Abstract
The biotechnological and industrial uses of thermostable and organic solvent-tolerant enzymes are extensive and the investigation of such enzymes from microbiota present in oil reservoirs is a promising approach. Searching sequence databases for esterases from such microbiota, we have identified in silico a potentially secreted esterase from Acetomicrobium hydrogeniformans, named AhEst. The recombinant enzyme was produced in E. coli to be used in biochemical and biophysical characterization studies. AhEst presented hydrolytic activity on short-acyl-chain p-nitrophenyl ester substrates. AhEst activity was high and stable in temperatures up to 75 °C. Interestingly, high salt concentration induced a significant increase of catalytic activity. AhEst still retained ~ 50% of its activity in 30% concentration of several organic solvents. Synchrotron radiation circular dichroism and fluorescence spectroscopies confirmed that AhEst displays high structural stability in extreme conditions of temperature, salinity, and organic solvents. The enzyme is a good emulsifier agent and is able to partially reverse the wettability of an oil-wet carbonate substrate, making it of potential interest for use in enhanced oil recovery. All the traits observed in AhEst make it an interesting candidate for many industrial applications, such as those in which a significant hydrolytic activity at high temperatures is required.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- AhEst:
-
Acetomicrobium hydrogeniformans esterase
- CD:
-
Circular dichroism
- EOR:
-
Enhanced oil recovery
- HMM:
-
Hidden Markov models
- MRW:
-
Mean residue weight
- NATA:
-
N-Acetyl-tryptophanamide
- pNA:
-
p-Nitrophenyl acetate
- pNB:
-
p-Nitrophenyl butyrate
- SEC:
-
Size-exclusion chromatography
- SRCD:
-
Synchrotron radiation circular dichroism
References
Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, Stockinger H (2012) ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res 40(W1):W597–W603. https://doi.org/10.1093/nar/gks400
Atomi H, Sato T, Kanai T (2011) Application of hyperthermophiles and their enzymes. Curr Opin Biotechnol 22:618–626. https://doi.org/10.1016/j.copbio.2011.06.010
Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42(W1):W252–W258. https://doi.org/10.1093/nar/gku340
Bodour AA, Miller-Maier RM (1998) Application of a modified drop-collapse technique for surfactant quantitation and screening of biosurfactant-producing microorganisms. J Microbiol Methods 32(3):273–280. https://doi.org/10.1016/S0167-7012(98)00031-1
Bornscheuer UT (2002) Microbial carboxyl esterases: classification, properties and application in biocatalysis. FEMS Microbiol Rev 26:73–81. https://doi.org/10.1111/j.1574-6976.2002.tb00599.x
Colin PY, Kintses B, Gielen F, Miton CM, Fischer G, Mohamed MF, Hyvönen M, Morgavi DP, Janssen DB, Hollfelder F (2015) Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics. Nat Commun 6:10008. https://doi.org/10.1038/ncomms10008
Cooper DG, Goldenberg BG (1987) Surface-active agents from two Bacillus species. Appl Environ Microbiol 53(2):224–229
Das P, Mukherjee S, Sivapathasekaran C, Sen R (2010) Microbial surfactants of marine origin: potential and prospects. In: Sen R (ed) Biosurfactants—advances in experimental medicine and biology. Landes Bioscience and Springer Science + Business Media, LLC, Austin, pp 88–101
Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7(10):e1002195. https://doi.org/10.1371/journal.pcbi.1002195
Elleuche S, Schäfers C, Blank S, Schröder C, Antranikian G (2015) Exploration of extremophiles for high temperature biotechnological processes. Curr Opin Microbiol 25:113–119. https://doi.org/10.1016/j.mib.2015.05.011
Garnier J, Gibrat JF, Robson B (1996) GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 266:540–553. https://doi.org/10.1016/S0076-6879(96)66034-0
Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Humana Press, Totowa, pp 571–607
Hania WB, Bouanane-Darenfed A, Cayol JL, Ollivier B, Fardeau ML (2016) Reclassification of Anaerobaculum mobile, Anaerobaculum thermoterrenum, Anaerobaculum hydrogeniformans as Acetomicrobium mobile comb. nov., Acetomicrobium thermoterrenum comb. nov., and Acetomicrobium hydrogeniformans comb. nov, respectively, and emendation of the genus Acetomicrobium. Int J Syst Evol Microbiol 66(3):1506–1509. https://doi.org/10.1099/ijsem.0.000910
Harrison JP, Gheeraert N, Tsigelnitskiy D, Cockell CS (2013) The limits for life under multiple extremes. Trends Microbiol 21:204–212. https://doi.org/10.1016/j.tim.2013.01.006
Hotta Y, Ezaki S, Atomi H, Imanaka T (2002) Extremely stable and versatile carboxylesterase from hyperthermophilic archeon. Appl Environ Microbiol 68:3925–3931
Jaeger KE, Dijkstra BW, Reetz MT (1999) Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu Rev Microbiol 53:315–351. https://doi.org/10.1146/annurev.micro.53.1.315
James NG, Ross JA, Stefl M, Jameson DM (2011) Application of phasor plots to in vitro protein studies. Anal Biochem 410:70–76. https://doi.org/10.1016/j.ab.2010.11.011
Khusainova A (2016) Enhanced oil recovery with application of enzymes. Ph.D. thesis, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
Khusainova A, Nielsen SM, Pedersen HH, Woodley JM, Shapiro A (2015) Study of wettability of calcite surfaces using oil–brine–enzyme systems for enhanced oil recovery applications. J Pet Sci Eng 27:53–64. https://doi.org/10.1016/j.petrol.2014.12.014
Klose DP, Wallace BA, Janes RW (2010) 2Struc: the secondary structure server. Bioinformatics 26(20):2624–2625. https://doi.org/10.1093/bioinformatics/btq480
Lees JG, Smith BR, Wien F, Miles AJ, Wallace BA (2004) CDtool—an integrated software package for circular dichroism spectroscopic data processing, analysis, and archiving. Anal Biochem 332(2):285–289. https://doi.org/10.1016/j.ab.2004.06.002
Lees JG, Miles AJ, Wien F, Wallace BA (2006) A reference database for circular dichroism spectroscopy covering fold and secondary structure space. Bioinformatics 22(16):1955–1962. https://doi.org/10.1093/bioinformatics/btl327
Levisson M, van der Oost J, Kengen SWM (2007) Characterization and structural modeling of a new type of thermostable esterase from Thermotoga maritima. FEBS J 274(11):2832–2842. https://doi.org/10.1111/j.1742-4658.2007.05817.x
Levisson M, van der Oost J, Kengen SWM (2009) Carboxylic ester hydrolases from hyperthermophiles. Extremophlies 13(4):567–581. https://doi.org/10.1007/s00792-009-0260-4
Levisson M, Han GW, Deller MC, Xu Q, Biely P, Hendriks S, Ten Eyck LF, Flensburg C, Roversi P, Miller MD, McMullan D, von Delft F, Kreusch A, Deacon AM, van der Oost J, Lesley SA, Elsliger MA, Kengen SW, Wilson IA (2012) Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima. Proteins 80(6):1545–1559. https://doi.org/10.1002/prot.24041
Lopes JLS, Yoneda JS, Martins JM, DeMarco R, Jameson DM, Castro AM, Bossolan NRS, Wallace BA, Araujo APU (2016) Environmental factors modulating the stability and enzymatic activity of the Petrotoga mobilis esterase (PmEst). PLoS One 11(6):e0158146. https://doi.org/10.1371/journal.pone.0158146
López-López O, Cerdán ME, González-Siso MI (2014) New extremophilic lipases and esterases from metagenomics. Curr Protein Pept Sci 15(5):445–455. https://doi.org/10.2174/1389203715666140228153801
Maune MW, Tanner RS (2012) Description of Anaerobaculum hydrogeniformans sp. nov., an anaerobe that produces hydrogen from glucose, and emended description of the genus Anaerobaculum. Int J Syst Evol Microbiol 62:832–838. https://doi.org/10.1099/ijs.0.024349-0
Nasiri H (2011) Enzymes for enhanced oil recovery (EOR). Ph.D. thesis, University of Bergen, Norway
Nasiri H, Spildo K, Skauge A (2009) Use of enzymes to improve waterflood performance. In: International symposium of the society of core analysts, Noordwijk, The Netherlands
Panda T, Gowrishankar BS (2005) Production and applications of esterases. Appl Microbiol Biotechnol 67:160–169. https://doi.org/10.1007/s00253-004-1840-y
Park SY, Kim JT, Kang SG, Woo JH, Lee JH, Choi HT, Kim SJ (2007) A new esterase showing similarity to putative dienelactone hydrolase from a strict marine bacterium, Vibrio sp. GMD509. Appl Microbiol Biotechnol 77:107–115. https://doi.org/10.1007/s00253-007-1134-2
Park YJ, Yoon SJ, Lee HB (2010) A novel dienelactone hydrolase from the thermoacidophilic archaeon Sulfolobus solfataricus P1: purification, characterization, and expression. Biochim Biophys Acta 1800(11):1164–1172. https://doi.org/10.1016/j.bbagen.2010.07.006
Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptide from transmembrane regions. Nat Methods 8(10):785–786. https://doi.org/10.1038/nmeth.1701
Pikuta EV, Hoover RB, Tang J (2007) Microbial extremophiles at the limits of life. Crit Rev Microbiol 33:183–209. https://doi.org/10.1080/10408410701451948
Punta M, Coggill PC, Eberhard RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (2012) The Pfam protein families database. Nucleic Acids Res 40(database issue):D290–D301. https://doi.org/10.1093/nar/gkr1065
Rhee JK, Ahn DG, Kim YG, Oh JW (2005) New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl Environ Microbiol 71(2):817–825. https://doi.org/10.1128/AEM.71.2.817-825.2005
Ross JA, Jameson DM (2008) Frequency domain fluorometry: applications to intrinsic protein fluorescence. Photochem Photobiol Sci 7(11):1301–1312. https://doi.org/10.1039/b804450n
Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D (2004) BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 32(database issue):D431–D433. https://doi.org/10.1093/nar/gkh081
Schreck SD, Grunden AM (2014) Biotechnological applications of halophilic lipases and thioesterases. Appl Microbiol Biotechnol 98:1011. https://doi.org/10.1007/s00253-013-5417-5
Seethepalli A, Adibhatla B, Mohanty KK (2004) Wettability alteration during surfactant flooding of carbonate reservoirs. In: SPE/DOE symposium on improved oil recovery, 17–21 April, Tulsa, Oklahoma. SPE 89423. https://doi.org/10.2118/89423-ms
Sheng JJ (2013) Comparison of the effects of wettability alteration and IFT reduction on oil recovery in carbonate reservoirs. Asia Pac J Chem Eng 8:154–161. https://doi.org/10.1002/apj.1640
Sreerama N, Woody RW (2000) Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal Biochem 287:252–260. https://doi.org/10.1006/abio.2000.4880
Stefl M, James NG, Ross JA, Jameson DM (2011) Application of phasor plots to in vitro time-resolved fluorescence measurements. Anal Biochem 410:62–69. https://doi.org/10.1016/j.ab.2010.11.010
Urbieta MS, Donati ER, Chan K-G, Shahar S, Sin LL, Goh KM (2015) Thermophiles in the genomic era: biodiversity, science, and applications. Biotechnol Adv 33:633–647. https://doi.org/10.1016/j.biotechadv.2015.04.007
Vieille C, Zeikus GJ (2001) Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 65(1):1–43. https://doi.org/10.1128/MMBR.65.1.1-43.2001
Weber G (1960) Fluorescence-polarization spectrum and electronic energy transfer in proteins. Biochem J 75:345–352
Whitmore L, Wallace BA (2008) Protein secondary structure analyses from circular dichroism spectroscopy: methods and reference databases. Biopolymers 89:392–400. https://doi.org/10.1002/bip.20853
Wu Y, Shuler PJ, Blanco M, Tang Y, Goddard WA (2006) A study of wetting behavior and surfactant EOR in carbonates with model compounds. In: SPE/DOE symposium on improved oil recovery, Tulsa, USA. Society of Petroleum Engineers. https://doi.org/10.2118/99612-ms
Yoneda JS, Miles AJ, Araujo APU, Wallace BA (2017) Differential dehydration effects on globular proteins and intrinsically disordered proteins during film formation. Protein Sci 26(4):718–726. https://doi.org/10.1002/pro.3118
Zhua Y, Li J, Cai H, Ni H, Xiao A, Hou L (2013) Characterization of a new and thermostable esterase from a metagenomic library. Microbiol Res 168(9):589–597. https://doi.org/10.1016/j.micres.2013.04.004
Acknowledgements
Authors are grateful for the support of paired UK–Brazil partnering grants from the Biotechnology and Biological Sciences Research Council (BBSRC) and Sao Paulo Research Foundation (FAPESP) Grant FAPPA to APUA and BAW. We thank the beamline access to the AU-CD beamline on ASTRID2 at ISA Synchrotron (Aarhus, Denmark) (to JLSL and PSK).
Funding
This study was supported by Biotechnology and Biological Sciences Research Council (BBSRC) Grant N012763 to BAW; Sao Paulo Research Foundation (FAPESP) Grant FAPPA 15/50347-2 to APUA; National Council for Scientific and Technological Development (CNPq) Grants 407337/2013-0 to APUA; 406429/2016-2 and 303513/2016-0 to JLSL and Grant 150417/2016-0 to PSK; Petrobras (Petróleo Brasileiro S.A.) Grant to NRSB and DTI fellowships to JMM and RFG (cooperation agreement 0050.0079046.12.9, resources regulated by the Brazilian National Agency of Petroleum, Natural Gas and Biofuels—ANP resolution 05/2015).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
Communicated by F. Robb.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Kumagai, P.S., Gutierrez, R.F., Lopes, J.L.S. et al. Characterization of esterase activity from an Acetomicrobium hydrogeniformans enzyme with high structural stability in extreme conditions. Extremophiles 22, 781–793 (2018). https://doi.org/10.1007/s00792-018-1038-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00792-018-1038-3