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Wu S, Xu G, Su Y, Huang H, Xu X, Zhang Y, Tian J, Zhang W, Zhang Z, Liu B. Mining and rational design of psychrophilic catalases using metagenomics and deep learning models. Appl Microbiol Biotechnol 2024; 108:31. [PMID: 38175233 DOI: 10.1007/s00253-023-12926-1] [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: 07/29/2023] [Revised: 09/21/2023] [Accepted: 09/30/2023] [Indexed: 01/05/2024]
Abstract
A complete catalase-encoding gene, designated soiCat1, was obtained from soil samples via metagenomic sequencing, assembly, and gene prediction. soiCat1 showed 73% identity to a catalase-encoding gene of Mucilaginibacter rubeus strain P1, and the amino acid sequence of soiCAT1 showed 99% similarity to the catalase of a psychrophilic bacterium, Pedobacter cryoconitis. soiCAT1 was identified as a psychrophilic enzyme due to the low optimum temperature predicted by the deep learning model Preoptem, which was subsequently validated through analysis of enzymatic properties. Experimental results showed that soiCAT1 has a very narrow range of optimum temperature, with maximal specific activity occurring at the lowest test temperature (4 °C) and decreasing with increasing reaction temperature from 4 to 50 °C. To rationally design soiCAT1 with an improved temperature range, soiCAT1 was engineered through site-directed mutagenesis based on molecular evolution data analyzed through position-specific amino acid possibility calculation. Compared with the wild type, one mutant, soiCAT1S205K, exhibited an extended range of optimum temperature ranging from 4 to 20 °C. The strategies used in this study may shed light on the mining of genes of interest and rational design of desirable proteins. KEY POINTS: • Numerous putative catalases were mined from soil samples via metagenomics. • A complete sequence encoding a psychrophilic catalase was obtained. • A mutant psychrophilic catalase with an extended range of optimum temperature was engineered through site-directed mutagenesis.
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Affiliation(s)
- Shuning Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China
- College of Forestry, Shanxi Agricultural University, No.81 Longcheng Street, Taiyuan, 030031, Shanxi, China
| | - Guoshun Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Yongping Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China
- College of Forestry, Shanxi Agricultural University, No.81 Longcheng Street, Taiyuan, 030031, Shanxi, China
| | - Huoqing Huang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Xinxin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China
| | - Yuhong Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China
| | - Zhiwei Zhang
- College of Forestry, Shanxi Agricultural University, No.81 Longcheng Street, Taiyuan, 030031, Shanxi, China.
| | - Bo Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China.
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Ramasamy KP, Mahawar L, Rajasabapathy R, Rajeshwari K, Miceli C, Pucciarelli S. Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules. Front Microbiol 2023; 14:1197797. [PMID: 37396361 PMCID: PMC10312091 DOI: 10.3389/fmicb.2023.1197797] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Climate change and the induced environmental disturbances is one of the major threats that have a strong impact on bacterial communities in the Antarctic environment. To cope with the persistent extreme environment and inhospitable conditions, psychrophilic bacteria are thriving and displaying striking adaptive characteristics towards severe external factors including freezing temperature, sea ice, high radiation and salinity which indicates their potential in regulating climate change's environmental impacts. The review illustrates the different adaptation strategies of Antarctic microbes to changing climate factors at the structural, physiological and molecular level. Moreover, we discuss the recent developments in "omics" approaches to reveal polar "blackbox" of psychrophiles in order to gain a comprehensive picture of bacterial communities. The psychrophilic bacteria synthesize distinctive cold-adapted enzymes and molecules that have many more industrial applications than mesophilic ones in biotechnological industries. Hence, the review also emphasizes on the biotechnological potential of psychrophilic enzymes in different sectors and suggests the machine learning approach to study cold-adapted bacteria and engineering the industrially important enzymes for sustainable bioeconomy.
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Affiliation(s)
| | - Lovely Mahawar
- Department of Plant Physiology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Nitra, Slovakia
| | - Raju Rajasabapathy
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | | | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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Stoyancheva G, Dishliyska V, Miteva‐Staleva J, Kostadinova N, Abrashev R, Angelova M, Krumova E. Sequencing and gene expression analysis of catalase genes in Antarctic fungal strain Penicillium griseofulvum P29. Polar Biol 2022. [DOI: 10.1007/s00300-021-03001-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yusof NA, Hashim NHF, Bharudin I. Cold Adaptation Strategies and the Potential of Psychrophilic Enzymes from the Antarctic Yeast, Glaciozyma antarctica PI12. J Fungi (Basel) 2021; 7:jof7070528. [PMID: 34209103 PMCID: PMC8306469 DOI: 10.3390/jof7070528] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/19/2021] [Accepted: 06/25/2021] [Indexed: 12/20/2022] Open
Abstract
Psychrophilic organisms possess several adaptive strategies which allow them to sustain life at low temperatures between −20 to 20 °C. Studies on Antarctic psychrophiles are interesting due to the multiple stressors that exist on the permanently cold continent. These organisms produce, among other peculiarities, cold-active enzymes which not only have tremendous biotechnological potential but are valuable models for fundamental research into protein structure and function. Recent innovations in omics technologies such as genomics, transcriptomics, proteomics and metabolomics have contributed a remarkable perspective of the molecular basis underpinning the mechanisms of cold adaptation. This review critically discusses similar and different strategies of cold adaptation in the obligate psychrophilic yeast, Glaciozyma antarctica PI12 at the molecular (genome structure, proteins and enzymes, gene expression) and physiological (antifreeze proteins, membrane fluidity, stress-related proteins) levels. Our extensive studies on G. antarctica have revealed significant insights towards the innate capacity of- and the adaptation strategies employed by this psychrophilic yeast for life in the persistent cold. Furthermore, several cold-active enzymes and proteins with biotechnological potential are also discussed.
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Affiliation(s)
- Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia;
| | - Noor Haza Fazlin Hashim
- Water Quality Laboratory, National Water Research Institute Malaysia (NAHRIM), Ministry of Environment and Water, Jalan Putra Permai, Seri Kembangan 43300, Selangor, Malaysia;
| | - Izwan Bharudin
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
- Correspondence:
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Chabot M, Morales E, Cummings J, Rios N, Giatpaiboon S, Mogul R. Simple kinetics, assay, and trends for soil microbial catalases. Anal Biochem 2020; 610:113901. [PMID: 32841648 DOI: 10.1016/j.ab.2020.113901] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/03/2020] [Indexed: 12/17/2022]
Abstract
In this report, we expand upon the enzymology and ecology of soil catalases through development and application of a simple kinetic model and field-amenable assay based upon volume displacement. Through this approach, we (A) directly relate apparent Michaelis-Menten terms to the catalase reaction mechanism, (B) obtain upper estimates of the intrinsic rate constants for the catalase community (k3'), along with moles of catalase per 16S rRNA gene copy number, (C) utilize catalase specific activities (SAs) to obtain biomass estimates of soil and permafrost communities (LOD, ~104 copy number gdw-1), and (D) relate kinetic trends to changes in bacterial community structure. In addition, this novel kinetic approach simultaneously incorporates barometric adjustments to afford comparisons across field measurements. As per our model, and when compared to garden soils, biological soil crusts exhibited ~2-fold lower values for k3', ≥105-fold higher catalase moles per biomass (250-1200 zmol copy number-1), and ~104-fold higher SAs per biomass (74-230 fkat copy number-1); whereas the highest SAs were obtained from permafrost and high-elevation soil communities (5900-6700 fkat copy number-1). In sum, the total trends suggest that microbial communities which experience higher degrees of native oxidative stress possess higher basal intracellular catalase concentrations and SAs per biomass.
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Affiliation(s)
- Michael Chabot
- Cal Poly Pomona, Chemistry & Biochemistry Department, 3801 W. Temple Ave., Pomona, CA, 91768, USA
| | - Ernesto Morales
- Cal Poly Pomona, Chemistry & Biochemistry Department, 3801 W. Temple Ave., Pomona, CA, 91768, USA
| | - Jacob Cummings
- Cal Poly Pomona, Chemistry & Biochemistry Department, 3801 W. Temple Ave., Pomona, CA, 91768, USA
| | - Nicholas Rios
- Cal Poly Pomona, Chemistry & Biochemistry Department, 3801 W. Temple Ave., Pomona, CA, 91768, USA
| | - Scott Giatpaiboon
- Cal Poly Pomona, Chemistry & Biochemistry Department, 3801 W. Temple Ave., Pomona, CA, 91768, USA
| | - Rakesh Mogul
- Cal Poly Pomona, Chemistry & Biochemistry Department, 3801 W. Temple Ave., Pomona, CA, 91768, USA.
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Fongaro G, Maia GA, Rogovski P, Cadamuro RD, Lopes JC, Moreira RS, Camargo AF, Scapini T, Stefanski FS, Bonatto C, Marques Souza DS, Stoco PH, Duarte RTD, Cabral da Cruz AC, Wagner G, Treichel H. Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools. Curr Genomics 2020; 21:240-252. [PMID: 33071618 PMCID: PMC7521039 DOI: 10.2174/1389202921999200601144137] [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: 01/10/2020] [Revised: 02/02/2020] [Accepted: 04/20/2020] [Indexed: 12/03/2022] Open
Abstract
Abstract: Genomic and proteomic advances in extremophile microorganism studies are increasingly demonstrating their ability to produce a variety of enzymes capable of converting biomass into bioenergy. Such microorganisms are found in environments with nutritional restrictions, anaerobic environments, high salinity, varying pH conditions and extreme natural environments such as hydrothermal vents, soda lakes, and Antarctic sediments. As extremophile microorganisms and their enzymes are found in widely disparate locations, they generate new possibilities and opportunities to explore biotechnological prospecting, including biofuels (biogas, hydrogen and ethanol) with an aim toward using multi-omics tools that shed light on biotechnological breakthroughs.
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Affiliation(s)
- Gislaine Fongaro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Guilherme Augusto Maia
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Paula Rogovski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rafael Dorighello Cadamuro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Joana Camila Lopes
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Renato Simões Moreira
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Aline Frumi Camargo
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Thamarys Scapini
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Fábio Spitza Stefanski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Charline Bonatto
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Doris Sobral Marques Souza
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Patrícia Hermes Stoco
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Tadeu Delgado Duarte
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Ariadne Cristiane Cabral da Cruz
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Glauber Wagner
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Helen Treichel
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
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Monsalves MT, Ollivet-Besson GP, Amenabar MJ, Blamey JM. Isolation of a Psychrotolerant and UV-C-Resistant Bacterium from Elephant Island, Antarctica with a Highly Thermoactive and Thermostable Catalase. Microorganisms 2020; 8:E95. [PMID: 31936717 PMCID: PMC7022778 DOI: 10.3390/microorganisms8010095] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/30/2019] [Accepted: 01/07/2020] [Indexed: 12/23/2022] Open
Abstract
Microorganisms present in Antarctica have to deal not only with cold temperatures but also with other environmental conditions, such as high UV radiation, that trigger the generation of reactive oxygen species. Therefore, Antarctic microorganisms must have an important antioxidant defense system to prevent oxidative damage. One of these defenses are antioxidant enzymes, such as catalase, which is involved in the detoxification of hydrogen peroxide produced under oxidative conditions. Here, we reported the isolation and partial characterization of an Antarctic bacterium belonging to the Serratia genus that was resistant to UV-C radiation and well-adapted to cold temperatures. This microorganism, denominated strain I1P, was efficient at decreasing reactive oxygen species levels produced after UV-C irradiation. Genomic and activity assays suggested that the enzymatic antioxidant defense mechanisms of strain I1P, especially its catalase enzyme, may confer UV resistance. This catalase was active in a wide range of temperatures (20-70 °C), showing optimal activity at 50 °C (at pH 7.0), a remarkable finding considering its psychrotolerant origin. In addition, this enzyme was thermostable, retaining around 60% of its activity after 6 h of incubation at 50 °C. The antioxidant defense systems of strain I1P, including its surprisingly thermoactive and thermostable catalase enzyme, make this microorganism a good source of biocompounds with potential biotechnological applications.
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Affiliation(s)
- María T. Monsalves
- Fundación Científica y Cultural Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago 7750132, Chile; (M.T.M.); (G.P.O.-B.); (M.J.A.)
| | - Gabriela P. Ollivet-Besson
- Fundación Científica y Cultural Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago 7750132, Chile; (M.T.M.); (G.P.O.-B.); (M.J.A.)
| | - Maximiliano J. Amenabar
- Fundación Científica y Cultural Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago 7750132, Chile; (M.T.M.); (G.P.O.-B.); (M.J.A.)
| | - Jenny M. Blamey
- Fundación Científica y Cultural Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago 7750132, Chile; (M.T.M.); (G.P.O.-B.); (M.J.A.)
- Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central, Santiago 9170022, Chile
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Enzymes from Marine Polar Regions and Their Biotechnological Applications. Mar Drugs 2019; 17:md17100544. [PMID: 31547548 PMCID: PMC6835263 DOI: 10.3390/md17100544] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
The microorganisms that evolved at low temperatures express cold-adapted enzymes endowed with unique catalytic properties in comparison to their mesophilic homologues, i.e., higher catalytic efficiency, improved flexibility, and lower thermal stability. Cold environments are therefore an attractive research area for the discovery of enzymes to be used for investigational and industrial applications in which such properties are desirable. In this work, we will review the literature on cold-adapted enzymes specifically focusing on those discovered in the bioprospecting of polar marine environments, so far largely neglected because of their limited accessibility. We will discuss their existing or proposed biotechnological applications within the framework of the more general applications of cold-adapted enzymes.
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Yuzugullu Karakus Y, Isik S. Partial characterization of Bacillus pumilus catalase partitioned in poly(ethylene glycol)/sodium sulfate aqueous two-phase systems. Prep Biochem Biotechnol 2019; 49:391-399. [PMID: 30767698 DOI: 10.1080/10826068.2019.1573197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aqueous two-phase partitioning system (ATPS) was used to extract and purify catalase from Bacillus pumilus. The system parameters for effective purification of catalase were optimized. The best catalase recovery (123%) with a 4.6-fold purification was obtained in the bottom phase of ATPS including the mixture of 15% (w/w) PEG4000, 10% (w/w) Na2SO4 and 3% (w/w) NaCl at pH 5.0. The purified enzyme was characterized regarding its activity and stability. The highest enzyme activity was observed at pH 7.0 and 37 °C on hydrogen peroxide. The enzyme was quite stable at temperatures between 30 and 55 °C and a pH range of 7.0-9.0. The Km and Vmax values were determined from Lineweaver-Burk plot as 11 mM and 1667 µmole ml-1 min-1, respectively. Overall, it can be said that ATPS is a rapid, reasonable, straightforward and cost-effective process for catalase purification in comparison to the chromatographic methods.
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Affiliation(s)
| | - Semih Isik
- b The Graduate School of Natural and Applied Sciences , Kocaeli University , Kocaeli , Turkey
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Samson M, Yang T, Omar M, Xu M, Zhang X, Alphonse U, Rao Z. Improved thermostability and catalytic efficiency of overexpressed catalase from B. pumilus ML 413 (KatX2) by introducing disulfide bond C286-C289. Enzyme Microb Technol 2018; 119:10-16. [DOI: 10.1016/j.enzmictec.2018.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 06/25/2018] [Accepted: 08/08/2018] [Indexed: 01/14/2023]
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Raveendran S, Parameswaran B, Ummalyma SB, Abraham A, Mathew AK, Madhavan A, Rebello S, Pandey A. Applications of Microbial Enzymes in Food Industry. Food Technol Biotechnol 2018; 56:16-30. [PMID: 29795993 DOI: 10.17113/ftb.56.01.18.5491] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The use of enzymes or microorganisms in food preparations is an age-old process. With the advancement of technology, novel enzymes with wide range of applications and specificity have been developed and new application areas are still being explored. Microorganisms such as bacteria, yeast and fungi and their enzymes are widely used in several food preparations for improving the taste and texture and they offer huge economic benefits to industries. Microbial enzymes are the preferred source to plants or animals due to several advantages such as easy, cost-effective and consistent production. The present review discusses the recent advancement in enzyme technology for food industries. A comprehensive list of enzymes used in food processing, the microbial source of these enzymes and the wide range of their application are discussed.
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Affiliation(s)
- Sindhu Raveendran
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | - Binod Parameswaran
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | - Sabeela Beevi Ummalyma
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India.,Institute of Bioresources and Sustainable Development, 795001 Imphal, India
| | - Amith Abraham
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | - Anil Kuruvilla Mathew
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | | | - Sharrel Rebello
- Communicable Disease Research Laboratory, St. Joseph's College, 680121 Irinjalakuda, India
| | - Ashok Pandey
- CSIR-Indian Institute of Toxicology Research (CSIR-IITR), 226001 Lucknow, India
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Jia X, Lin X, Lin C, Lin L, Chen J. Enhanced alkaline catalase production by Serratia marcescens FZSF01: Enzyme purification, characterization, and recombinant expression. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Cloning, Expression, and Characterization of a Novel Thermophilic Monofunctional Catalase from Geobacillus sp. CHB1. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7535604. [PMID: 27579320 PMCID: PMC4992532 DOI: 10.1155/2016/7535604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/03/2016] [Indexed: 12/11/2022]
Abstract
Catalases are widely used in many scientific areas. A catalase gene (Kat) from Geobacillus sp. CHB1 encoding a monofunctional catalase was cloned and recombinant expressed in Escherichia coli (E. coli), which was the first time to clone and express this type of catalase of genus Geobacillus strains as far as we know. This Kat gene was 1,467 bp in length and encoded a catalase with 488 amino acid residuals, which is only 81% similar to the previously studied Bacillus sp. catalase in terms of amino acid sequence. Recombinant catalase was highly soluble in E. coli and made up 30% of the total E. coli protein. Fermentation broth of the recombinant E. coli showed a high catalase activity level up to 35,831 U/mL which was only lower than recombinant Bacillus sp. WSHDZ-01 among the reported catalase production strains. The purified recombinant catalase had a specific activity of 40,526 U/mg and K m of 51.1 mM. The optimal reaction temperature of this recombinant enzyme was 60°C to 70°C, and it exhibited high activity over a wide range of reaction temperatures, ranging from 10°C to 90°C. The enzyme retained 94.7% of its residual activity after incubation at 60°C for 1 hour. High yield and excellent thermophilic properties are valuable features for this catalase in industrial applications.
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Heterologous expression and characterization of a new heme-catalase in Bacillus subtilis 168. ACTA ACUST UNITED AC 2016; 43:729-40. [DOI: 10.1007/s10295-016-1758-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/29/2016] [Indexed: 01/09/2023]
Abstract
Abstract
Reactive oxygen species (ROS) is an inherent consequence to all aerobically living organisms that might lead to the cells being lethal and susceptible to oxidative stress. Bacillus pumilus is characterized by high-resistance oxidative stress that stimulated our interest to investigate the heterologous expression and characterization of heme-catalase as potential biocatalyst. Results indicated that recombinant enzyme significantly exhibited the high catalytic activity of 55,784 U/mg expressed in Bacillus subtilis 168 and 98.097 µmol/min/mg peroxidatic activity, the apparent K m of catalytic activity was 59.6 ± 13 mM with higher turnover rate (K cat = 322.651 × 103 s−1). The pH dependence of catalatic and peroxidatic activity was pH 7.0 and pH 4.5 respectively with temperature dependence of 40 °C and the recombinant heme-catalase exhibited a strong Fe2+ preference. It was further revealed that catalase KatX2 improved the resistance oxidative stress of B. subtilis. These findings suggest that this B. pumilus heme-catalase can be considered among the industrially relevant biocatalysts due to its exceptional catalytic rate and high stability and it can be a potential candidate for the improvement of oxidative resistance of industrially produced strains.
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Kauldhar BS, Sooch BS. Tailoring nutritional and process variables for hyperproduction of catalase from a novel isolated bacterium Geobacillus sp. BSS-7. Microb Cell Fact 2016; 15:7. [PMID: 26762530 PMCID: PMC5377025 DOI: 10.1186/s12934-016-0410-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/05/2016] [Indexed: 11/25/2022] Open
Abstract
Background Catalase (EC 1.11.1.6) is one of the important industrial enzyme employed in diagnostic and analytical methods in the form of biomarkers and biosensors in addition to their enormous applications in textile, paper, food and pharmaceutical sectors. The present study demonstrates the utility of a newly isolated and adapted strain of genus Geobacillus possessing unique combination of several industrially important extremophilic properties for the hyper production of catalase. The bacterium can grow over a wide range of pH (3–12) and temperature (10–90 °C) with extraordinary capability to produce catalase. Results A novel extremophilic strain belonging to genus Geobacillus was exploited for the production of catalase by tailoring its nutritional requirements and process variables. One variable at a time traditional approach followed by computational designing was applied to customize the fermentation process. A simple fermentation media containing only three components namely sucrose (0.55 %, w/v), yeast extract (1.0 %, w/v) and BaCl2 (0.08 %, w/v) was designed for the hyperproduction of catalase. A controlled and optimum air supply caused a tremendous increase in the enzyme production on moving the bioprocess from the flask to bioreactor level. The present paper reports high quantum of catalase production (105,000 IU/mg of cells) in a short fermentation time of 12 h. To the best of our knowledge, there is no report in the literature that matches the performance of the developed protocol for the catalase production. This is the first serious study covering intracellular catalase production from thermophilic genus Geobacillus. Conclusions An increase in intracellular catalase production by 214.72 % was achieved in the optimized medium when transferred from the shake flask to the fermenter level. The extraordinary high production of catalase from Geobacillus sp. BSS-7 makes the isolated strain a prospective candidate for bulk catalase production on an industrial scale.
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Affiliation(s)
- Baljinder Singh Kauldhar
- Enzyme Biotechnology Laboratory, Department of Biotechnology, Punjabi University, Patiala, 147002, Punjab, India.
| | - Balwinder Singh Sooch
- Enzyme Biotechnology Laboratory, Department of Biotechnology, Punjabi University, Patiala, 147002, Punjab, India.
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Sooch BS, Kauldhar BS, Puri M. Recent insights into microbial catalases: Isolation, production and purification. Biotechnol Adv 2014; 32:1429-47. [DOI: 10.1016/j.biotechadv.2014.09.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 09/10/2014] [Accepted: 09/18/2014] [Indexed: 01/08/2023]
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Mafra ACO, Furlan FF, Badino AC, Tardioli PW. Gluconic acid production from sucrose in an airlift reactor using a multi-enzyme system. Bioprocess Biosyst Eng 2014; 38:671-80. [DOI: 10.1007/s00449-014-1306-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 10/10/2014] [Indexed: 10/24/2022]
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V Garay-Flores R, P Segura-Ceniceros E, De León-Gámez R, Balvantín-García C, L Martínez-Hernández J, Betancourt-Galindo R, Rosa Paredes Ramírez A, Noé Aguilar C, Ilyina A. Production of glucose oxidase and catalase by Aspergillus niger free and immobilized in alginate-polyvinyl alcohol beads. J GEN APPL MICROBIOL 2014; 60:262-9. [PMID: 25742978 DOI: 10.2323/jgam.60.262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The production of glucose oxidase (GOX) and catalase (CAT) by submerged fermentation of the free and immobilized xerophytic fungus Aspergillus niger under equal conditions was compared. To immobilize fungal spores, entrapment in PVA/alginate beads treated with NaNO3/CaCl2 was performed. The yield of immobilization in the beads with a diameter less than 1mm was equal to 100%. Fungus growth and substrate consumption were evaluated in both fermentation systems, demonstrating the lag-period presence in the case of the first cycle of immobilized fungus use. The enzyme production by immobilized fungus reuse was carried out. In these cases, greater enzymatic GOX activity was detected, while CAT activity decreased. SEM micrographs for the beads with immobilized fungus applied in the first and second fermentation cycles were obtained, presenting fungus spreading inside the sphere, spore presence and branching hyphae. Immobilization of A. niger on PVA/alginate beads is effective for GOX and CAT production at least on 2-3 repeated fermentative cycles. Thus, immobilization enables repeated use of microbial cells.
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Affiliation(s)
- Rocio V Garay-Flores
- Coahuila Autonomous University, Nanobioscience Group of Chemistry Faculty and Medical School
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Alkaliphilic bacteria: applications in industrial biotechnology. J Ind Microbiol Biotechnol 2011; 38:769-90. [DOI: 10.1007/s10295-011-0968-x] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 03/26/2011] [Indexed: 11/26/2022]
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Zeng HW, Cai YJ, Liao XR, Qian SL, Zhang F, Zhang DB. Optimization of catalase production and purification and characterization of a novel cold-adapted Cat-2 from mesophilic bacterium Serratia marcescens SYBC-01. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0116-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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