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Hussian CHAC, Rahman RNZRA, Leow ATC, Salleh AB, Ali MSM, Latip W. Enhancement in T1 lipase purification recovery using the novel construct pGEX4T1/His-T1. Prep Biochem Biotechnol 2024; 54:526-534. [PMID: 37647127 DOI: 10.1080/10826068.2023.2252052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The Geobacillus zalihae strain T1 produces a thermostable T1 lipase that could be used for industrial purposes. Previously, the GST-T1 lipase was purified through two chromatographic steps: affinity and ion exchange (IEX) but the recovery yield was only 33%. To improve the recovery yield to over 80%, the GST tag from the pGEX system was replaced with a poly-histidine at the N-terminal of the T1 lipase sequence. The novel construct of pGEX/His-T1 lipase was developed by site-directed mutagenesis, where the XbaI restriction site was introduced upstream of the GST tag, allowing the removal of tag via double digestion using XbaI and EcoRI (existing cutting site in the pGEX system). Fragment of 6 × His-T1 lipase fusion was synthesized, cloned into the pGEX4T1 system, and expressed in Escherichia coli BL21 (DE3) pLysS, resulting in lipase-specific activity at 236 U/mg. The single purification step of His-T1 lipase was successfully achieved using nickel Sepharose 6FF with an optimized concentration of 5 mM imidazole for binding, yielding the recovery of 98%, 1,353 U/mg lipase activity, and a 5.7-fold increase in purification fold. His-T1 lipase was characterized and was found to be stable at pH 5-9, active at 70 °C, and optimal at pH 9.
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Affiliation(s)
- Che Haznie Ayu Che Hussian
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Adam Thean Chor Leow
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Malaysia
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Khaswal A, Chaturvedi N, Mishra SK, Kumar PR, Paul PK. Current status and applications of genus Geobacillus in the production of industrially important products-a review. Folia Microbiol (Praha) 2022; 67:389-404. [PMID: 35229277 DOI: 10.1007/s12223-022-00961-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/19/2022] [Indexed: 11/25/2022]
Abstract
The genus Geobacillus is one of the most important genera which mainly comprises gram-positive thermophilic bacterial strains including obligate aerobes, denitrifiers and facultative anaerobes having capability of endospore formation as well. The genus Geobacillus is widely distributed in nature and mostly abundant in extreme locations such as cool soils, hot springs, hydrothermal vents, marine trenches, hay composts and dairy plants. Due to plasticity towards environmental adaptation, the Geobacillus sp. shows remarkable genome diversification and acquired many beneficial properties, which facilitates their exploitation for many biotechnological applications. Many thermophiles are of biotechnological importance and having considerable interest in commercial applications for the production of industrially important products. Recently, due to catabolic versatility especially in the degradation of hemicellulose and starch containing agricultural waste and rapid growth rates, these microorganisms show potential for the production of biofuels, thermostable enzymes and bioremediation. This review mainly summarizes the status of Geobacillus sp. including its notable properties, biotechnological studies and its potential application in the production of industrially important products.
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Affiliation(s)
- Ashutosh Khaswal
- Department of Biotechnology, IMS Engineering College, Uttar Pradesh, Ghaziabad, India
| | - Neha Chaturvedi
- Department of Biotechnology, IMS Engineering College, Uttar Pradesh, Ghaziabad, India
| | - Santosh Kumar Mishra
- Department of Biotechnology, IMS Engineering College, Uttar Pradesh, Ghaziabad, India.
| | - Priya Ranjan Kumar
- Department of Biotechnology, IMS Engineering College, Uttar Pradesh, Ghaziabad, India
| | - Prabir Kumar Paul
- Department of Biotechnology, IMS Engineering College, Uttar Pradesh, Ghaziabad, India
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Thermostable lipases and their dynamics of improved enzymatic properties. Appl Microbiol Biotechnol 2021; 105:7069-7094. [PMID: 34487207 DOI: 10.1007/s00253-021-11520-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 10/20/2022]
Abstract
Thermal stability is one of the most desirable characteristics in the search for novel lipases. The search for thermophilic microorganisms for synthesising functional enzyme biocatalysts with the ability to withstand high temperature, and capacity to maintain their native state in extreme conditions opens up new opportunities for their biotechnological applications. Thermophilic organisms are one of the most favoured organisms, whose distinctive characteristics are extremely related to their cellular constituent particularly biologically active proteins. Modifications on the enzyme structure are critical in optimizing the stability of enzyme to thermophilic conditions. Thermostable lipases are one of the most favourable enzymes used in food industries, pharmaceutical field, and actively been studied as potential biocatalyst in biodiesel production and other biotechnology application. Particularly, there is a trade-off between the use of enzymes in high concentration of organic solvents and product generation. Enhancement of the enzyme stability needs to be achieved for them to maintain their enzymatic activity regardless the environment. Various approaches on protein modification applied since decades ago conveyed a better understanding on how to improve the enzymatic properties in thermophilic bacteria. In fact, preliminary approach using advanced computational analysis is practically conducted before any modification is being performed experimentally. Apart from that, isolation of novel extremozymes from various microorganisms are offering great frontier in explaining the crucial native interaction within the molecules which could help in protein engineering. In this review, the thermostability prospect of lipases and the utility of protein engineering insights into achieving functional industrial usefulness at their high temperature habitat are highlighted. Similarly, the underlying thermodynamic and structural basis that defines the forces that stabilize these thermostable lipase is discussed. KEY POINTS: • The dynamics of lipases contributes to their non-covalent interactions and structural stability. • Thermostability can be enhanced by well-established genetic tools for improved kinetic efficiency. • Molecular dynamics greatly provides structure-function insights on thermodynamics of lipase.
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Adetunji AI, Olaniran AO. Production strategies and biotechnological relevance of microbial lipases: a review. Braz J Microbiol 2021; 52:1257-1269. [PMID: 33904151 PMCID: PMC8324693 DOI: 10.1007/s42770-021-00503-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/16/2021] [Indexed: 01/14/2023] Open
Abstract
Lipases are enzymes that catalyze the breakdown of lipids into long-chain fatty acids and glycerol in oil-water interface. In addition, they catalyze broad spectrum of bioconversion reactions including esterification, inter-esterification, among others in non-aqueous and micro-aqueous milieu. Lipases are universally produced from plants, animals, and microorganisms. However, lipases from microbial origin are mostly preferred owing to their lower production costs, ease of genetic manipulation etc. The secretion of these biocatalysts by microorganisms is influenced by nutritional and physicochemical parameters. Optimization of the bioprocess parameters enhanced lipase production. In addition, microbial lipases have gained intensified attention for a wide range of applications in food, detergent, and cosmetics industries as well as in environmental bioremediation. This review provides insights into strategies for production of microbial lipases for potential biotechnological applications.
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Affiliation(s)
- Adegoke Isiaka Adetunji
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville campus), Private Bag X54001, Durban, 4000, Republic of South Africa.
| | - Ademola Olufolahan Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville campus), Private Bag X54001, Durban, 4000, Republic of South Africa
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Ishak SNH, Kamarudin NHA, Ali MSM, Leow ATC, Rahman RNZRA. Ion-Pair Interaction and Hydrogen Bonds as Main Features of Protein Thermostability in Mutated T1 Recombinant Lipase Originating from Geobacillus zalihae. Molecules 2020; 25:E3430. [PMID: 32731607 PMCID: PMC7435748 DOI: 10.3390/molecules25153430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/04/2020] [Accepted: 07/09/2020] [Indexed: 01/19/2023] Open
Abstract
A comparative structure analysis between space- and an Earth-grown T1 recombinant lipase from Geobacillus zalihae had shown changes in the formation of hydrogen bonds and ion-pair interactions. Using the space-grown T1 lipase validated structure having incorporated said interactions, the recombinant T1 lipase was re-engineered to determine the changes brought by these interactions to the structure and stability of lipase. To understand the effects of mutation on T1 recombinant lipase, five mutants were developed from the structure of space-grown T1 lipase and biochemically characterized. The results demonstrate an increase in melting temperature up to 77.4 °C and 76.0 °C in E226D and D43E, respectively. Moreover, the mutated lipases D43E and E226D had additional hydrogen bonds and ion-pair interactions in their structures due to the improvement of stability, as observed in a longer half-life and an increased melting temperature. The biophysical study revealed differences in β-Sheet percentage between less stable (T118N) and other mutants. As a conclusion, the comparative analysis of the tertiary structure and specific residues associated with ion-pair interactions and hydrogen bonds could be significant in revealing the thermostability of an enzyme with industrial importance.
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Affiliation(s)
- Siti Nor Hasmah Ishak
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd. Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Kohli I, Joshi NC, Mohapatra S, Varma A. Extremophile - An Adaptive Strategy for Extreme Conditions and Applications. Curr Genomics 2020; 21:96-110. [PMID: 32655304 PMCID: PMC7324872 DOI: 10.2174/1389202921666200401105908] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/27/2020] [Accepted: 03/19/2020] [Indexed: 11/22/2022] Open
Abstract
The concurrence of microorganisms in niches that are hostile like extremes of temperature, pH, salt concentration and high pressure depends upon novel molecular mechanisms to enhance the stability of their proteins, nucleic acids, lipids and cell membranes. The structural, physiological and genomic features of extremophiles that make them capable of withstanding extremely selective environmental conditions are particularly fascinating. Highly stable enzymes exhibiting several industrial and biotechnological properties are being isolated and purified from these extremophiles. Successful gene cloning of the purified extremozymes in the mesophilic hosts has already been done. Various extremozymes such as amylase, lipase, xylanase, cellulase and protease from thermophiles, halothermophiles and psychrophiles are of industrial interests due to their enhanced stability at forbidding conditions. In this review, we made an attempt to point out the unique features of extremophiles, particularly thermophiles and psychrophiles, at the structural, genomic and proteomic levels, which allow for functionality at harsh conditions focusing on the temperature tolerance by them.
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Affiliation(s)
- Isha Kohli
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Naveen C. Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Swati Mohapatra
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Noida, India
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Ktata A, Krayem N, Aloulou A, Bezzine S, Sayari A, Chamkha M, Karray A. Purification, biochemical and molecular study of lipase producing from a newly thermoalkaliphilic Aeribacillus pallidus for oily wastewater treatment. J Biochem 2019; 167:89-99. [DOI: 10.1093/jb/mvz083] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/08/2019] [Indexed: 11/12/2022] Open
Abstract
AbstractTreatment of oily wastewater is constantly a challenge; biological wastewater treatment is an effective, cheap and eco-friendly technology. A newly thermostable, haloalkaline, solvent tolerant and non-induced lipase from Aeribacillus pallidus designated as GPL was purified and characterized of biochemical and molecular study for apply in wastewater treatment. The GPL showed a maximum activity at 65°C and pH 10 after 22 h of incubation, with preference to TC4 substrates. Pure enzyme was picked up after one chromatographic step. It displayed an important resistance at high temperature, pH, NaCl, at the presence of detergents and organic solvents. In fact, GPL exhibited a prominent stability in wide range of organic solvents at 50% (v/v) concentration for 2 h of incubation. The efficiency of the GPL in oil wastewater hydrolysis was established at 50°C for 1 h, the oil removal efficiency was established at 96, 11% and the oil biodegradation was confirmed through fourier transform infrared (FT-IR) spectroscopy. The gene that codes for this lipase was cloned and sequenced and its open reading frame encoded 236 amino acid residues. The deduced amino acids sequence of the GPL shows an important level of identity with Geobacillus lipases.
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Affiliation(s)
- Ameni Ktata
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS Route de Soukra, km 3.5, université de Sfax-Tunisie, BP 1173 3038 Sfax, Tunisia
| | - Najeh Krayem
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS Route de Soukra, km 3.5, université de Sfax-Tunisie, BP 1173 3038 Sfax, Tunisia
| | - Ahmed Aloulou
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS Route de Soukra, km 3.5, université de Sfax-Tunisie, BP 1173 3038 Sfax, Tunisia
| | - Sofiane Bezzine
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS Route de Soukra, km 3.5, université de Sfax-Tunisie, BP 1173 3038 Sfax, Tunisia
| | - Adel Sayari
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS Route de Soukra, km 3.5, université de Sfax-Tunisie, BP 1173 3038 Sfax, Tunisia
| | - Mohamed Chamkha
- Centre de Biotechnologie de Sfax, Route Sidi Mansour Km 6, BP 1177 3018 Sfax, Tunisia
| | - Aida Karray
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS Route de Soukra, km 3.5, université de Sfax-Tunisie, BP 1173 3038 Sfax, Tunisia
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Low molecular weight alkaline thermostable α-amylase from Geobacillus sp. nov. Heliyon 2019; 5:e02171. [PMID: 31388592 PMCID: PMC6667821 DOI: 10.1016/j.heliyon.2019.e02171] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/30/2019] [Accepted: 07/24/2019] [Indexed: 01/11/2023] Open
Abstract
Industrial demands for enzymes that are stable in a broad range of conditions are increasing. Such enzymes, one of which is α-amylase, could be produced by extremophiles. This study reports a thermostable α-amylase produced by a newly isolated Geobacillus sp. nov. from a geothermal area. The phylogenetic analysis of the 16S rRNA gene showed that the isolate formed a separate branch with 95% homology to Geobacillus sp. After precipitation using ammonium sulphate followed by ion-exchange chromatography, the enzyme produced a specific activity of 25.1 (U/mg) with a purity of 6.5-fold of the crude extract. The molecular weight of the enzyme was approximately 12.2 kDa. The optimum activity was observed at 75 °C and pH 8. The activity increased in the presence of Ba2+ and Fe2+ but decreased in the presence of K+ and Mg2+. Ca2+ and Mn2+ increased the activity slightly. The activity completely diminished with the addition of Cu2+. EDTA and PMSF also sharply reduced enzyme activity. Although the stability was moderate, the low molecular weight could be an important feature for its future applications.
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Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species. Appl Microbiol Biotechnol 2018; 102:10425-10437. [PMID: 30310966 DOI: 10.1007/s00253-018-9422-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022]
Abstract
The genus Geobacillus comprises thermophilic bacilli capable of endospore formation. The members of this genus provide thermostable proteins and can be used in whole cell applications at elevated temperatures; therefore, these organisms are of biotechnological importance. While these applications have been described in previous reviews, the present paper highlights the environmental adaptations and genome diversifications of Geobacillus spp. and their applications in evolutionary-protein engineering. Despite their obligate thermophilic properties, Geobacillus spp. are widely distributed in nature. Because several isolates demonstrate remarkable properties for cell reproduction in their respective niches, they seem to exist not only as endospores but also as vegetative cells in diverse environments. This suggests their excellence in environmental adaptation via genome diversification; in fact, evidence suggests that Geobacillus spp. were derived from Bacillus spp. while diversifying their genomes via horizontal gene transfer. Moreover, when subjected to an environmental stressor, Geobacillus spp. diversify their genomes using inductive mutations and transposable elements to produce derivative cells that are adaptive to the stressor. Notably, inductive mutations in Geobacillus spp. occur more rapidly and frequently than the stress-induced mutagenesis observed in other microorganisms. Owing to this, Geobacillus spp. can efficiently generate mutant genes coding for thermostable enzyme variants from the thermolabile enzyme genes under appropriate selection pressures. This phenomenon provides a new approach to generate thermostable enzymes, termed as thermoadaptation-directed enzyme evolution, thereby expanding the biotechnological potentials of Geobacillus spp. In this review, we have discussed this approach using successful examples and major challenges yet to be addressed.
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Lebre PH, Aliyu H, De Maayer P, Cowan DA. In silico characterization of the global Geobacillus and Parageobacillus secretome. Microb Cell Fact 2018; 17:156. [PMID: 30285747 PMCID: PMC6171300 DOI: 10.1186/s12934-018-1005-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/26/2018] [Indexed: 11/17/2022] Open
Abstract
Background Geobacillus and Parageobacillus are two ecologically diverse thermophilic genera within the phylum Firmicutes. These taxa have long been of biotechnological interest due to their ability to secrete thermostable enzymes and other biomolecules that have direct applications in various industrial and clinical fields. Despite the commercial and industrial interest in these microorganisms, the full scope of the secreted protein, i.e. the secretome, of Geobacillus and Parageobacillus species remains largely unexplored, with most studies focusing on single enzymes. A genome-wide exploration of the global secretome can provide a platform for understanding the extracellular functional “protein cloud” and the roles that secreted proteins play in the survival and adaptation of these biotechnologically relevant organisms. Results In the present study, the global secretion profile of 64 Geobacillus and Parageobacillus strains, comprising 772 distinct proteins, was predicted using comparative genomic approaches. Thirty-one of these proteins are shared across all strains used in this study and function in cell-wall/membrane biogenesis as well as transport and metabolism of carbohydrates, amino acids and inorganic ions. An analysis of the clustering patterns of the secretomes of the 64 strains according to shared functional orthology revealed a correlation between the secreted profiles of different strains and their phylogeny, with Geobacillus and Parageobacillus species forming two distinct functional clades. Conclusions The in silico characterization of the global secretome revealed a metabolically diverse set of secreted proteins, which include proteases, glycoside hydrolases, nutrient binding proteins and toxins. Electronic supplementary material The online version of this article (10.1186/s12934-018-1005-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Habibu Aliyu
- Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Pieter De Maayer
- School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
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Adetunji AI, Olaniran AO. Immobilization and characterization of lipase from an indigenous Bacillus aryabhattai SE3-PB isolated from lipid-rich wastewater. Prep Biochem Biotechnol 2018; 48:898-905. [PMID: 30265208 DOI: 10.1080/10826068.2018.1514517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Extracellular lipase from an indigenous Bacillus aryabhattai SE3-PB was immobilized in alginate beads by entrapment method. After optimization of immobilization conditions, maximum immobilization efficiencies of 77% ± 1.53% and 75.99% ± 3.49% were recorded at optimum concentrations of 2% (w/v) sodium alginate and 0.2 M calcium chloride, respectively, for the entrapped enzyme. Biochemical properties of both free and immobilized lipase revealed no change in the optimum temperature and pH of both enzyme preparations, with maximum activity attained at 60 °C and 9.5, respectively. In comparison to free lipase, the immobilized enzyme exhibited improved stability over the studied pH range (8.5-9.5) and temperature (55-65 °C) when incubated for 3 h. Furthermore, the immobilized lipase showed enhanced enzyme-substrate affinity and higher catalytic efficiency when compared to soluble enzyme. The entrapped enzyme was also found to be more stable, retaining 61.51% and 49.44% of its original activity after being stored for 30 days at 4 °C and 25 °C, respectively. In addition, the insolubilized enzyme exhibited good reusability with 18.46% relative activity after being repeatedly used for six times. These findings suggest the efficient and sustainable use of the developed immobilized lipase for various biotechnological applications.
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Affiliation(s)
- Adegoke Isiaka Adetunji
- a Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science , University of KwaZulu-Natal (Westville Campus) , Durban , Republic of South Africa
| | - Ademola Olufolahan Olaniran
- a Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science , University of KwaZulu-Natal (Westville Campus) , Durban , Republic of South Africa
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Isiaka Adetunji A, Olufolahan Olaniran A. Optimization of culture conditions for enhanced lipase production by an indigenousBacillus aryabhattaiSE3-PB using response surface methodology. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1514985] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Adegoke Isiaka Adetunji
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, Republic of South Africa
| | - Ademola Olufolahan Olaniran
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, Republic of South Africa
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Mohamed RA, Salleh AB, Leow ATC, Yahaya NM, Abdul Rahman MB. Ability of T1 Lipase to Degrade Amorphous P(3HB): Structural and Functional Study. Mol Biotechnol 2018; 59:284-293. [PMID: 28580552 DOI: 10.1007/s12033-017-0012-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
An enzyme with broad substrate specificity would be an asset for industrial application. T1 lipase apparently has the same active site residues as polyhydroxyalkanoates (PHA) depolymerase. Sequences of both enzymes were studied and compared, and a conserved lipase box pentapeptide region around the nucleophilic serine was detected. The alignment of 3-D structures for both enzymes showed their active site residues were well aligned with an RMSD value of 1.981 Å despite their sequence similarity of only 53.8%. Docking of T1 lipase with P(3HB) gave forth high binding energy of 5.4 kcal/mol, with the distance of 4.05 Å between serine hydroxyl (OH) group of TI lipase to the carbonyl carbon of the substrate, similar to the native PhaZ7 Pl . This suggests the possible ability of T1 lipase to bind P(3HB) in its active site. The ability of T1 lipase in degrading amorphous P(3HB) was investigated on 0.2% (w/v) P(3HB) plate. Halo zone was observed around the colony containing the enzyme which confirms that T1 lipase is indeed able to degrade amorphous P(3HB). Results obtained in this study highlight the fact that T1 lipase is a versatile hydrolase enzyme which does not only record triglyceride degradation activity but amorphous P(3HB) degradation activity as well.
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Affiliation(s)
- Rauda A Mohamed
- Laboratory of Enzyme Technology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Laboratory of Enzyme Technology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Adam Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Normi M Yahaya
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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Pervasiveness of UVC254-resistant Geobacillus strains in extreme environments. Appl Microbiol Biotechnol 2018; 102:1869-1887. [DOI: 10.1007/s00253-017-8712-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/09/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]
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15
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Characterization of a Novel Alkalophilic Lipase From Aneurinibacillus thermoaerophilus: Lid Heterogeneity and Assignment to Family I.5. Protein J 2017; 36:478-488. [PMID: 28975457 DOI: 10.1007/s10930-017-9743-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Recent investigations of Aneurinibacillus thermoaerophilus strains have allowed identification of a unique solvent tolerant lipase, distinct from known lipases. This work reports the expression and purification of this lipase (LipAT) and the first characterization of its structure and temperature and pH-dependent behaviour. LipAT has a secondary structural content compatible with the canonical lipase α/β hydrolase fold, and is dimeric at neutral pH. The protein was folded from pH 5 to 10, and association into folded aggregates at pH 7 and 8 likely protected its secondary structures from thermal unfolding. The enzyme was active from 25 to 65 °C under neutral pH, but its maximal activity was detected at pH 10 and 45 °C. The ability of LipAT to recover from high temperature was investigated. Heating at 70 °C and pH 10 followed by cooling prevented the restoration of activity, while similar treatments performed at pH 8 (where folded aggregates may form) allowed recovery of 50% of the initial activity. In silico analyses revealed a high conservation (85% or more) for the main lipase signature sequences in LipAT despite an overall low residue identity (60% identity compared to family I.5 lipases). In contrast, the active site lid region in LipAT is very distinct showing only 25% amino acid sequence identity to other homologous lipases in this region. Comparison of lids among lipases from the I.5 family members and LipAT reveals that this region should be a primary target for elucidation, optimisation and prediction of structure-function relationships in lipases.
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Identification of lipolytic enzymes isolated from bacteria indigenous to Eucalyptus wood species for application in the pulping industry. ACTA ACUST UNITED AC 2017; 15:114-124. [PMID: 28794998 PMCID: PMC5545822 DOI: 10.1016/j.btre.2017.07.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/21/2017] [Accepted: 07/11/2017] [Indexed: 11/20/2022]
Abstract
Phenol red screening plates is the best method for detecting lipolytic activity. Substrate specificity is affected by temperature and pH. Essential to test substrates at various pH and temperature to determine optima. Lipolytic enzymes indigenous to Eucalyptus sp. can assist in pitch control.
This study highlights the importance of determining substrate specificity at variable experimental conditions. Lipases and esterases were isolated from microorganisms cultivated from Eucalyptus wood species and then concentrated (cellulases removed) and characterized. Phenol red agar plates supplemented with 1% olive oil or tributyrin was ascertained to be the most favourable method of screening for lipolytic activity. Lipolytic activity of the various enzymes were highest at 45–61 U/ml at the optimum temperature and pH of between at 30–35 °C and pH 4–5, respectively. Change in pH influenced the substrate specificity of the enzymes tested. The majority of enzymes tested displayed a propensity for longer aliphatic acyl chains such as dodecanoate (C12), myristate (C14), palmitate (C16) and stearate (C18) indicating that they could be characterised as potential lipases. Prospective esterases were also detected with specificity towards acetate (C2), butyrate (C4) and valerate (C5). Enzymes maintained up to 95% activity at the optimal pH and temperature for 2–3 h. It is essential to test substrates at various pH and temperature when determining optimum activity of lipolytic enzymes, a method rarely employed. The stability of the enzymes at acidic pH and moderate temperatures makes them excellent candidates for application in the treatment of pitch during acid bi-sulphite pulping, which would greatly benefit the pulp and paper industry.
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17
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Aliyu H, Lebre P, Blom J, Cowan D, De Maayer P. Phylogenomic re-assessment of the thermophilic genus Geobacillus. Syst Appl Microbiol 2016; 39:527-533. [DOI: 10.1016/j.syapm.2016.09.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/21/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022]
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Facile modulation of enantioselectivity of thermophilic Geobacillus zalihae lipase by regulating hydrophobicity of its Q114 oxyanion. Enzyme Microb Technol 2016; 93-94:174-181. [DOI: 10.1016/j.enzmictec.2016.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/20/2016] [Accepted: 08/30/2016] [Indexed: 01/04/2023]
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20
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Koc M, Cokmus C, Cihan AC. The genotypic diversity and lipase production of some thermophilic bacilli from different genera. Braz J Microbiol 2016; 46:1065-76. [PMID: 26691464 PMCID: PMC4704621 DOI: 10.1590/s1517-838246420140942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 04/12/2015] [Indexed: 11/26/2023] Open
Abstract
Thermophilic 32 isolates and 20 reference bacilli were subjected to
Rep-PCR and ITS-PCR fingerprinting for determination of their
genotypic diversity, before screening lipase activities. By these methods, all the
isolates and references could easily be differentiated up to subspecies level from
each other. In screening assay, 11 isolates and 7 references were found to be lipase
producing. Their extracellular lipase activities were measured quantitatively by
incubating in both tributyrin and olive oil broths at 60 °C and pH 7.0. During the
24, 48 and 72-h period of incubation, the changes in the lipase activities, culture
absorbance, wet weight of biomass and pH were all measured. The activity was
determined by using pNPB in 50 mM phosphate buffer at pH 7.0 at 60
°C. The lipase production of the isolates in olive oil broths varied between 0.008
and 0.052, whereas these values were found to be 0.002-0.019 (U/mL) in the case of
tyributyrin. For comparison, an index was established by dividing the lipase
activities to cell biomass (U/mg). The maximum thermostable lipase production was
achieved by the isolates F84a, F84b, and G. thermodenitrificans DSM
465T (0.009, 0.008 and 0.008 U/mg) within olive oil broth, whereas
G. stearothermophilus A113 displayed the highest lipase activity
than its type strain in tyributyrin. Therefore, as some of these isolates displayed
higher activities in comparison to references, new lipase producing bacilli were
determined by presenting their genotypic diversity with DNA fingerprinting
techniques.
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Affiliation(s)
- Melih Koc
- Biology Department, Faculty of Science, Ankara University, Ankara, Turkey
| | | | - Arzu Coleri Cihan
- Biology Department, Faculty of Science, Ankara University, Ankara, Turkey
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Lipase-Secreting Bacillus Species in an Oil-Contaminated Habitat: Promising Strains to Alleviate Oil Pollution. BIOMED RESEARCH INTERNATIONAL 2015; 2015:820575. [PMID: 26180812 PMCID: PMC4477129 DOI: 10.1155/2015/820575] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/04/2015] [Indexed: 11/17/2022]
Abstract
Lipases are of great interest for different industrial applications due to their diversity and versatility. Among different lipases, microbial lipases are preferable due to their broad substrate specificity, and higher stability with lower production costs compared to the lipases from plants and animals. In the past, a vast number of bacterial species have been reported as potential lipases producers. In this study, the lipases-producing bacterial species were isolated from an oil spillage area in the conventional night market. Isolated species were identified as Bacillus species by biochemical tests which indicate their predominant establishment, and further screened on the agar solid surfaces using lipid and gelatin as the substrates. Out of the ten strains tested, four potential strains were subjected to comparison analysis of the lipolytic versus proteolytic activities. Strain 10 exhibited the highest lipolytic and proteolytic activity. In all the strains, the proteolytic activity is higher than the lipolytic activity except for strain 8, suggesting the possibility for substrate-based extracellular gene induction. The simultaneous secretion of both the lipase and protease is a mean of survival. The isolated bacterial species which harbour both lipase and protease enzymes could render potential industrial-based applications and solve environmental issues.
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Yuan D, Lan D, Xin R, Yang B, Wang Y. Screening and characterization of a thermostable lipase from marine Streptomyces sp. strain W007. Biotechnol Appl Biochem 2015; 63:41-50. [PMID: 25639796 DOI: 10.1002/bab.1338] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 12/26/2014] [Indexed: 12/31/2022]
Abstract
A screening method along with the combination of genome sequence of microorganism, pairwise alignment, and lipase classification was used to search the thermostable lipase. Then, a potential thermostable lipase (named MAS1) from marine Streptomyces sp. strain W007 was expressed in Pichia pastoris X-33, and the biochemical properties were characterized. Lipase MAS1 belongs to the subfamily I.7, and it has 38% identity to the well-characterized Bacillus subtilis thermostable lipases in the subfamily I.4. The purified enzyme was estimated to be 29 kDa. The enzyme showed optimal temperature at 40 °C, and retained more than 80% of initial activity after 1 H incubation at 60 °C, suggesting that MAS1 was a thermostable lipase. MAS1 was an alkaline enzyme with optimal pH value at 7.0 and had stable activity for 12 H of incubation at pH 6.0-9.0. It was stable and retained about 90% of initial activity in the presence of Cu(2+) , Ca(2+) , Ni(2+) , and Mg(2+) , whereas 89.05% of the initial activity was retained when ethylene diamine tetraacetic acid was added. MAS1 showed the tolerance to organic solvents, but was inhibited by various surfactants. MAS1 was verified to be a triglyceride lipase and could hydrolyze triacylglycerol and diacylglycerol. The result represents a good example for researchers to discover thermostable lipase for industrial application.
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Affiliation(s)
- Dongjuan Yuan
- College of Light Industry and Food Sciences, Key Lab of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, People's Republic of China
| | - Dongming Lan
- College of Light Industry and Food Sciences, Key Lab of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, People's Republic of China
| | - Ruipu Xin
- College of Light Industry and Food Sciences, Key Lab of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, People's Republic of China
| | - Bo Yang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, People's Republic of China
| | - Yonghua Wang
- College of Light Industry and Food Sciences, Key Lab of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, People's Republic of China
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de Melo MR, Moraes TC, da Rocha CB, Moreira Gasparin FG, Colabone Celligoi MAP. Effect of carbon source on lipase production by Aeromonas sp. isolated from dairy effluent. BMC Proc 2014. [PMCID: PMC4211096 DOI: 10.1186/1753-6561-8-s4-p245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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24
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Jang HM, Lee JW, Ha JH, Park JM. Effects of organic loading rates on reactor performance and microbial community changes during thermophilic aerobic digestion process of high-strength food wastewater. BIORESOURCE TECHNOLOGY 2013; 148:261-269. [PMID: 24055968 DOI: 10.1016/j.biortech.2013.08.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 06/02/2023]
Abstract
To evaluate the applicability of single-stage thermophilic aerobic digestion (TAD) process treating high-strength food wastewater (FWW), TAD process was operated at four organic loading rates (OLRs) from 9.2 to 37.2 kg COD/m(3)d. The effects of OLRs on microbial community changes were also examined. The highest volumetric removal rate (13.3 kg COD/m(3)d) and the highest thermo-stable protease activity (0.95 unit/mL) were detected at OLR=18.6 kg COD/m(3)d. Denaturing gradient gel electrophoresis (DGGE) profiles and quantitative PCR (qPCR) results showed significant microbial community shifts in response to changes in OLR. In particular, DGGE and phylogenetic analysis demonstrate that the presence of Bacillus sp. (phylum of Firmicutes) was strongly correlated with efficient removal of organic particulates from high-strength food wastewater.
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Affiliation(s)
- Hyun Min Jang
- School of Environmental Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea
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25
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Mahadevan GD, Neelagund SE. Thermostable lipase from Geobacillus sp. Iso5: bioseparation, characterization and native structural studies. J Basic Microbiol 2013; 54:386-96. [PMID: 23775834 DOI: 10.1002/jobm.201200656] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 11/13/2012] [Indexed: 11/09/2022]
Abstract
The extracellular thermoalkaline lipase from Geobacillus sp. Iso5 was purified to homogeneity by ultrafiltration, 6% cross-linked agarose and Phenyl spehrose HIC column chromatography. The final purified lipase resulted in 8.7-fold with 6.2% yield. The relative molecular weight of the enzyme was determined to be a monomer of 47 kDa by SDS-PAGE and MALDI-TOF MS/MS spectroscopy. The purified enzyme exhibit optimum activity at 70 °C and pH 8.0. The enzyme retained above 90% activity at temperatures of 70 °C and about 35% activity at 85 °C for 2 h. However, the stability of the enzyme decreased at the temperature over 90 °C. The enzyme activity was promoted in the presence of Ca(2+) and Mg(2+) and strongly inhibited by HgCl2 , PMSF, DTT, K(+) , Co(2+) , and Zn (2+) . EDTA did not affect the enzyme activity. The secondary structure of purified lipase contains 36% α-helix and 64% β-sheet which was determined by Circular dichromism, FTIR, and Raman Spectroscopy.
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Affiliation(s)
- Gurumurthy D Mahadevan
- Department of PG Studies and Research in Biochemistry, Jnana Sahyadri, Kuvempu University, Shankaraghatta, Karnataka, India
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26
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Unraveling the lipolytic activity of thermophilic bacteria isolated from a volcanic environment. BIOMED RESEARCH INTERNATIONAL 2013; 2013:703130. [PMID: 23738330 PMCID: PMC3662197 DOI: 10.1155/2013/703130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 03/25/2013] [Indexed: 11/17/2022]
Abstract
In a bioprospecting effort towards novel thermostable lipases, we assessed the lipolytic profile of 101 bacterial strains isolated from the volcanic area of Santorini, Aegean Sea, Greece. Screening of lipase activity was performed both in agar plates and liquid cultures using olive oil as carbon source. Significant differences were observed between the two screening methods with no clear correlation between them. While the percentage of lipase producing strains identified in agar plates was only 17%, lipolytic activity in liquid culture supernatants was detected for 74% of them. Nine strains exhibiting elevated extracellular lipase activities were selected for lipase production and biochemical characterization. The majority of lipase producers revealed high phylogenetic similarity with Geobacillus species and related genera, whilst one of them was identified as Aneurinibacillus sp. Lipase biosynthesis strongly depended on the carbon source that supplemented the culture medium. Olive oil induced lipase production in all strains, but maximum enzyme yields for some of the strains were also obtained with Tween-80, mineral oil, and glycerol. Partially purified lipases revealed optimal activity at 70–80°C and pH 8-9. Extensive thermal stability studies revealed marked thermostability for the majority of the lipases as well as a two-step thermal deactivation pattern.
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Rahman MZA, Salleh AB, Rahman RNZRA, Rahman MBA, Basri M, Leow TC. Unlocking the mystery behind the activation phenomenon of T1 lipase: a molecular dynamics simulations approach. Protein Sci 2012; 21:1210-21. [PMID: 22692819 PMCID: PMC3537241 DOI: 10.1002/pro.2108] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 06/04/2012] [Accepted: 06/04/2012] [Indexed: 12/30/2022]
Abstract
The activation of lipases has been postulated to proceed by interfacial activation, temperature switch activation, or aqueous activation. Recently, based on molecular dynamics (MD) simulation experiments, the T1 lipase activation mechanism was proposed to involve aqueous activation in addition to a double-flap mechanism. Because the open conformation structure is still unavailable, it is difficult to validate the proposed theory unambiguously to understand the behavior of the enzyme. In this study, we try to validate the previous reports and uncover the mystery behind the activation process using structural analysis and MD simulations. To investigate the effects of temperature and environmental conditions on the activation process, MD simulations in different solvent environments (water and water-octane interface) and temperatures (20, 50, 70, 80, and 100°C) were performed. Based on the structural analysis of the lipases in the same family of T1 lipase (I.5 lipase family), we proposed that the lid domain comprises α6 and α7 helices connected by a loop, thus forming a helix-loop-helix motif involved in interfacial activation. Throughout the MD simulations experiments, lid displacements were only observed in the water-octane interface, not in the aqueous environment with respect to the temperature effect, suggesting that the activation process is governed by interfacial activation coupled with temperature switch activation. Examining the activation process in detail revealed that the large structural rearrangement of the lid domain was caused by the interaction between the hydrophobic residues of the lid with octane, a nonpolar solvent, and this conformation was found to be thermodynamically favorable.
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Affiliation(s)
| | - Abu Bakar Salleh
- Institute of Bioscience, Universiti Putra Malaysia43400 Serdang, Selangor
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia43400 Serdang, Selangor
| | - Raja Noor Zaliha Raja Abdul Rahman
- Institute of Bioscience, Universiti Putra Malaysia43400 Serdang, Selangor
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia43400 Serdang, Selangor
| | | | - Mahiran Basri
- Institute of Bioscience, Universiti Putra Malaysia43400 Serdang, Selangor
- Faculty of Science, Universiti Putra Malaysia43400 Serdang, Selangor
| | - Thean Chor Leow
- Institute of Bioscience, Universiti Putra Malaysia43400 Serdang, Selangor
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia43400 Serdang, Selangor
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Kumar S, Karan R, Kapoor S, S P S, S K K. Screening and isolation of halophilic bacteria producing industrially important enzymes. Braz J Microbiol 2012; 43:1595-603. [PMID: 24031991 PMCID: PMC3769037 DOI: 10.1590/s1517-838220120004000044] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 12/15/2011] [Accepted: 06/07/2012] [Indexed: 11/22/2022] Open
Abstract
Halophiles are excellent sources of enzymes that are not only salt stable but also can withstand and carry out reactions efficiently under extreme conditions. The aim of the study was to isolate and study the diversity among halophilic bacteria producing enzymes of industrial value. Screening of halophiles from various saline habitats of India led to isolation of 108 halophilic bacteria producing industrially important hydrolases (amylases, lipases and proteases). Characterization of 21 potential isolates by morphological, biochemical and 16S rRNA gene analysis found them related to Marinobacter, Virgibacillus, Halobacillus, Geomicrobium, Chromohalobacter, Oceanobacillus, Bacillus, Halomonas and Staphylococcus genera. They belonged to moderately halophilic group of bacteria exhibiting salt requirement in the range of 3–20%. There is significant diversity among halophiles from saline habitats of India. Preliminary characterization of crude hydrolases established them to be active and stable under more than one extreme condition of high salt, pH, temperature and presence of organic solvents. It is concluded that these halophilic isolates are not only diverse in phylogeny but also in their enzyme characteristics. Their enzymes may be potentially useful for catalysis under harsh operational conditions encountered in industrial processes. The solvent stability among halophilic enzymes seems a generic novel feature making them potentially useful in non-aqueous enzymology.
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Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Technology , Delhi, New Delhi , India
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29
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Complete genome sequence of the thermophilic bacterium Geobacillus thermoleovorans CCB_US3_UF5. J Bacteriol 2012; 194:1239. [PMID: 22328744 DOI: 10.1128/jb.06580-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Geobacillus thermoleovorans CCB_US3_UF5 is a thermophilic bacterium isolated from a hot spring in Malaysia. Here, we report the complete genome of G. thermoleovorans CCB_US3_UF5, which shows high similarity to the genome of Geobacillus kaustophilus HTA 426 in terms of synteny and orthologous genes.
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30
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Abstract
Lipases are ubiquitous enzymes, widespread in nature. They were first isolated from bacteria in the early nineteenth century and the associated research continuously increased due to the particular characteristics of these enzymes. This chapter reviews the main sources, structural properties, and industrial applications of these highly studied enzymes.
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Affiliation(s)
- Leticia Casas-Godoy
- Equipe de Catalyse et Ingénierie Moléculaire Enzymatique, Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, Université de Toulouse, INSA, UPS, INP, LISBP, Toulouse, France
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31
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Jing F, Cantu DC, Tvaruzkova J, Chipman JP, Nikolau BJ, Yandeau-Nelson MD, Reilly PJ. Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity. BMC BIOCHEMISTRY 2011; 12:44. [PMID: 21831316 PMCID: PMC3176148 DOI: 10.1186/1471-2091-12-44] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 08/10/2011] [Indexed: 11/24/2022]
Abstract
Background Acyl-acyl carrier protein thioesterases (acyl-ACP TEs) catalyze the hydrolysis of the thioester bond that links the acyl chain to the sulfhydryl group of the phosphopantetheine prosthetic group of ACP. This reaction terminates acyl chain elongation of fatty acid biosynthesis, and in plant seeds it is the biochemical determinant of the fatty acid compositions of storage lipids. Results To explore acyl-ACP TE diversity and to identify novel acyl ACP-TEs, 31 acyl-ACP TEs from wide-ranging phylogenetic sources were characterized to ascertain their in vivo activities and substrate specificities. These acyl-ACP TEs were chosen by two different approaches: 1) 24 TEs were selected from public databases on the basis of phylogenetic analysis and fatty acid profile knowledge of their source organisms; and 2) seven TEs were molecularly cloned from oil palm (Elaeis guineensis), coconut (Cocos nucifera) and Cuphea viscosissima, organisms that produce medium-chain and short-chain fatty acids in their seeds. The in vivo substrate specificities of the acyl-ACP TEs were determined in E. coli. Based on their specificities, these enzymes were clustered into three classes: 1) Class I acyl-ACP TEs act primarily on 14- and 16-carbon acyl-ACP substrates; 2) Class II acyl-ACP TEs have broad substrate specificities, with major activities toward 8- and 14-carbon acyl-ACP substrates; and 3) Class III acyl-ACP TEs act predominantly on 8-carbon acyl-ACPs. Several novel acyl-ACP TEs act on short-chain and unsaturated acyl-ACP or 3-ketoacyl-ACP substrates, indicating the diversity of enzymatic specificity in this enzyme family. Conclusion These acyl-ACP TEs can potentially be used to diversify the fatty acid biosynthesis pathway to produce novel fatty acids.
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Affiliation(s)
- Fuyuan Jing
- Department of Biochemistry, Biophysics, and Molecular Biology, Biorenewables Research Laboratory Building, Iowa State University, Ames, Iowa 50011-3270, USA
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Isolation and identification of lipase producing thermophilic Geobacillus sp. SBS-4S: Cloning and characterization of the lipase. J Biosci Bioeng 2011; 111:272-8. [DOI: 10.1016/j.jbiosc.2010.11.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/15/2010] [Accepted: 11/19/2010] [Indexed: 11/23/2022]
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Guncheva M, Zhiryakova D. Catalytic properties and potential applications of Bacillus lipases. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2010.09.002] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Cheong KW, Leow TC, Rahman RNZRA, Basri M, Rahman MBA, Salleh AB. Reductive Alkylation Causes the Formation of a Molten Globule-Like Intermediate Structure in Geobacillus zalihae Strain T1 Thermostable Lipase. Appl Biochem Biotechnol 2010; 164:362-75. [DOI: 10.1007/s12010-010-9140-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 11/29/2010] [Indexed: 11/28/2022]
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Sequential optimization of production of a thermostable and organic solvent tolerant lipase by recombinant Escherichia coli. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0170-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Sifour M, Saeed H, Zaghloul T, Berekaa M, Abdel-Fatt Y. Purification and Properties of a Lipase from Thermophilic Geobacillus stearothermophilus Strain-5. ACTA ACUST UNITED AC 2010. [DOI: 10.3923/ijbc.2010.203.212] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Dinsdale AE, Halket G, Coorevits A, Van Landschoot A, Busse HJ, De Vos P, Logan NA. Emended descriptions of Geobacillus thermoleovorans and Geobacillus thermocatenulatus. Int J Syst Evol Microbiol 2010; 61:1802-1810. [PMID: 20817844 DOI: 10.1099/ijs.0.025445-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nineteen thermophilic, aerobic, endospore-forming bacterial strains were subjected to 16S rRNA gene sequence analysis. Eight of these strains had been received as cultures of Geobacillus kaustophilus, G. lituanicus, G. stearothermophilus, 'G. thermoleovorans subsp. stromboliensis', G. vulcani, 'Bacillus caldolyticus', 'B. caldotenax' and 'B. caldovelox', but they showed close relationships with the type strain of G. thermoleovorans, as did two other strains received as G. thermoleovorans. All strains underwent further taxonomic analysis by API and other phenotypic tests and fatty acid methyl ester analysis, and selected strains were analysed for their polar lipids and for DNA relatedness. The 11 strains that formed the G. thermoleovorans 16S rRNA cluster also showed some phenotypic similarities, and DNA relatedness data support the reassignment of the strains received as G. kaustophilus, G. lituanicus, 'G. thermoleovorans subsp. stromboliensis', G. vulcani, 'B. caldolyticus', 'B. caldotenax' and 'B. caldovelox', and one of the G. stearothermophilus strains, as members of the species G. thermoleovorans. Four other strains received as G. kaustophilus were misnamed; two were identified as G. stearothermophilus and two appeared to be closely related to Anoxybacillus rupiensis. One strain received as G. stearothermophilus remained unidentified. On the basis of a single strain, Geobacillus thermocatenulatus was shown to represent a distinct species, but study of the type strain of Geobacillus gargensis showed this species to be a later heterotypic synonym of Geobacillus thermocatenulatus. Emended descriptions of Geobacillus thermoleovorans and Geobacillus thermocatenulatus are therefore presented.
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Affiliation(s)
- Anna E Dinsdale
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow, G4 0BA, UK
| | - Gillian Halket
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow, G4 0BA, UK
| | - An Coorevits
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Department of Applied Engineering Sciences, Laboratory of Biochemistry and Brewing, University College Ghent, Schoonmeersstraat 52, B-9000 Ghent, Belgium
| | - Anita Van Landschoot
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Department of Applied Engineering Sciences, Laboratory of Biochemistry and Brewing, University College Ghent, Schoonmeersstraat 52, B-9000 Ghent, Belgium
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie & Hygiene, Veterinärmedizinische Universität, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Paul De Vos
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Niall A Logan
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow, G4 0BA, UK
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Wang Y, Wei DQ, Wang JF. Molecular dynamics studies on T1 lipase: insight into a double-flap mechanism. J Chem Inf Model 2010; 50:875-8. [PMID: 20443585 DOI: 10.1021/ci900458u] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
T1 lipase is isolated from the palm Geobacillus zalihae strain T1 in Malaysia, functioning as a secreted protein responsible for the catalyzing hydrolysis of long-chain triglycerides into fatty acids and glycerol at high temperatures. In the current study, using 30 ns molecular dynamics simulations at different temperatures, an aqueous activation was detected for T1 lipase. This aqueous activation in T1 lipase was mainly caused by a double-flap movement mechanism. The double flaps were constituted by the hydrophobic helices 6 and 9. Helix 6 employed two major components with the hydrophilic part at the surface and the hydrophobic part inside. In the aqueous solution, the hydrophobic part could provide enough power for helix 6 to move away, driving the protein into an open configuration and exposing the catalytic triad. Our findings could provide structural evidence to support the double-flap movement, revealing the catalytic mechanism for T1 lipase.
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Affiliation(s)
- Ying Wang
- College of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
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Ren Y, Strobel G, Sears J, Park M. Geobacillus sp., a thermophilic soil bacterium producing volatile antibiotics. MICROBIAL ECOLOGY 2010; 60:130-136. [PMID: 20091406 DOI: 10.1007/s00248-009-9630-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 12/16/2009] [Indexed: 05/28/2023]
Abstract
Geobacillus, a bacterial genus, is represented by over 25 species of Gram-positive isolates from various man-made and natural thermophilic areas around the world. An isolate of this genus (M-7) has been acquired from a thermal area near Yellowstone National Park, MT and partially characterized. The cells of this organism are globose (ca. 0.5 mu diameter), and they are covered in a matrix capsule which gives rise to elongate multicelled bacilliform structures (ranging from 3 to 12 mum) as seen by light and atomic force microscopy, respectively. The organism produces unique petal-shaped colonies (undulating margins) on nutrient agar, and it has an optimum pH of 7.0 and an optimum temperature range of 55-65 degrees C. The partial 16S rRNA sequence of this organism has 97% similarity with Geobacillus stearothermophilus, one of its closest relatives genetically. However, uniquely among all members of this genus, Geobacillus sp. (M-7) produces volatile organic substances (VOCs) that possess potent antibiotic activities. Some of the more notable components of the VOCs are benzaldehyde, acetic acid, butanal, 3-methyl-butanoic acid, 2-methyl-butanoic acid, propanoic acid, 2-methyl-, and benzeneacetaldehyde. An exposure of test organisms such as Aspergillus fumigatus, Botrytis cinerea, Verticillium dahliae, and Geotrichum candidum produced total inhibition of growth on a 48-h exposure to Geobacillus sp.(M-7) cells (ca.10(7)) and killing at a 72-h exposure at higher bacterial cell concentrations. A synthetic mixture of those available volatile compounds, at the ratios occurring in Geobacillus sp. (M-7), mimicked the bioactivity of this organism.
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Affiliation(s)
- Yuhao Ren
- Department of Plant Sciences, Montana State University, Bozeman, MT 59717, USA
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Identification and characterization of thermophilic bacteria isolated from hot springs in Turkey. J Microbiol Methods 2009; 79:321-8. [DOI: 10.1016/j.mimet.2009.09.026] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 09/29/2009] [Accepted: 09/30/2009] [Indexed: 11/17/2022]
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Miñana-Galbis D, Pinzón DL, Lorén JG, Manresa À, Oliart-Ros RM. Reclassification of Geobacillus pallidus (Scholz et al. 1988) Banat et al. 2004 as Aeribacillus pallidus gen. nov., comb. nov. Int J Syst Evol Microbiol 2009; 60:1600-1604. [PMID: 19700455 DOI: 10.1099/ijs.0.003699-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although Anoxybacillus and Geobacillus, two genera of thermophilic bacteria close to the genus Bacillus, have only been described recently, the number of species in these genera has increased rapidly. Four thermophilic, lipolytic strains (DR01, DR02, DR03 and DR04) isolated from a hot spring in Veracruz (Mexico), which could not be identified phenotypically, were subjected to 16S rRNA gene sequence analysis. Three strains were identified as belonging to the genus Anoxybacillus, but strain DR03 was identified as Geobacillus pallidus. This result led us to perform a phylogenetic analysis of the genera Anoxybacillus and Geobacillus based on 16S rRNA gene sequences from all the type strains of these genera. Phylogenetic trees showed three major clusters, Anoxybacillus-Geobacillus tepidamans, Geobacillus sensu stricto and Geobacillus pallidus, while the 16S rRNA gene sequences of G. pallidus (DR03 and the type strain) showed low similarity to sequences of Anoxybacillus (92.5-95.1 %) and Geobacillus (92.8-94.5 %) species, as well as to Bacillus subtilis (92.2-92.4 %). In addition, G. pallidus could be differentiated from Anoxybacillus and Geobacillus on the basis of DNA G+C content and fatty acid and polar lipid profiles. From these results, it is proposed that Geobacillus pallidus should be classified in a novel genus, for which we propose the name Aeribacillus, as Aeribacillus pallidus gen. nov., comb. nov. The type strain of Aeribacillus pallidus is H12(T) (=ATCC 51176(T) =DSM 3670(T) =LMG 19006(T)).
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Affiliation(s)
- David Miñana-Galbis
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Dora L Pinzón
- Unidad de Investigación y Desarrollo en Alimentos, Instituto Tecnológico de Veracruz, Av. Miguel A. de Quevedo 2779, 91860 Veracruz, Ver., Mexico
| | - J Gaspar Lorén
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Àngels Manresa
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Rosa M Oliart-Ros
- Unidad de Investigación y Desarrollo en Alimentos, Instituto Tecnológico de Veracruz, Av. Miguel A. de Quevedo 2779, 91860 Veracruz, Ver., Mexico
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Wu TY, Mohammad AW, Jahim JM, Anuar N. A holistic approach to managing palm oil mill effluent (POME): Biotechnological advances in the sustainable reuse of POME. Biotechnol Adv 2009; 27:40-52. [DOI: 10.1016/j.biotechadv.2008.08.005] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Revised: 08/19/2008] [Accepted: 08/21/2008] [Indexed: 10/21/2022]
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