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Zeb A, Khan Y, He H, Zhang D, Shen S. Molecular identification of Halomonas AZ07 and its multifunctional enzymatic activities to degrade Pyropia yezoensis under high-temperature condition. Mol Biol Rep 2024; 51:816. [PMID: 39012539 DOI: 10.1007/s11033-024-09724-x] [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] [Received: 04/12/2024] [Accepted: 06/13/2024] [Indexed: 07/17/2024]
Abstract
BACKGROUND Pyropia yezoensis a commercially important red seaweed species, is susceptible to various microorganisms infections, among which bacterial infections are the most prominent ones. Pyropia yezoensis is often affected by harmful bacterial communities under high temperatures that can lead to its degradation and economic losses. The current study aimed to explore Pyropia yezoensis-associated microbiota and further identify potential isolates, which can degrade Pyropia yezoensis under high-temperature conditions. METHODS AND RESULTS The 16S rRNA gene sequencing was used to identify the agarolytic bacterial species. The results showed that Chromohalobacter sp. strain AZ6, Pseudoalteromonas sp. strain AZ, Psychrobacter sp. strain AZ3, Vibrio sp. strain AZ, and Halomonas sp. strain AZ07 exhibited algicidal properties as these strains were more abundant at high temperature (25 °C). Among the five isolated strains, the potential isolate Halomonas sp. strain AZ07 showed high production of agarolytic enzymes, including lipase, protease, cellulase, and amylase. This study confirmed that the isolated strain could produce these four different enzymes. The strain Halomonas AZ07 was co-treated with Pyropia yezoensis cells under two different temperature environments, including 13 °C and 25 °C. The degradation of Pyropia yezoensis occurred at the optimum temperature of 25 °C and effectively degraded their cell wall, proteins, lipids, and carbohydrates. CONCLUSION The successful cultivation of Pyropia yezoensis in coastal farm environments is dependent on specific temperature and environmental factors, and lower temperatures have been observed to be particularly beneficial for the survival and growth of Pyropia yezoensis. The temperature below 13 °C was confirmed to be the best niche for the symbiotic relationship of microbiota associated with Pyropia yezoensis for its growth, development, and production.
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Affiliation(s)
- Aurang Zeb
- Department of Cell Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215006, China
| | - Yasmin Khan
- Department of Biology, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hongyan He
- Department of Cell Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215006, China
| | - Dongren Zhang
- Department of Cell Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215006, China
| | - Songdong Shen
- Department of Cell Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215006, China.
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2
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Salazar-Alekseyeva K, Herndl GJ, Baltar F. Influence of Salinity on the Extracellular Enzymatic Activities of Marine Pelagic Fungi. J Fungi (Basel) 2024; 10:152. [PMID: 38392824 PMCID: PMC10890631 DOI: 10.3390/jof10020152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 02/24/2024] Open
Abstract
Even though fungi are ubiquitous in the biosphere, the ecological knowledge of marine fungi remains rather rudimentary. Also, little is known about their tolerance to salinity and how it influences their activities. Extracellular enzymatic activities (EEAs) are widely used to determine heterotrophic microbes' enzymatic capabilities and substrate preferences. Five marine fungal species belonging to the most abundant pelagic phyla (Ascomycota and Basidiomycota) were grown under non-saline and saline conditions (0 g/L and 35 g/L, respectively). Due to their sensitivity and specificity, fluorogenic substrate analogues were used to determine hydrolytic activity on carbohydrates (β-glucosidase, β-xylosidase, and N-acetyl-β-D-glucosaminidase); peptides (leucine aminopeptidase and trypsin); lipids (lipase); organic phosphorus (alkaline phosphatase), and sulfur compounds (sulfatase). Afterwards, kinetic parameters such as maximum velocity (Vmax) and half-saturation constant (Km) were calculated. All fungal species investigated cleaved these substrates, but some species were more efficient than others. Moreover, most enzymatic activities were reduced in the saline medium, with some exceptions like sulfatase. In non-saline conditions, the average Vmax ranged between 208.5 to 0.02 μmol/g biomass/h, and in saline conditions, 88.4 to 0.02 μmol/g biomass/h. The average Km ranged between 1553.2 and 0.02 μM with no clear influence of salinity. Taken together, our results highlight a potential tolerance of marine fungi to freshwater conditions and indicate that changes in salinity (due to freshwater input or evaporation) might impact their enzymatic activities spectrum and, therefore, their contribution to the oceanic elemental cycles.
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Affiliation(s)
- Katherine Salazar-Alekseyeva
- Bio-Oceanography and Marine Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
- Bioprocess Engineering Group, Department of Agrotechnology and Food Sciences, Wageningen University and Research, 6708 WG Wageningen, The Netherlands
| | - Gerhard J Herndl
- Bio-Oceanography and Marine Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), University of Utrecht, 1790 AB Texel, The Netherlands
| | - Federico Baltar
- Bio-Oceanography and Marine Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
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3
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Sun X, Zhang G, Shi Y, Zhu D, Cheng L. Efficient flocculation pretreatment of coal gasification wastewater by halophilic bacterium Halovibrio variabilis TG-5. Extremophiles 2024; 28:11. [PMID: 38240933 DOI: 10.1007/s00792-023-01328-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/28/2023] [Indexed: 01/23/2024]
Abstract
The isolated halophilic bacterial strain Halovibrio variabilis TG-5 showed a good performance in the pretreatment of coal gasification wastewater. With the optimum culture conditions of pH = 7, a temperature of 46 °C, and a salinity of 15%, the chemical oxygen demand and volatile phenol content of pretreated wastewater were decreased to 1721 mg/L and 94 mg/L, respectively. The removal rates of chemical oxygen demand and volatile phenol were over 90% and 70%, respectively. At the optimum salinity conditions of 15%, the total yield of intracellular compatible solutes and the extracellular transient released yield under hypotonic conditions were increased to 6.88 g/L and 3.45 g/L, respectively. The essential compatible solutes such as L-lysine, L-valine, and betaine were important in flocculation mechanism in wastewater pretreatment. This study provided a new method for pretreating coal gasification wastewater by halophilic microorganisms, and revealed the crucial roles of compatible solutes in the flocculation process.
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Affiliation(s)
- Xin Sun
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- Tianjin Key Laboratory of Brine Chemical Engineering and Resource Eco-Utilization, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Gangsheng Zhang
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- Tianjin Key Laboratory of Brine Chemical Engineering and Resource Eco-Utilization, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Yamin Shi
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- Tianjin Key Laboratory of Brine Chemical Engineering and Resource Eco-Utilization, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Daling Zhu
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- Tianjin Key Laboratory of Brine Chemical Engineering and Resource Eco-Utilization, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Lin Cheng
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- Tianjin Key Laboratory of Brine Chemical Engineering and Resource Eco-Utilization, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
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4
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Salazar-Alekseyeva K, Herndl GJ, Baltar F. Release of cell-free enzymes by marine pelagic fungal strains. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1209265. [PMID: 38025900 PMCID: PMC10658710 DOI: 10.3389/ffunb.2023.1209265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023]
Abstract
Fungi are ubiquitous organisms that secrete different enzymes to cleave large molecules into smaller ones so that can then be assimilated. Recent studies suggest that fungi are also present in the oceanic water column harboring the enzymatic repertoire necessary to cleave carbohydrates and proteins. In marine prokaryotes, the cell-free fraction is an important contributor to the oceanic extracellular enzymatic activities (EEAs), but the release of cell-free enzymes by marine fungi remains unknown. Here, to study the cell-free enzymatic activities of marine fungi and the potential influence of salinity on them, five strains of marine fungi that belong to the most abundant pelagic phyla (Ascomycota and Basidiomycota), were grown under non-saline and saline conditions (0 g/L and 35 g/L, respectively). The biomass was separated from the medium by filtration (0.2 μm), and the filtrate was used to perform fluorogenic enzymatic assays with substrate analogues of carbohydrates, lipids, organic phosphorus, sulfur moieties, and proteins. Kinetic parameters such as maximum velocity (Vmax) and half-saturation constant (Km) were obtained. The species studied were able to release cell-free enzymes, and this represented up to 85.1% of the respective total EEA. However, this differed between species and enzymes, with some of the highest contributions being found in those with low total EEA, with some exceptions. This suggests that some of these contributions to the enzymatic pool might be minimal compared to those with higher total EEA. Generally, in the saline medium, the release of cell-free enzymes degrading carbohydrates was reduced compared to the non-saline medium, but those degrading lipids and sulfur moieties were increased. For the remaining substrates, there was not a clear influence of the salinity. Taken together, our results suggest that marine fungi are potential contributors to the oceanic dissolved (i.e., cell-free) enzymatic pool. Our results also suggest that, under salinity changes, a potential effect of global warming, the hydrolysis of organic matter by marine fungal cell-free enzymes might be affected and hence, their potential contribution to the oceanic biogeochemical cycles.
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Affiliation(s)
- Katherine Salazar-Alekseyeva
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- Department of Agrotechnology and Food Sciences, Bioprocess Engineering Group, Wageningen University and Research, Wageningen, Netherlands
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), University of Utrecht, Texel, Netherlands
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
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5
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Hassani II, Quadri I, Yadav A, Bouchard S, Raoult D, Hacène H, Desnues C. Assessment of diversity of archaeal communities in Algerian chott. Extremophiles 2023; 27:2. [PMID: 36469177 DOI: 10.1007/s00792-022-01287-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Halophilic archaea are the dominant type of microorganisms in hypersaline environments. The diversity of halophilic archaea in Zehrez-Chergui (Saharian chott) was analyzed and compared by both analysis of a library of PCR amplified 16S rRNA genes and by cultivation approach. This work, represents the first of its type in Algeria. A total cell count was estimated at 3.8 × 103 CFU/g. The morphological, biochemical, and physiological characterizations of 45 distinct strains, suggests that all of them might be members of the class Halobacteria. Among stains, 23 were characterized phylogenetically and are related to 6 genera of halophilic archaea.The dominance of the genus Halopiger, has not been reported yet in other hypersaline environments. The 100 clones obtained by the molecular approach, were sequenced, and analyzed. The ribosomal library of 61 OTUs showed that the archaeal diversity included uncultured haloarcheon, Halomicrobium, Natronomonas, Halomicroarcula, Halapricum, Haloarcula, Halosimplex, Haloterrigena, Halolamina, Halorubellus, Halorussus and Halonotius. The results of rarefaction analysis indicated that the analysis of an increasing number of clones would have revealed additional diversity. Surprisingly, no halophilic archaea were not shared between the two approaches. Combining both types of methods was considered the best approach to acquire better information on the characteristics of soil halophilic archaea.
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Affiliation(s)
- Imene Ikram Hassani
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie, USTHB Université, Bab Ezzouar, Algeria.
| | - Inès Quadri
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie, USTHB Université, Bab Ezzouar, Algeria
| | - Archana Yadav
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Sonia Bouchard
- Faculté de Médecine, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD 198, Inserm U1095, 27 Boulevard Jean Moulin, 13385, Marseille, France
| | - Didier Raoult
- Faculté de Médecine, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD 198, Inserm U1095, 27 Boulevard Jean Moulin, 13385, Marseille, France
| | - Hocine Hacène
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie, USTHB Université, Bab Ezzouar, Algeria
| | - Christelle Desnues
- Faculté de Médecine, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD 198, Inserm U1095, 27 Boulevard Jean Moulin, 13385, Marseille, France
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6
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Moopantakath J, Imchen M, Anju VT, Busi S, Dyavaiah M, Martínez-Espinosa RM, Kumavath R. Bioactive molecules from haloarchaea: Scope and prospects for industrial and therapeutic applications. Front Microbiol 2023; 14:1113540. [PMID: 37065149 PMCID: PMC10102575 DOI: 10.3389/fmicb.2023.1113540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
Marine environments and salty inland ecosystems encompass various environmental conditions, such as extremes of temperature, salinity, pH, pressure, altitude, dry conditions, and nutrient scarcity. The extremely halophilic archaea (also called haloarchaea) are a group of microorganisms requiring high salt concentrations (2–6 M NaCl) for optimal growth. Haloarchaea have different metabolic adaptations to withstand these extreme conditions. Among the adaptations, several vesicles, granules, primary and secondary metabolites are produced that are highly significant in biotechnology, such as carotenoids, halocins, enzymes, and granules of polyhydroxyalkanoates (PHAs). Among halophilic enzymes, reductases play a significant role in the textile industry and the degradation of hydrocarbon compounds. Enzymes like dehydrogenases, glycosyl hydrolases, lipases, esterases, and proteases can also be used in several industrial procedures. More recently, several studies stated that carotenoids, gas vacuoles, and liposomes produced by haloarchaea have specific applications in medicine and pharmacy. Additionally, the production of biodegradable and biocompatible polymers by haloarchaea to store carbon makes them potent candidates to be used as cell factories in the industrial production of bioplastics. Furthermore, some haloarchaeal species can synthesize nanoparticles during heavy metal detoxification, thus shedding light on a new approach to producing nanoparticles on a large scale. Recent studies also highlight that exopolysaccharides from haloarchaea can bind the SARS-CoV-2 spike protein. This review explores the potential of haloarchaea in the industry and biotechnology as cellular factories to upscale the production of diverse bioactive compounds.
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Affiliation(s)
- Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - V. T. Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Rosa María Martínez-Espinosa
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
- Rosa María Martínez-Espinosa,
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- *Correspondence: Ranjith Kumavath, ,
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7
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Oyewusi HA, Akinyede KA, Abdul Wahab R, Huyop F. In silico analysis of a putative dehalogenase from the genome of halophilic bacterium Halomonas smyrnensis AAD6T. J Biomol Struct Dyn 2023; 41:319-335. [PMID: 34854349 DOI: 10.1080/07391102.2021.2006085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Microbial-assisted removal of natural or synthetic pollutants is the prevailing green, low-cost technology to treat polluted environments. However, the challenge with enzyme-assisted bioremediation is the laborious nature of dehalogenase-producing microorganisms' bioprospecting. This bottleneck could be circumvented by in-silico analysis of certain microorganisms' whole-genome sequences to predict their protein functions and enzyme versatility for improved biotechnological applications. Herein, this study performed structural analysis on a dehalogenase (DehHsAAD6) from the genome of Halomonas smyrnensis AAD6 by molecular docking and molecular dynamic (MD) simulations. Other bioinformatics tools were also employed to identify substrate preference (haloacids and haloacetates) of the DehHsAAD6. The DehHsAAD6 preferentially degraded haloacids and haloacetates (-3.2-4.8 kcal/mol) and which formed three hydrogen bonds with Tyr12, Lys46, and Asp182. MD simulations data revealed the higher stability of DehHsAAD6-haloacid- (RMSD 0.22-0.3 nm) and DehHsAAD6-haloacetates (RMSF 0.05-0.14 nm) complexes, with the DehHsAAD6-L-2CP complex being the most stable. The detail of molecular docking calculations ranked complexes with the lowest binding free energies as: DehHsAAD6-L-2CP complex (-4.8 kcal/mol) = DehHsAAD6-MCA (-4.8 kcal/mol) < DehHsAAD6-TCA (-4.5 kcal/mol) < DehHsAAD6-2,3-DCP (-4.1 kcal/mol) < DehHsAAD6-D-2CP (-3.9 kcal/mol) < DehHsAAD6-2,2-DCP (-3.5 kcal/mol) < DehHsAAD6-3CP (-3.2 kcal/mol). In a nutshell, the study findings offer valuable perceptions into the elucidation of possible reaction mechanisms of dehalogenases for extended substrate specificity and higher catalytic activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Science Technology, Biochemistry unit, The Federal Polytechnic P.M.B, Ado Ekiti, Ekiti State, Nigeria
| | - Kolajo Adedamola Akinyede
- Department of Science Technology, Biochemistry unit, The Federal Polytechnic P.M.B, Ado Ekiti, Ekiti State, Nigeria.,Department of Medical Bioscience, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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8
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Phenotypic characteristics, phylogenetic analysis and characterization of alkaline proteases of marine bacteria Geomicrobium halophilum, Oceanobacillus oncorhynchi, and Oceanobacillus khimchii. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01095-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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9
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Ahmad A, Rahamtullah, Mishra R. Structural and functional adaptation in extremophilic microbial α-amylases. Biophys Rev 2022; 14:499-515. [PMID: 35528036 PMCID: PMC9043155 DOI: 10.1007/s12551-022-00931-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/12/2022] [Indexed: 01/26/2023] Open
Abstract
Maintaining stable native conformation of a protein under a given ecological condition is the prerequisite for survival of organisms. Extremophilic bacteria and archaea have evolved to adapt under extreme conditions of temperature, pH, salt, and pressure. Molecular adaptations of proteins under these conditions are essential for their survival. These organisms have the capability to maintain stable, native conformations of proteins under extreme conditions. The enzymes produced by the extremophiles are also known as extremozyme, which are used in several industries. Stability and functionality of extremozymes under varying temperature, pH, and solvent conditions are the most desirable requirement of industry. α-Amylase is one of the most important enzymes used in food, pharmaceutical, textile, and detergent industries. This enzyme is produced by diverse microorganisms including various extremophiles. Therefore, understanding its stability is important from fundamental as well as an applied point of view. Each class of extremophiles has a distinctive set of dominant non-covalent interactions which are important for their stability. Static information obtained by comparative analysis of amino acid sequence and atomic resolution structure provides information on the prevalence of particular amino acids or a group of non-covalent interactions. Protein folding studies give the information about thermodynamic and kinetic stability in order to understand dynamic aspect of molecular adaptations. In this review, we have summarized information on amino acid sequence, structure, stability, and adaptability of α-amylases from different classes of extremophiles.
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Affiliation(s)
- Aziz Ahmad
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rahamtullah
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
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10
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A novel acidic and SDS tolerant halophilic lipase from moderate halophile Nesterenkonia sp. strain F: molecular cloning, structure analysis and biochemical characterization. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-01005-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Regassa H, Bose D, Mukherjee A. Review of Microorganisms and Their Enzymatic Products for Industrial Bioprocesses. Ind Biotechnol (New Rochelle N Y) 2021. [DOI: 10.1089/ind.2021.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Hailemeleak Regassa
- Faculty of Applied Sciences & Biotechnology, Shoolini University of Biotechnology & Management Sciences, Solan, Himachal Pradesh, India
| | - Debajyoti Bose
- Faculty of Applied Sciences & Biotechnology, Shoolini University of Biotechnology & Management Sciences, Solan, Himachal Pradesh, India
| | - Alivia Mukherjee
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK, Canada
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12
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Solat N, Shafiei M. A novel pH and thermo-tolerant halophilic alpha-amylase from moderate halophile Nesterenkonia sp. strain F: gene analysis, molecular cloning, heterologous expression and biochemical characterization. Arch Microbiol 2021; 203:3641-3655. [PMID: 33993325 DOI: 10.1007/s00203-021-02359-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
A novel pH and thermo-tolerate halophilic alpha-amylase from moderately halophilic bacterium, Nesterenkonia sp.strain F was cloned and expressed in Escherichia coli. 16S rRNA sequence of the strain shared 99.46% similarities with closely related type species. Also, the genome sequence shared ANI values below 92% and dDDH values below 52% with the closely related type species. Consequently, it is proposed that strain F represents a novel species. The AmyF gene was 1390 bp long and encodes an alpha-amylase of 463 amino acid residues with pI of 4.62. The deduced AmyF shared very low sequence similarity (< 24%) with functionally characterized recombinant halophilic alpha-amylases. The recombinant alpha-amylase was successfully purified from Ni-NTA columns with a molecular mass of about 52 KDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active over a wide range of temperature (25-75 °C) and pH (4-9) with optimum activity at 45 °C and 7.5, respectively. Also, although it was active over a various concentrations of NaCl and KCl (0-4 M), increasing activity of the enzyme was observed with increasing concentration of these salts. Low concentrations of Ca2+ ion had no activating effect, but high concentrations of the ion (40-200 mM) enhanced activity of AmyF. The enzyme activity was increased by increasing concentrations of Mg2+, Zn2+, Hg2+ and Fe3+. However, it was inhibited only at very high concentrations of these metal ions. Cu2+ did not decrease the amylase activity and the highest activity was observed at 100 mM of the ion. These properties indicate wide potential applications of this recombinant enzyme in starch processing industries. This is the first isolation, cloning and characterization of a gene encoding alpha-amylase from Nesternkonia genus.
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Affiliation(s)
- Nastaran Solat
- Department of Genetics, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Biotechnology and Bioscience Research Center, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Shafiei
- Department of Genetics, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran. .,Biotechnology and Bioscience Research Center, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
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13
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Gómez-Villegas P, Vigara J, Romero L, Gotor C, Raposo S, Gonçalves B, Léon R. Biochemical Characterization of the Amylase Activity from the New Haloarchaeal Strain Haloarcula sp. HS Isolated in the Odiel Marshlands. BIOLOGY 2021; 10:biology10040337. [PMID: 33923574 PMCID: PMC8073556 DOI: 10.3390/biology10040337] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022]
Abstract
Alpha-amylases are a large family of α,1-4-endo-glycosyl hydrolases distributed in all kingdoms of life. The need for poly-extremotolerant amylases encouraged their search in extreme environments, where archaea become ideal candidates to provide new enzymes that are able to work in the harsh conditions demanded in many industrial applications. In this study, a collection of haloarchaea isolated from Odiel saltern ponds in the southwest of Spain was screened for their amylase activity. The strain that exhibited the highest activity was selected and identified as Haloarcula sp. HS. We demonstrated the existence in both, cellular and extracellular extracts of the new strain, of functional α-amylase activities, which showed to be moderately thermotolerant (optimum around 60 °C), extremely halotolerant (optimum over 25% NaCl), and calcium-dependent. The tryptic digestion followed by HPLC-MS/MS analysis of the partially purified cellular and extracellular extracts allowed to identify the sequence of three alpha-amylases, which despite sharing a low sequence identity, exhibited high three-dimensional structure homology, conserving the typical domains and most of the key consensus residues of α-amylases. Moreover, we proved the potential of the extracellular α-amylase from Haloarcula sp. HS to treat bakery wastes under high salinity conditions.
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Affiliation(s)
- Patricia Gómez-Villegas
- Laboratory of Biochemistry, Department of Chemistry, Marine International Campus of Excellence (CEIMAR), University of Huelva, Avda. de las Fuerzas Armadas s/n, 21071 Huelva, Spain; (P.G.-V.); (J.V.)
| | - Javier Vigara
- Laboratory of Biochemistry, Department of Chemistry, Marine International Campus of Excellence (CEIMAR), University of Huelva, Avda. de las Fuerzas Armadas s/n, 21071 Huelva, Spain; (P.G.-V.); (J.V.)
| | - Luis Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio 49, 41092 Seville, Spain; (L.R.); (C.G.)
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio 49, 41092 Seville, Spain; (L.R.); (C.G.)
| | - Sara Raposo
- CIMA—Centre for Marine and Environmental Research, FCT, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal; (S.R.); (B.G.)
| | - Brígida Gonçalves
- CIMA—Centre for Marine and Environmental Research, FCT, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal; (S.R.); (B.G.)
| | - Rosa Léon
- Laboratory of Biochemistry, Department of Chemistry, Marine International Campus of Excellence (CEIMAR), University of Huelva, Avda. de las Fuerzas Armadas s/n, 21071 Huelva, Spain; (P.G.-V.); (J.V.)
- Correspondence: ; Tel.: +34-959-219-951
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14
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Paul JS, Gupta N, Beliya E, Tiwari S, Jadhav SK. Aspects and Recent Trends in Microbial α-Amylase: a Review. Appl Biochem Biotechnol 2021; 193:2649-2698. [PMID: 33715051 DOI: 10.1007/s12010-021-03546-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/26/2021] [Indexed: 10/21/2022]
Abstract
α-Amylases are the oldest and versatile starch hydrolysing enzymes which can replace chemical hydrolysis of starch in industries. It cleaves the α-(1,4)-D-glucosidic linkage of starch and other related polysaccharides to yield simple sugars like glucose, maltose and limit dextrin. α-Amylase covers about 30% shares of the total enzyme market. On account of their superior features, α-amylase is the most widely used among all the existing amylases for hydrolysis of polysaccharides. Endo-acting α-amylase of glycoside hydrolase family 13 is an extensively used biocatalyst and has various biotechnological applications like in starch processing, detergent, textile, paper and pharmaceutical industries. Apart from these, it has some novel applications including polymeric material for drug delivery, bioremediating agent, biodemulsifier and biofilm inhibitor. The present review will accomplish the research gap by providing the unexplored aspects of microbial α-amylase. It will allow the readers to know about the works that have already been done and the latest trends in this field. The manuscript has covered the latest immobilization techniques and the site-directed mutagenesis approaches which are readily being performed to confer the desirable property in wild-type α-amylases. Furthermore, it will state the inadequacies and the numerous obstacles coming in the way of its production during upstream and downstream steps and will also suggest some measures to obtain stable and industrial-grade α-amylase.
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Affiliation(s)
- Jai Shankar Paul
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India
| | - Nisha Gupta
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India
| | - Esmil Beliya
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India.,Department of Botany, Govt. College, Bichhua, Chhindwara, MP, 480111, India
| | - Shubhra Tiwari
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India
| | - Shailesh Kumar Jadhav
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India.
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15
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A Novel Carboxylesterase Derived from a Compost Metagenome Exhibiting High Stability and Activity towards High Salinity. Genes (Basel) 2021; 12:genes12010122. [PMID: 33478024 PMCID: PMC7835964 DOI: 10.3390/genes12010122] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/09/2021] [Accepted: 01/13/2021] [Indexed: 01/08/2023] Open
Abstract
Halotolerant lipolytic enzymes have gained growing interest, due to potential applications under harsh conditions, such as hypersalinity and presence of organic solvents. In this study, a lipolytic gene, est56, encoding 287 amino acids was identified by functional screening of a compost metagenome. Subsequently, the gene was heterologously expressed, and the recombinant protein (Est56) was purified and characterized. Est56 is a mesophilic (Topt 50 °C) and moderate alkaliphilic (pHopt 8) enzyme, showing high thermostability at 30 and 40 °C. Strikingly, Est56 is halotolerant as it exhibited high activity and stability in the presence of up to 4 M NaCl or KCl. Est56 also displayed enhanced stability against high temperatures (50 and 60 °C) and urea (2, 4, and 6 M) in the presence of NaCl. In addition, the recently reported halotolerant lipolytic enzymes were summarized. Phylogenetic analysis grouped these enzymes into 13 lipolytic protein families. The majority (45%) including Est56 belonged to family IV. To explore the haloadaptation of halotolerant enzymes, the amino acid composition between halotolerant and halophilic enzymes was statistically compared. The most distinctive feature of halophilic from non-halophilic enzymes are the higher content of acidic residues (Asp and Glu), and a lower content of lysine, aliphatic hydrophobic (Leu, Met and Ile) and polar (Asn) residues. The amino acid composition and 3-D structure analysis suggested that the high content of acidic residues (Asp and Glu, 12.2%) and low content of lysine residues (0.7%), as well as the excess of surface-exposed acidic residues might be responsible for the haloadaptation of Est56.
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16
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Kasirajan L, Maupin-Furlow JA. Halophilic archaea and their potential to generate renewable fuels and chemicals. Biotechnol Bioeng 2020; 118:1066-1090. [PMID: 33241850 DOI: 10.1002/bit.27639] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/27/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
Lignocellulosic biofuels and chemicals have great potential to reduce our dependence on fossil fuels and mitigate air pollution by cutting down on greenhouse gas emissions. Chemical, thermal, and enzymatic processes are used to release the sugars from the lignocellulosic biomass for conversion to biofuels. These processes often operate at extreme pH conditions, high salt concentrations, and/or high temperature. These harsh treatments add to the cost of the biofuels, as most known biocatalysts do not operate under these conditions. To increase the economic feasibility of biofuel production, microorganisms that thrive in extreme conditions are considered as ideal resources to generate biofuels and value-added products. Halophilic archaea (haloarchaea) are isolated from hypersaline ecosystems with high salt concentrations approaching saturation (1.5-5 M salt concentration) including environments with extremes in pH and/or temperature. The unique traits of haloarchaea and their enzymes that enable them to sustain catalytic activity in these environments make them attractive resources for use in bioconversion processes that must occur across a wide range of industrial conditions. Biocatalysts (enzymes) derived from haloarchaea occupy a unique niche in organic solvent, salt-based, and detergent industries. This review focuses on the use of haloarchaea and their enzymes to develop and improve biofuel production. The review also highlights how haloarchaea produce value-added products, such as antibiotics, carotenoids, and bioplastic precursors, and can do so using feedstocks considered "too salty" for most microbial processes including wastes from the olive-mill, shell fish, and biodiesel industries.
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Affiliation(s)
- Lakshmi Kasirajan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Coimbatore, India
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Genetics Institute, University of Florida, Gainesville, Florida, USA
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17
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Shah F, Mishra S. In vitro optimization for enhanced cellulose degrading enzyme from Bacillus licheniformis KY962963 associated with a microalgae Chlorococcum sp. using OVAT and statistical modeling. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-03697-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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18
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Oyewusi HA, Huyop F, Wahab RA. Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos. J Biomol Struct Dyn 2020; 40:1979-1994. [PMID: 33094694 DOI: 10.1080/07391102.2020.1835727] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The high dependency and surplus use of agrochemical products have liberated enormous quantities of toxic halogenated pollutants into the environment and threaten the well-being of humankind. Herein, this study performed molecular docking, molecular dynamic (MD) simulations, molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis, to identify the order of which the enzyme degrades different substrates, haloacids, haloacetate and chlorpyrifos. The study discovered that the DehH2 favored the degradation of haloacids and haloacetates (-3.3 - 4.6 kcal/mol) and formed three hydrogen bonds with Asp125, Arg201 and Lys202. Despite the inconclusive molecular docking result, chlorpyrifos was consistently shown to be the least favored substrate of the DehH2 in MD simulations and MM-PBSA calculations. Results of MD simulations revealed the DehH2-haloacid- (RMSD 0.15 - 0.25 nm) and DehH2-haloacetates (RMSF 0.05 - 0.25 nm) were more stable, with the DehH2-L-2CP complex being the most stable while the least was the DehH2-chlorpyrifos (RMSD 0.295 nm; RMSF 0.05 - 0.59 nm). The Molecular Mechanics Poisson-Boltzmann Surface Area calculations showed the DehH2-L-2CP complex (-24.27 kcal/mol) having the lowest binding energy followed by DehH2-MCA (-22.78 kcal/mol), DehH2-D-2CP (-21.82 kcal/mol), DehH2-3CP (-21.11 kcal/mol), DehH2-2,2-DCP (-18.34 kcal/mol), DehH2-2,3-DCP (-8.34 kcal/mol), DehH2-TCA (-7.62 kcal/mol), while chlorpyrifos was unable to spontaneously bind to DehH2 (+127.16 kcal/mol). In a nutshell, the findings of this study offer valuable insights into the rational tailoring of the DehH2 for expanding its substrate specificity and catalytic activity in the near future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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19
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Karan R, Mathew S, Muhammad R, Bautista DB, Vogler M, Eppinger J, Oliva R, Cavallo L, Arold ST, Rueping M. Understanding High-Salt and Cold Adaptation of a Polyextremophilic Enzyme. Microorganisms 2020; 8:microorganisms8101594. [PMID: 33081237 PMCID: PMC7602713 DOI: 10.3390/microorganisms8101594] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/27/2022] Open
Abstract
The haloarchaeon Halorubrum lacusprofundi is among the few polyextremophilic organisms capable of surviving in one of the most extreme aquatic environments on Earth, the Deep Lake of Antarctica (−18 °C to +11.5 °C and 21–28%, w/v salt content). Hence, H. lacusprofundi has been proposed as a model for biotechnology and astrobiology to investigate potential life beyond Earth. To understand the mechanisms that allow proteins to adapt to both salinity and cold, we structurally (including X-ray crystallography and molecular dynamics simulations) and functionally characterized the β-galactosidase from H. lacusprofundi (hla_bga). Recombinant hla_bga (produced in Haloferax volcanii) revealed exceptional stability, tolerating up to 4 M NaCl and up to 20% (v/v) of organic solvents. Despite being cold-adapted, hla_bga was also stable up to 60 °C. Structural analysis showed that hla_bga combined increased surface acidity (associated with halophily) with increased structural flexibility, fine-tuned on a residue level, for sustaining activity at low temperatures. The resulting blend enhanced structural flexibility at low temperatures but also limited protein movements at higher temperatures relative to mesophilic homologs. Collectively, these observations help in understanding the molecular basis of a dual psychrophilic and halophilic adaptation and suggest that such enzymes may be intrinsically stable and functional over an exceptionally large temperature range.
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Affiliation(s)
- Ram Karan
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
- Correspondence: (R.K.); (S.T.A.); (M.R.)
| | - Sam Mathew
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Reyhan Muhammad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia;
| | - Didier B. Bautista
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Malvina Vogler
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Jorg Eppinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Romina Oliva
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Luigi Cavallo
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia;
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
- Correspondence: (R.K.); (S.T.A.); (M.R.)
| | - Magnus Rueping
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
- Correspondence: (R.K.); (S.T.A.); (M.R.)
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20
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Verma DK, Vasudeva G, Sidhu C, Pinnaka AK, Prasad SE, Thakur KG. Biochemical and Taxonomic Characterization of Novel Haloarchaeal Strains and Purification of the Recombinant Halotolerant α-Amylase Discovered in the Isolate. Front Microbiol 2020; 11:2082. [PMID: 32983058 PMCID: PMC7490331 DOI: 10.3389/fmicb.2020.02082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/07/2020] [Indexed: 11/13/2022] Open
Abstract
Haloarchaea are salt-loving archaea and potential source of industrially relevant halotolerant enzymes. In the present study, three reddish-pink, extremely halophilic archaeal strains, namely wsp1 (wsp-water sample Pondicherry), wsp3, and wsp4, were isolated from the Indian Solar saltern. The phylogenetic analysis based on 16S rRNA gene sequences suggests that both wsp3 and wsp4 strains belong to Halogeometricum borinquense while wsp1 is closely related to Haloferax volcanii species. The comparative genomics revealed an open pangenome for both genera investigated here. Whole-genome sequence analysis revealed that these isolates have multiple copies of industrially/biotechnologically important unique genes and enzymes. Among these unique enzymes, for recombinant expression and purification, we selected four putative α-amylases identified in these three isolates. We successfully purified functional halotolerant recombinant Amy2, from wsp1 using pelB signal sequence-based secretion strategy using Escherichia coli as an expression host. This method may prove useful to produce functional haloarchaeal secretory recombinant proteins suitable for commercial or research applications. Biochemical analysis of Amy2 suggests the halotolerant nature of the enzyme having maximum enzymatic activity observed at 1 M NaCl. We also report the isolation and characterization of carotenoids purified from these isolates. This study highlights the presence of several industrially important enzymes in the haloarchaeal strains which may potentially have improved features like stability and salt tolerance suitable for industrial applications.
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Affiliation(s)
- Dipesh Kumar Verma
- G. N. Ramachandran Protein Centre, Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Gunjan Vasudeva
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Chandni Sidhu
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Anil K Pinnaka
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Senthil E Prasad
- Biochemical Engineering Research and Process Development Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Krishan Gopal Thakur
- G. N. Ramachandran Protein Centre, Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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21
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Martínez-Espinosa RM. Heterologous and Homologous Expression of Proteins from Haloarchaea: Denitrification as Case of Study. Int J Mol Sci 2019; 21:E82. [PMID: 31877629 PMCID: PMC6981372 DOI: 10.3390/ijms21010082] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/05/2019] [Accepted: 12/18/2019] [Indexed: 12/23/2022] Open
Abstract
Haloarchaea (halophilic microbes belonging to the Archaea domain) are microorganisms requiring mid or even high salt concentrations to be alive. The molecular machinery of these organisms is adapted to such conditions, which are stressful for most life forms. Among their molecular adaptations, halophilic proteins are characterized by their high content of acidic amino acids (Aspartate (Asp) and glumate (Glu)), being only stable in solutions containing high salt concentration (between 1 and 4 M total salt concentration). Recent knowledge about haloarchaeal peptides, proteins, and enzymes have revealed that many haloarchaeal species produce proteins of interest due to their potential applications in biotechnology-based industries. Although proteins of interest are usually overproduced in recombinant prokaryotic or eukaryotic expression systems, these procedures do not accurately work for halophilic proteins, mainly if such proteins contain metallocofactors in their structures. This work summarizes the main challenges of heterologous and homologous expression of enzymes from haloarchaea, paying special attention to the metalloenzymes involved in the pathway of denitrification (anaerobic reduction of nitrate to dinitrogen), a pathway with significant implications in wastewater treatment, climate change, and biosensor design.
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Affiliation(s)
- Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences and Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Ap. 99, E-03080 Alicante, Spain
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22
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A new GH13 subfamily represented by the α-amylase from the halophilic archaeon Haloarcula hispanica. Extremophiles 2019; 24:207-217. [PMID: 31734852 DOI: 10.1007/s00792-019-01147-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/05/2019] [Indexed: 01/16/2023]
Abstract
α-Amylase catalyzes the endohydrolysis of α-1,4-glucosidic linkages in starch and related α-glucans. In the CAZy database, most α-amylases have been classified into the family GH13 counting at present more than 80,000 sequences and ~ 30 different enzyme specificities. The family has already been divided into 42 subfamilies, but additional subfamilies are still emerging. The present bioinformatics study was undertaken in an effort to propose a novel GH13 subfamily around the experimentally characterized α-amylase from the halophilic archaeon Haloarcula hispanica, which until now has not been assigned to any GH13 subfamily. The in silico analysis resulted in collecting a convincing group of putative haloarchaeal α-amylase homologues sharing sequence similarities mainly in their conserved sequence regions (CSRs) and forming a cluster in the evolutionary tree, which is well separated from representatives of established GH13 subfamilies. One of the most exclusive sequence features of the novel GH13 subfamily is the tyrosine (Tyr79 in H. hispanica α-amylase numbering) succeeding the glycine at the beginning of the CSR-VI at the β2 strand of the catalytic TIM-barrel. Evolutionarily, the novel GH13 α-amylase subfamily was most closely related to two clusters of GH13 subfamilies with the specificity of α-amylase, i.e. subfamilies GH13_5, 6 and 7 as well as GH13_15, 24, 27 and 28.
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23
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Edbeib MF, Aksoy HM, Kaya Y, Wahab RA, Huyop F. Haloadaptation: insights from comparative modeling studies between halotolerant and non-halotolerant dehalogenases. J Biomol Struct Dyn 2019; 38:3452-3461. [PMID: 31422756 DOI: 10.1080/07391102.2019.1657498] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Halophiles are extremophilic microorganisms that grow optimally at high salt concentrations by producing a myriad of equally halotolerant enzymes. Structural haloadaptation of these enzymes adept to thriving under high-salt environments, though are not fully understood. Herein, the study attempts an in silico investigation to identify and comprehend the evolutionary structural adaptation of a halotolerant dehalogenase, DehHX (GenBank accession number: KR297065) of the halotolerant Pseudomonas halophila, over its non-halotolerant counterpart, DehMX1 (GenBank accession number KY129692) produced by Pseudomonas aeruginosa. GC content of the halotolerant DehHX DNA sequence was distinctively higher (58.9%) than the non-halotolerant dehalogenases (55% average GC). Its acidic residues, Asp and Glu were 8.27% and 12.06%, respectively, compared to an average 5.5% Asp and 7% Glu, in the latter; but lower contents of basic and hydrophobic residues in the DehHX. The secondary structure of DehHX interestingly revealed a lower incidence of α-helix forming regions (29%) and a higher percentage of coils (57%), compared to 49% and 29% in the non-halotolerant homologues, respectively. Simulation models showed the DehHX is stable under a highly saline environment (25% w/v) by adopting a highly negative-charged surface with a concomitant weakly interacting hydrophobic core. The study thus, established that a halotolerant dehalogenase undergoes notable evolutionary structural changes related to GC content over its non-halotolerant counterpart, in order to adapt and thrive under highly saline environments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed Faraj Edbeib
- Department of Animal Production, Faculty of Agriculture, Baniwalid University, Baniwalid, Libya.,Department of Plant Protection, Agricultural Faculty, Ondokuz Mayis University, Samsun, Turkey
| | - Hasan Murat Aksoy
- Department of Plant Protection, Agricultural Faculty, Ondokuz Mayis University, Samsun, Turkey
| | - Yilmaz Kaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey.,Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Fahrul Huyop
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey.,Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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Amoozegar MA, Safarpour A, Noghabi KA, Bakhtiary T, Ventosa A. Halophiles and Their Vast Potential in Biofuel Production. Front Microbiol 2019; 10:1895. [PMID: 31507545 PMCID: PMC6714587 DOI: 10.3389/fmicb.2019.01895] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/31/2019] [Indexed: 11/13/2022] Open
Abstract
Global warming and the limitations of using fossil fuels are a main concern of all societies, and thus, the development of alternative fuel sources is crucial to improving the current global energy situation. Biofuels are known as the best alternatives of unrenewable fuels and justify increasing extensive research to develop new and less expensive methods for their production. The most frequent biofuels are bioethanol, biobutanol, biodiesel, and biogas. The production of these biofuels is the result of microbial activity on organic substrates like sugars, starch, oil crops, non-food biomasses, and agricultural and animal wastes. Several industrial production processes are carried out in the presence of high concentrations of NaCl and therefore, researchers have focused on halophiles for biofuel production. In this review, we focus on the role of halophilic microorganisms and their current utilization in the production of all types of biofuels. Also, the outstanding potential of them and their hydrolytic enzymes in the hydrolysis of different kind of biomasses and the production of biofuels are discussed.
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Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Atefeh Safarpour
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Kambiz Akbari Noghabi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Tala Bakhtiary
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
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Salgaonkar BB, Sawant DT, Harinarayanan S, Bragança JM. Alpha-amylase Production by Extremely Halophilic ArchaeonHalococcusStrain GUVSC8. STARCH-STARKE 2019. [DOI: 10.1002/star.201800018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Bhakti B. Salgaonkar
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani; K K Birla, Goa Campus; NH-17B Zuarinagar 403 726 Goa India
- Department of Microbiology, Goa University; Taleigao Plateau; 403 206 Goa India
| | - Divya T. Sawant
- Department of Microbiology, Goa University; Taleigao Plateau; 403 206 Goa India
| | - Saranya Harinarayanan
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani; K K Birla, Goa Campus; NH-17B Zuarinagar 403 726 Goa India
| | - Judith M. Bragança
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani; K K Birla, Goa Campus; NH-17B Zuarinagar 403 726 Goa India
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Jujjavarapu SE, Dhagat S. Evolutionary Trends in Industrial Production of α-amylase. Recent Pat Biotechnol 2019; 13:4-18. [PMID: 30810102 DOI: 10.2174/2211550107666180816093436] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/09/2018] [Accepted: 07/27/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Amylase catalyzes the breakdown of long-chain carbohydrates to yield maltotriose, maltose, glucose and dextrin as end products. It is present in mammalian saliva and helps in digestion. OBJECTIVE Their applications in biotechnology include starch processing, biofuel, food, paper, textile and detergent industries, bioremediation of environmental pollutants and in clinical and medical applications. The commercial microbial strains for production of α-amylase are Bacillus subtilis, B. licheniformis, B. amyloliquefaciens and Aspergillus oryzae. Industrial production of enzymes requires high productivity and cannot use wild-type strains for enzyme production. The yield of enzyme from bacteria can be increased by varying the physiological and genetic properties of strains. RESULTS The genetic properties of a bacterium can be improved by enhancing the expression levels of the gene and secretion of the enzyme outside the cells, thereby improving the productivity by preventing degradation of enzymes. Overall, the strain for specific productivity should have the maximum ability for synthesis and secretion of an enzyme of interest. Genetic manipulation of α-amylase can also be used for the production of enzymes with different properties, for example, by recombinant DNA technology. CONCLUSION This review summarizes different techniques in the production of recombinant α- amylases along with the patents in this arena. The washing out of enzymes in reactions became a limitation in utilization of these enzymes in industries and hence immobilization of these enzymes becomes important. This paper also discusses the immobilization techniques for used α-amylases.
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Affiliation(s)
| | - Swasti Dhagat
- Department of Biotechnology, National Institute of Technology Raipur, Raipur-492010, India
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Cabrera MÁ, Blamey JM. Biotechnological applications of archaeal enzymes from extreme environments. Biol Res 2018; 51:37. [PMID: 30290805 PMCID: PMC6172850 DOI: 10.1186/s40659-018-0186-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 09/25/2018] [Indexed: 11/10/2022] Open
Abstract
To date, many industrial processes are performed using chemical compounds, which are harmful to nature. An alternative to overcome this problem is biocatalysis, which uses whole cells or enzymes to carry out chemical reactions in an environmentally friendly manner. Enzymes can be used as biocatalyst in food and feed, pharmaceutical, textile, detergent and beverage industries, among others. Since industrial processes require harsh reaction conditions to be performed, these enzymes must possess several characteristics that make them suitable for this purpose. Currently the best option is to use enzymes from extremophilic microorganisms, particularly archaea because of their special characteristics, such as stability to elevated temperatures, extremes of pH, organic solvents, and high ionic strength. Extremozymes, are being used in biotechnological industry and improved through modern technologies, such as protein engineering for best performance. Despite the wide distribution of archaea, exist only few reports about these microorganisms isolated from Antarctica and very little is known about thermophilic or hyperthermophilic archaeal enzymes particularly from Antarctica. This review summarizes current knowledge of archaeal enzymes with biotechnological applications, including two extremozymes from Antarctic archaea with potential industrial use, which are being studied in our laboratory. Both enzymes have been discovered through conventional screening and genome sequencing, respectively.
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Affiliation(s)
- Ma Ángeles Cabrera
- Fundación Científica y Cultural Biociencia, José Domingo Cañas, 2280, Santiago, Chile.,Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O´Higgins, 3363, Santiago, Chile
| | - Jenny M Blamey
- Fundación Científica y Cultural Biociencia, José Domingo Cañas, 2280, Santiago, Chile. .,Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O´Higgins, 3363, Santiago, Chile.
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Mohammadzadeh Rostami F, Shahsafi M. Evaluation and Isolation of Halophilic Bacteria from the Meyghan Lake in Arak, Iran. MEDICAL LABORATORY JOURNAL 2018. [DOI: 10.29252/mlj.12.6.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Karray F, Ben Abdallah M, Kallel N, Hamza M, Fakhfakh M, Sayadi S. Extracellular hydrolytic enzymes produced by halophilic bacteria and archaea isolated from hypersaline lake. Mol Biol Rep 2018; 45:1297-1309. [PMID: 30062501 DOI: 10.1007/s11033-018-4286-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 07/26/2018] [Indexed: 02/04/2023]
Abstract
The screening of bacteria and archaea from Chott El Jerid, a hypersaline lake in the south of Tunisia, led to the isolation of 68 extremely halophilic prokaryotes growing in media with 15-25% of salt. Assessment of 68 partial 16S rRNA analyzed by amplified rDNA restriction analysis (ARDRA) revealed 15 different bacterial and archaeal taxonomic groups. Based on ARDRA results, phenotypic and hydrolytic activity tests, 20 archaeal and 6 bacterial isolates were selected for sequencing. The halophilic isolates were identified as members of the genera: Salicola, Bacillus, Halorubrum, Natrinema and Haloterrigena. Most of these isolates are able to produce hydrolytic enzymes such as amylase, protease, lipase, cellulase, xylanase, pectinase and some of them showed combined activities. Natrinema genus is an excellent candidate for lipase production. These results indicated that the extremely halophilic archaea and bacteria from Chott El Jerid are a potential source of hydrolytic enzymes and may possess commercial value.
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Affiliation(s)
- Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia.
| | - Manel Ben Abdallah
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
| | - Najwa Kallel
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
| | - Manel Hamza
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
| | - Manel Fakhfakh
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
| | - Sami Sayadi
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
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Molecular Cloning and Characterization of a Novel α-Amylase from Antarctic Sea Ice Bacterium Pseudoalteromonas sp. M175 and Its Primary Application in Detergent. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3258383. [PMID: 30050926 PMCID: PMC6040283 DOI: 10.1155/2018/3258383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/06/2018] [Accepted: 05/02/2018] [Indexed: 11/17/2022]
Abstract
A novel cold-adapted and salt-tolerant α-amylase gene (amy175) from Antarctic sea ice bacterium Pseudoalteromonas sp. M175 was successfully cloned and expressed. The open reading frame (ORF) of amy175 had 1722 bp encoding a protein of 573 amino acids residues. Multiple alignments indicated Amy175 had seven highly conserved sequences and the putative catalytic triad (Asp244, Glu286, and Asp372). It was the first identified member of GH13_36 subfamily which contained QPDLN in the CSR V. The recombinant enzyme (Amy175) was purified to homogeneity with a molecular mass of about 62 kDa on SDS-PAGE. It had a mixed enzyme specificity of α-amylase and α-glucosidase. Amy175 displayed highest activity at pH 8.0 and 25°C and exhibited extreme salt-resistance with the maximum activity at 1 M NaCl. Amy175 was strongly stimulated by Mg2+, Ni2+, K+, 1 mM Ca2+, 1 mM Ba2+, 1 mM Pb2+, 1 mM sodium dodecyl sulphate (SDS), and 10% dimethyl sulfoxide (DMSO) but was significantly inhibited by Cu2+, Mn2+, Hg2+, 10 mM β-mercaptoethanol (β-ME), and 10% Tween 80. Amy175 demonstrated excellent resistance towards all the tested commercial detergents, and wash performance analysis displayed that the addition of Amy175 improved the stain removal efficiency. This study demonstrated that Amy175 would be proposed as a novel α-amylase source for industrial application in the future.
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Gonzalez-Ordenes F, Cea PA, Fuentes-Ugarte N, Muñoz SM, Zamora RA, Leonardo D, Garratt RC, Castro-Fernandez V, Guixé V. ADP-Dependent Kinases From the Archaeal Order Methanosarcinales Adapt to Salt by a Non-canonical Evolutionarily Conserved Strategy. Front Microbiol 2018; 9:1305. [PMID: 29997580 PMCID: PMC6028617 DOI: 10.3389/fmicb.2018.01305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/29/2018] [Indexed: 11/13/2022] Open
Abstract
Halophilic organisms inhabit hypersaline environments where the extreme ionic conditions and osmotic pressure have driven the evolution of molecular adaptation mechanisms. Understanding such mechanisms is limited by the common difficulties encountered in cultivating such organisms. Within the Euryarchaeota, for example, only the Halobacteria and the order Methanosarcinales include readily cultivable halophilic species. Furthermore, only the former have been extensively studied in terms of their component proteins. Here, in order to redress this imbalance, we investigate the halophilic adaptation of glycolytic enzymes from the ADP-dependent phosphofructokinase/glucokinase family (ADP-PFK/GK) derived from organisms of the order Methanosarcinales. Structural analysis of proteins from non-halophilic and halophilic Methanosarcinales shows an almost identical composition and distribution of amino acids on both the surface and within the core. However, these differ from those observed in Halobacteria or Eukarya. Proteins from Methanosarcinales display a remarkable increase in surface lysine content and have no reduction to the hydrophobic core, contrary to the features ubiquitously observed in Halobacteria and which are thought to be the main features responsible for their halophilic properties. Biochemical characterization of recombinant ADP-PFK/GK from M. evestigatum (halophilic) and M. mazei (non-halophilic) shows the activity of both these extant enzymes to be only moderately inhibited by salt. Nonetheless, its activity over time is notoriously stabilized by salt. Furthermore, glycine betaine has a protective effect against KCl inhibition and enhances the thermal stability of both enzymes. The resurrection of the last common ancestor of ADP-PFK/GK from Methanosarcinales shows that the ancestral enzyme displays an extremely high salt tolerance and thermal stability. Structure determination of the ancestral protein reveals unique traits such as an increase in the Lys and Glu content at the protein surface and yet no reduction to the volume of the hydrophobic core. Our results suggest that the halophilic character is an ancient trait in the evolution of this protein family and that proteins from Methanosarcinales have adapted to highly saline environments by a non-canonical strategy, different from that currently proposed for Halobacteria. These results open up new avenues for the search and development of novel salt tolerant biocatalysts.
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Affiliation(s)
- Felipe Gonzalez-Ordenes
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo A Cea
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Nicolás Fuentes-Ugarte
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sebastián M Muñoz
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ricardo A Zamora
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Diego Leonardo
- São Carlos Institute of Physics, University of São Paulo at São Carlos, São Paulo, Brazil
| | - Richard C Garratt
- São Carlos Institute of Physics, University of São Paulo at São Carlos, São Paulo, Brazil
| | - Victor Castro-Fernandez
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Victoria Guixé
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Cuebas-Irizarry MF, Irizarry-Caro RA, López-Morales C, Badillo-Rivera KM, Rodríguez-Minguela CM, Montalvo-Rodríguez R. Cloning and Molecular Characterization of an Alpha-Glucosidase (MalH) from the Halophilic Archaeon Haloquadratum walsbyi. Life (Basel) 2017; 7:life7040046. [PMID: 29160840 PMCID: PMC5745559 DOI: 10.3390/life7040046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/15/2017] [Accepted: 11/18/2017] [Indexed: 11/16/2022] Open
Abstract
We report the heterologous expression and molecular characterization of the first extremely halophilic alpha-glucosidase (EC 3.2.1.20) from the archaeon Haloquadratum walsbyi. A 2349 bp region (Hqrw_2071) from the Hqr. walsbyi C23 annotated genome was PCR-amplified and the resulting amplicon ligated into plasmid pET28b(+), expressed in E. coli Rosetta cells, and the resulting protein purified by Ni-NTA affinity chromatography. The recombinant protein showed an estimated molecular mass of 87 kDa, consistent with the expected value of the annotated protein, and an optimal activity for the hydrolysis of α-PNPG was detected at 40 °C, and at pH 6.0. Enzyme activity values were the highest in the presence of 3 M NaCl or 3-4 M KCl. However, specific activity values were two-fold higher in the presence of 3-4 M KCl when compared to NaCl suggesting a cytoplasmic localization. Phylogenetic analyses, with respect to other alpha-glucosidases from members of the class Halobacteria, showed that the Hqr. walsbyi MalH was most similar (up to 41%) to alpha-glucosidases and alpha-xylosidases of Halorubrum. Moreover, computational analyses for the detection of functional domains, active and catalytic sites, as well as 3D structural predictions revealed a close relationship with an E. coli YicI-like alpha-xylosidase of the GH31 family. However, the purified enzyme did not show alpha-xylosidase activity. This narrower substrate range indicates a discrepancy with annotations from different databases and the possibility of specific substrate adaptations of halophilic glucosidases due to high salinity. To our knowledge, this is the first report on the characterization of an alpha-glucosidase from the halophilic Archaea, which could serve as a new model to gain insights into carbon metabolism in this understudied microbial group.
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Affiliation(s)
| | - Ricardo A Irizarry-Caro
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Carol López-Morales
- Biology Department, Box 9000, University of Puerto Rico, Mayagüez, PR 00681, USA.
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Amoozegar MA, Siroosi M, Atashgahi S, Smidt H, Ventosa A. Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. MICROBIOLOGY-SGM 2017; 163:623-645. [PMID: 28548036 DOI: 10.1099/mic.0.000463] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Halophilic archaea, also referred to as haloarchaea, dominate hypersaline environments. To survive under such extreme conditions, haloarchaea and their enzymes have evolved to function optimally in environments with high salt concentrations and, sometimes, with extreme pH and temperatures. These features make haloarchaea attractive sources of a wide variety of biotechnological products, such as hydrolytic enzymes, with numerous potential applications in biotechnology. The unique trait of haloarchaeal enzymes, haloenzymes, to sustain activity under hypersaline conditions has extended the range of already-available biocatalysts and industrial processes in which high salt concentrations inhibit the activity of regular enzymes. In addition to their halostable properties, haloenzymes can also withstand other conditions such as extreme pH and temperature. In spite of these benefits, the industrial potential of these natural catalysts remains largely unexplored, with only a few characterized extracellular hydrolases. Because of the applied impact of haloarchaea and their specific ability to live in the presence of high salt concentrations, studies on their systematics have intensified in recent years, identifying many new genera and species. This review summarizes the current status of the haloarchaeal genera and species, and discusses the properties of haloenzymes and their potential industrial applications.
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Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Siroosi
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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Janeček Š, Gabriško M. Remarkable evolutionary relatedness among the enzymes and proteins from the α-amylase family. Cell Mol Life Sci 2016; 73:2707-25. [PMID: 27154042 PMCID: PMC11108405 DOI: 10.1007/s00018-016-2246-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/17/2022]
Abstract
The α-amylase is a ubiquitous starch hydrolase catalyzing the cleavage of the α-1,4-glucosidic bonds in an endo-fashion. Various α-amylases originating from different taxonomic sources may differ from each other significantly in their exact substrate preference and product profile. Moreover, it also seems to be clear that at least two different amino acid sequences utilizing two different catalytic machineries have evolved to execute the same α-amylolytic specificity. The two have been classified in the Cabohydrate-Active enZyme database, the CAZy, in the glycoside hydrolase (GH) families GH13 and GH57. While the former and the larger α-amylase family GH13 evidently forms the clan GH-H with the families GH70 and GH77, the latter and the smaller α-amylase family GH57 has only been predicted to maybe define a future clan with the family GH119. Sequences and several tens of enzyme specificities found throughout all three kingdoms in many taxa provide an interesting material for evolutionarily oriented studies that have demonstrated remarkable observations. This review emphasizes just the three of them: (1) a close relatedness between the plant and archaeal α-amylases from the family GH13; (2) a common ancestry in the family GH13 of animal heavy chains of heteromeric amino acid transporter rBAT and 4F2 with the microbial α-glucosidases; and (3) the unique sequence features in the primary structures of amylomaltases from the genus Borrelia from the family GH77. Although the three examples cannot represent an exhaustive list of exceptional topics worth to be interested in, they may demonstrate the importance these enzymes possess in the overall scientific context.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia.
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius in Trnava, Nám. J. Herdu 2, 91701, Trnava, Slovakia.
| | - Marek Gabriško
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia
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Santorelli M, Maurelli L, Pocsfalvi G, Fiume I, Squillaci G, La Cara F, Del Monaco G, Morana A. Isolation and characterisation of a novel alpha-amylase from the extreme haloarchaeon Haloterrigena turkmenica. Int J Biol Macromol 2016; 92:174-184. [PMID: 27377461 DOI: 10.1016/j.ijbiomac.2016.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 10/21/2022]
Abstract
An extracellular halophilic alpha-amylase (AmyA) was produced by the haloarchaeon Haloterrigena turkmenica grown in medium enriched with 0.2% (w/v) starch. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and size exclusion chromatography (SEC) analyses showed a major band at 66.0kDa and a peak of 54.0kDa, respectively. Analysis of tryptic fragments of the protein present in the major SDS-PAGE band by nano-LC-ESI-MS/MS led to identification of the alpha-amylase catalytic region, encoded by the htur2110 gene, as the protein possessing the described activity. Optimal values for activity were 55°C, pH 8.5 and 2M NaCl, and high thermostability was showed at 55°C and 3M NaCl. AmyA activity was enhanced by Triton X-100 and was not influenced by n-hexane and chloroform. Starch hydrolysis produced different oligomers with maltose as the smallest end-product. The efficiency of AmyA in degrading starch contained in agronomic residues was tested in grape cane chosen as model substrate. Preliminary results showed that starch was degraded making the enzyme a potential candidate for utilization of agro-industrial waste in fuel and chemicals production. AmyA is one of the few investigated amylases produced by haloarchaea, and the first alpha-amylase described among microorganisms belonging to the genus Haloterrigena.
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Affiliation(s)
- Marco Santorelli
- Department of Chemical, Materials and Production Engineering, University of Naples "Federico II", P.le Tecchio 80, 80125 Napoli, Italy
| | - Luisa Maurelli
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Gabriella Pocsfalvi
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Immacolata Fiume
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Squillaci
- Institute of Agro-environmental and Forest Biology, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Francesco La Cara
- Institute of Agro-environmental and Forest Biology, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giovanni Del Monaco
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Alessandra Morana
- Institute of Agro-environmental and Forest Biology, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
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Eprintsev AT, Falaleeva MI, Lyashchenko MS, Gataullina MO, Kompantseva EI. Isoformes of Malate Dehydrogenase from Rhodovulum Steppense A-20s Grown Chemotrophically under Aerobic Conditions. APPL BIOCHEM MICRO+ 2016. [DOI: 10.1134/s0003683816020058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kumar S, Grewal J, Sadaf A, Hemamalini R, K. Khare S. Halophiles as a source of polyextremophilic α-amylase for industrial applications. AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.1.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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38
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Waditee-Sirisattha R, Kageyama H, Takabe T. Halophilic microorganism resources and their applications in industrial and environmental biotechnology. AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.1.42] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Kumar S, Khan RH, Khare SK. Structural elucidation and molecular characterization ofMarinobactersp. α-amylase. Prep Biochem Biotechnol 2015; 46:238-46. [DOI: 10.1080/10826068.2015.1015564] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Bajpai B, Chaudhary M, Saxena J. Production and Characterization of α-Amylase from an Extremely Halophilic Archaeon, Haloferax sp. HA10. Food Technol Biotechnol 2015; 53:11-17. [PMID: 27904327 DOI: 10.17113/ftb.53.01.15.3824] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Haloarchaea are found at very high concentrations in salt-conditioned environments, hence produce enzymes which are able to catalyze reactions under harsh conditions, typical of many industrial processes. In the present study, culture conditions for extracellular amylase production from Haloarchaea isolated from a solar saltern were optimized and the purified enzyme was characterized. Haloferax sp. HA10 showed maximum amylase production at 3 M NaCl, 37 °C, pH=7 and 1% starch content. Purified α-amylase was a calcium-dependent enzyme with an estimated molecular mass of about 66 kDa and many industrially useful properties. It was found to be stable in a broad range of pH (from 5 to 9) and NaCl concentrations (from 0.5 to 3.0 M), retaining 48% activity even at 4 M. The optimal temperature for Haloferax sp. HA10 amylase activity was 55 °C (99% activity), and 57% activity was retained at 80 °C, which dropped to 44% with the increase of temperature to 90 or 100 °C. It was able to sustain various surfactants and detergents. To the best of our knowledge the detergent-stable α-amylases from halophilic archaeon have not been reported yet.
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Affiliation(s)
- Bhakti Bajpai
- Department of Biotechnology, Ashok & Rita Patel Institute of Integrated Study & Research in
Biotechnology and Allied Sciences (ARIBAS), New Vallabh Vidya Nagar 388121, Gujarat, India
| | - Monika Chaudhary
- Department of Bioscience and Biotechnology, Banasthali University, Distt. Tonk 304022, Rajasthan, India; Present address: 13836 Jefferson Park Dr, Apt 9102, Herndon, VA-20171, USA
| | - Jyoti Saxena
- Biochemical Engineering Department, B.T. Kumaon Institute of Technology, Dwarahat 263653,
Uttarakhand, India
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Structural changes in halophilic and non-halophilic proteases in response to chaotropic reagents. Protein J 2015; 33:394-402. [PMID: 25008068 DOI: 10.1007/s10930-014-9571-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Halophilic enzymes have been established for their stability and catalytic abilities under harsh operational conditions. These have been documented to withstand denaturation at high temperature, pH, organic solvents, and chaotropic agents. However, this stability is modulated by salt. The present study targets an important aspect in understanding protein-urea/GdmCl interactions using proteases from halophilic Bacillus sp. EMB9 and non-halophilic subtilisin (Carlsberg) from Bacillus licheniformis as model systems. While, halophilic protease containing 1 % (w/v) NaCl (0.17 M) retained full activity towards urea (8 M), non-halophilic protease lost about 90 % activity under similar conditions. The secondary and tertiary structure were lost in non-halophilic but preserved for halophilic protein. This effect could be due to the possible charge screening and shielding of the protein surface by Ca(2+) and Na(+) ions rendering it stable against denaturation. The dialyzed halophilic protease almost behaved like the non-halophilic counterpart. Incorporation of NaCl (up to 5 %, w/v or 0.85 M) in dialyzed EMB9 protease containing urea/GdmCl, not only helped regain of proteolytic activity but also evaded denaturing action. Deciphering the basis of this salt modulated stability amidst a denaturing milieu will provide guidelines and templates for engineering stable proteins/enzymes for biotechnological applications.
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Attar A, Ogan A, Yucel S, Turan K. The potential of archaeosomes as carriers of pDNA into mammalian cells. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2015; 44:710-6. [DOI: 10.3109/21691401.2014.982800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Chloride Activated Halophilic α-Amylase from Marinobacter sp. EMB8: Production Optimization and Nanoimmobilization for Efficient Starch Hydrolysis. Enzyme Res 2015; 2015:859485. [PMID: 25667773 PMCID: PMC4312637 DOI: 10.1155/2015/859485] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/13/2014] [Accepted: 12/15/2014] [Indexed: 11/23/2022] Open
Abstract
Halophiles have been perceived as potential source of novel enzymes in recent years. The interest emanates from their ability to catalyze efficiently under high salt and organic solvents. Present work encompasses production optimization and nanoimmobilization of an α-amylase from moderately halophilic Marinobacter sp. EMB8. Media ingredients and culture conditions were optimized by “one-at-a-time approach.” Starch was found to be the best carbon source at 5% (w/v) concentration. Glucose acted as catabolic repressor for amylase production. Salt proved critical for amylase production and maximum production was attained at 5% (w/v) NaCl. Optimization of various culture parameters resulted in 48.0 IU/mL amylase production, a 12-fold increase over that of unoptimized condition (4.0 IU/mL). α-Amylase was immobilized on 3-aminopropyl functionalized silica nanoparticles using glutaraldehyde as cross-linking agent. Optimization of various parameters resulted in 96% immobilization efficiency. Starch hydrolyzing efficiency of immobilized enzyme was comparatively better. Immobilized α-amylase retained 75% of its activity after 5th cycle of repeated use.
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Lee MH, Rhee JK, Cha IT, Song EJ, Song HS, Yim KJ, Seo MJ, Choi JS, Choi HJ, Yoon C, Nam YD, Roh SW. Draft genome sequence of the agarolytic haloarchaeon Halobellus rufus type strain CBA1103. FEMS Microbiol Lett 2014; 362:1-3. [PMID: 25790488 DOI: 10.1093/femsle/fnu005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The extremely halophilic archaeon Halobellus rufus type strain CBA1103(T) (CECT 8423(T) and JCM 19434(T)) was isolated from non-purified solar salt and characterized as an agarase producer. The draft genome sequence contains 3852 303 bp with a G + C content of 64.1% and includes genomic information on various carbohydrate-active enzymes. This is the first sequenced genome of the genus Halobellus, and is expected to provide general sequence information for halophilic carbohydrate-active enzymes and opportunities for biotechnological applications of novel halophilic enzymes.
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Affiliation(s)
- Mi-Hwa Lee
- Fermentation Research Center, Korea Food Research Institute, Sungnam 463-746, Republic of Korea
| | - Jin-Kyu Rhee
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
| | - In-Tae Cha
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea Division of Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea
| | - Eun-Ji Song
- Fermentation Research Center, Korea Food Research Institute, Sungnam 463-746, Republic of Korea Korea University of Science and Technology, Daejeon 305-350, Republic of Korea
| | - Hye S Song
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
| | - Kyung J Yim
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
| | - Myung-Ji Seo
- Division of Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea
| | - Jong-Soon Choi
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Hak-Jong Choi
- World Institute of Kimchi, Gwangju 503-360, Republic of Korea
| | - Changmann Yoon
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
| | - Young-Do Nam
- Fermentation Research Center, Korea Food Research Institute, Sungnam 463-746, Republic of Korea Korea University of Science and Technology, Daejeon 305-350, Republic of Korea
| | - Seong W Roh
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea Korea University of Science and Technology, Daejeon 305-350, Republic of Korea
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Wu G, Qin Y, Cheng Q, Liu Z. Characterization of a novel alkali-stable and salt-tolerant α-amylase from marine bacterium Zunongwangia profunda. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.08.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Sen SK, Raut S, Satpathy S, Rout PR, Bandyopadhyay B, Das Mohapatra PK. Characterizing novel thermophilic amylase producing bacteria from taptapani hot spring, odisha, India. Jundishapur J Microbiol 2014; 7:e11800. [PMID: 25741425 PMCID: PMC4335550 DOI: 10.5812/jjm.11800] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 09/08/2013] [Accepted: 09/25/2013] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Amylases play a vital role in biotechnological studies and rank an important position in the world enzyme market (25% to 33%). Bioprocess method of amylase production is more effective than the other sources, since the technique is easy, cost effective, fast, and the enzymes of required properties can be procured. OBJECTIVES The current study aimed to report the characteristics of novel amylase producing bacterial strains isolated from Taptapani hot spring, Odisha, India. MATERIALS AND METHODS Bacterial strains were isolated by dilution plating method from the water samples collected from Taptapani Hot Spring, Odisha and screened for amylase production through starch hydrolysis. The bacterial isolates were identified morphologically, biochemically, and finally by 16S rDNA profiling. RESULTS Based on the morphological, physiological, biochemical characteristics and the molecular characterization, the isolates SS1, SS2, and SS3 were identified as Bacillus barbaricus, Aeromonas veroni, and Stenotrophomonas maltophilia, respectively. The approximate molecular weight of enzymes from SS1, SS2, and SS3 strains were 19 kDa, 56 kDa and 49 kDa, respectively. CONCLUSIONS The current report isolates, characterizes, and demonstrates the novel heat-adapted amylase-producing bacteria SS1, SS2 and SS3 from Taptapani hot spring, indicating its potentiality and stability under acidic conditions.
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Affiliation(s)
- Sudip Kumar Sen
- Department of Biotechnology, Gandhi Institute of Engineering and Technology, Gunupur, Odisha, India
| | - Sangeeta Raut
- Department of Biotechnology, Gandhi Institute of Engineering and Technology, Gunupur, Odisha, India
| | - Soumya Satpathy
- Department of Biotechnology, Gandhi Institute of Engineering and Technology, Gunupur, Odisha, India
| | - Prangya Ranjan Rout
- Department of Biotechnology, National Institute of Technology, Warangal, Andhra Pradesh, India
| | - Bidyut Bandyopadhyay
- Department of Biotechnology, Oriental Institute of Science and Technology, Midnapore, West Bengal, India
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Boyd ES, Hamilton TL, Swanson KD, Howells AE, Baxter BK, Meuser JE, Posewitz MC, Peters JW. [FeFe]-hydrogenase abundance and diversity along a vertical redox gradient in Great Salt Lake, USA. Int J Mol Sci 2014; 15:21947-66. [PMID: 25464382 PMCID: PMC4284687 DOI: 10.3390/ijms151221947] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 11/29/2022] Open
Abstract
The use of [FeFe]-hydrogenase enzymes for the biotechnological production of H2 or other reduced products has been limited by their sensitivity to oxygen (O2). Here, we apply a PCR-directed approach to determine the distribution, abundance, and diversity of hydA gene fragments along co-varying salinity and O2 gradients in a vertical water column of Great Salt Lake (GSL), UT. The distribution of hydA was constrained to water column transects that had high salt and relatively low O2 concentrations. Recovered HydA deduced amino acid sequences were enriched in hydrophilic amino acids relative to HydA from less saline environments. In addition, they harbored interesting variations in the amino acid environment of the complex H-cluster metalloenzyme active site and putative gas transfer channels that may be important for both H2 transfer and O2 susceptibility. A phylogenetic framework was created to infer the accessory cluster composition and quaternary structure of recovered HydA protein sequences based on phylogenetic relationships and the gene contexts of known complete HydA sequences. Numerous recovered HydA are predicted to harbor multiple N- and C-terminal accessory iron-sulfur cluster binding domains and are likely to exist as multisubunit complexes. This study indicates an important role for [FeFe]-hydrogenases in the functioning of the GSL ecosystem and provides new target genes and variants for use in identifying O2 tolerant enzymes for biotechnological applications.
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.
| | - Trinity L Hamilton
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Kevin D Swanson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Alta E Howells
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Bonnie K Baxter
- Department of Biology and the Great Salt Lake Institute, Westminster College, Salt Lake City, UT 84105, USA.
| | - Jonathan E Meuser
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - Matthew C Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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Siroosi M, Amoozegar MA, Khajeh K, Fazeli M, Rezaei MH. Purification and characterization of a novel extracellular halophilic and organic solvent-tolerant amylopullulanase from the haloarchaeon, Halorubrum sp. strain Ha25. Extremophiles 2014; 18:25-33. [PMID: 24122359 DOI: 10.1007/s00792-013-0589-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 09/26/2013] [Indexed: 10/26/2022]
Abstract
A halophilic archaeon, Halorubrum sp. strain Ha25, produced extracellular halophilic organic solvent-tolerant amylopullulanase. The maximum enzyme production was at high salt concentration, 3-4 M NaCl. Optimum pH and temperature for enzyme production were 7.0 and 40 °C, respectively. Molecular mass of purified enzyme was estimated to be about 140 kDa by SDS-PAGE. This enzyme was active on pullulan and starch as substrates. The apparent Km for the enzyme activity on pullulan was 4 mg/ml and for soluble starch was 1.8 mg/ml. Optimum temperature for amylolytic and pullulytic activities was 50 °C. Optimum pH for amylolytic activity was 7 and for pullulytic activity was 7.5. This enzyme was active over a wide range of concentrations (0-4.5 M) of NaCl. The effect of organic solvents on the enzyme activities showed that this enzyme was more stable in the presence of non-polar organic solvents than polar solvents. This study is the first report on amylopullulanase production in halophilic bacteria and archaea.
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49
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Mesbah NM, Wiegel J. Halophilic alkali- and thermostable amylase from a novel polyextremophilic Amphibacillus sp. NM-Ra2. Int J Biol Macromol 2014; 70:222-9. [PMID: 25008132 DOI: 10.1016/j.ijbiomac.2014.06.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 11/17/2022]
Abstract
Extracellular gluco-amylo-pullulanase from Amphibacillus sp. NM-Ra2 was purified to homogeneity by ethanol precipitation, anion exchange chromatography and gel filtration chromatography. Molecular mass of the enzyme was 50kDa (SDS-PAGE). The enzyme showed maximal activity at 1.9 M NaCl, pH50°C 8.0 and 54°C and was active from 0 to 4.3 M NaCl and 37 to 65°C. The enzyme was inhibited by EDTA and was stable and active in the presence of PMSF, DTT, H2O2, Triton-X-100, Tween 20 and Tween 80. Ca2+ is inessential for activity. The amylase was stimulated with K+ and inhibited with Cu2+ and Mg2+. Hg2+, Zn2+ and Fe2+ had no effect on activity. Amylase was stable and active in the presence of ethanol, methanol and benzene (25%, v/v). The enzyme hydrolyzed linear and branched polysaccharides including pullulan, glycogen and amylopectin, and hydrolyzed raw wheat starch and raw corn starch (14.6% and 13.5% over 2 h). Amylase activity was inhibited by soluble starch concentrations greater than 0.3%. The major products of soluble starch hydrolysis were maltose and maltotriose. The amylase, being halophilic and alkali-thermostable, in addition to being resistant to surfactants, oxidizing agents and organic solvents, can find applications in the starch processing, pharmaceutical, food and paper/pulp industries.
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Affiliation(s)
- Noha M Mesbah
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt.
| | - Juergen Wiegel
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
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50
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Zorgani MA, Patron K, Desvaux M. New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface. J Comput Aided Mol Des 2014; 28:721-34. [DOI: 10.1007/s10822-014-9754-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 05/16/2014] [Indexed: 11/24/2022]
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