for petroleum degradation abilities either individually or in pools using seawater microcosms for 21 days. Gas Chromatography-Flame Ionization Detector (GC-FID) and Gas Chromatography-Mass Spectrometry (GC-MS) analyses were carried out to evaluate crude oil degradation. The results showed that metagenomic clones 1A and 2B were able to biodegrade n-alkanes (C14 to C33) and isoprenoids (phytane and pristane), with rates ranging from 31% to 47%, respectively. The bacteria Dietzia maris CBMAI 705 and Micrococcus sp. CBMAI 636 showed higher rates reaching 99% after 21 days. The metagenomic clone pool biodegraded these compounds at rates ranging from 11% to 45%. Regarding aromatic compound biodegradation, metagenomic clones 2B and 10A were able to biodegrade up to 94% of phenanthrene and methylphenanthrenes (3-MP, 2-MP, 9-MP and 1-MP) with rates ranging from 55% to 70% after 21 days, while the bacteria Dietzia maris CBMAI 705 and Micrococcus sp. CBMAI 636 were able to biodegrade 63% and up to 99% of phenanthrene, respectively, and methylphenanthrenes (3-MP, 2-MP, 9-MP and 1-MP) with rates ranging from 23% to 99% after 21 days. In this work, isolated strains as well as metagenomic clones were capable of degrading several petroleum compounds, revealing an innovative strategy and a great potential for further biotechnological and bioremediation applications.
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Affiliation(s)
- Bruna Martins Dellagnezze
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil
| | - Gabriel Vasconcelos de Sousa
- Laboratory of Engineering and Petroleum Exploration, Darcy Ribeiro North Fluminense State University - LENEP/UENF, POB 119562, 27910-970 Macaé, RJ, Brazil
| | - Laercio Lopes Martins
- Laboratory of Engineering and Petroleum Exploration, Darcy Ribeiro North Fluminense State University - LENEP/UENF, POB 119562, 27910-970 Macaé, RJ, Brazil
| | - Daniela Ferreira Domingos
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil
| | - Elmer E G Limache
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil
| | | | - Georgiana Feitosa da Cruz
- Laboratory of Engineering and Petroleum Exploration, Darcy Ribeiro North Fluminense State University - LENEP/UENF, POB 119562, 27910-970 Macaé, RJ, Brazil
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil.
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Narihiro T, Suzuki A, Yoshimune K, Hori T, Hoshino T, Yumoto I, Yokota A, Kimura N, Kamagata Y. The combination of functional metagenomics and an oil-fed enrichment strategy revealed the phylogenetic diversity of lipolytic bacteria overlooked by the cultivation-based method. Microbes Environ 2014; 29:154-61. [PMID: 24859309 PMCID: PMC4103521 DOI: 10.1264/jsme2.me14002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. We used an indigenous forest soil (NS) and oil-fed enriched soil (OS) as microbial and genetic resources. Thirty-four strains (17 each) of lipolytic bacteria were isolated from the NS and OS microcosms. These isolates were classified into the (sub)phyla Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria, all of which are known to be the main microbial resources of commercially available lipolytic enzymes. Seven and 39 lipolytic enzymes were successfully retrieved from the metagenomic libraries of the NS and OS microcosms, respectively. The screening efficiency (a ratio of positive lipolytic clones to the total number of environmental clones) was markedly higher in the OS microcosm than in the NS microcosm. Moreover, metagenomic clones encoding the lipolytic enzymes associated with Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Armatimonadetes, and Planctomycetes and hitherto-uncultivated microbes were recovered from these libraries. The results of the present study indicate that functional metagenomics can be effectively used to capture as yet undiscovered lipolytic enzymes that have eluded the cultivation-based method, and these combined approaches may be able to provide an overview of lipolytic organisms potentially present in nature.
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Affiliation(s)
- Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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Bartasun P, Cieśliński H, Bujacz A, Wierzbicka-Woś A, Kur J. A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library. PLoS One 2013; 8:e55697. [PMID: 23383268 PMCID: PMC3561333 DOI: 10.1371/journal.pone.0055697] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/02/2013] [Indexed: 11/19/2022] Open
Abstract
The presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified and its UV-VIS absorbance spectrum and emission spectrum were assayed. Simultaneously, the same spectroscopic studies were carried out for rhodamine B in the absence or presence of RSFP protein or native E. coli proteins, respectively. The results of the spectroscopic studies suggested that the fluorescence of E. coli cells expressing rsfp gene under UV illumination is due to the interaction of rhodamine B molecules with the RSFP protein. Finally, this interaction was proved by a crystallographic study and then by site-directed mutagenesis of rsfp gene sequence. The crystal structures of RSFP apo form (1.98 Å) and complex RSFP/RB (1.90 Å) show a trimer of RSFP molecules located on the crystallographic six fold screw axis. The RSFP complex with rhodamine B revealed the binding site for RB, in the pocket located on the interface between symmetry related monomers.
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Affiliation(s)
- Paulina Bartasun
- Department of Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Hubert Cieśliński
- Department of Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Anna Bujacz
- Institute of Technical Biochemistry, Lódź University of Technology, Lódź, Poland
| | - Anna Wierzbicka-Woś
- Department of Microbiology, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Józef Kur
- Department of Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
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Faoro H, Glogauer A, Couto GH, de Souza EM, Rigo LU, Cruz LM, Monteiro RA, Pedrosa FDO. Characterization of a new Acidobacteria-derived moderately thermostable lipase from a Brazilian Atlantic Forest soil metagenome. FEMS Microbiol Ecol 2012; 81:386-94. [PMID: 22428990 DOI: 10.1111/j.1574-6941.2012.01361.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 02/25/2012] [Accepted: 03/06/2012] [Indexed: 11/28/2022] Open
Abstract
A clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of the Brazilian Atlantic Forest soil. The DNA insert of LP001 was fully sequenced, and 38 ORFs were identified. Comparison of ORFs, %G + C content and gene organization with sequenced bacterial genomes suggested that the fosmid DNA insert belongs to an organism of the Acidobacteria phylum. Protein domain analysis and inactivation by transposon insertion showed that the protein encoded by ORF29 was responsible for the lipase activity and was named LipAAc. The purified LipAAc lipase was capable of hydrolyzing a broad range of substrates, showing the highest activity against p-nitrophenol (pNP) decanoate. The lipase was active over a pH range of 5.0-10.0 and was insensitive to divalent cations. LipAAc is moderately thermostable with optimum temperature between 50 and 60 °C and was thermally activated (80% activity increase) after 1 h incubation at 50 °C. Phylogenetic analysis suggested that the LipAAc is a member of family I of bacterial lipases and clusters with other moderately thermostable lipases of this group. Comparisons of the DNA insert of fosmid LP001 with other acidobacterial genomes and sequence database suggest that lipAAc gene has a fungal origin and was acquired by horizontal transfer.
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Affiliation(s)
- Helisson Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
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