1
|
Thøgersen MS, Zervas A, Stougaard P, Ellegaard-Jensen L. Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland. Front Microbiol 2024; 15:1358787. [PMID: 38655082 PMCID: PMC11035741 DOI: 10.3389/fmicb.2024.1358787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024] Open
Abstract
The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.
Collapse
|
2
|
Zervas A, Stougaard P, Thøgersen MS. Complete genome sequence of "Bacillaceae sp. strain IKA-2": a cold-active, amylase-producing bacterium from ikaite columns in SW Greenland. Microbiol Resour Announc 2024; 13:e0088723. [PMID: 38134028 PMCID: PMC10868235 DOI: 10.1128/mra.00887-23] [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: 09/20/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
Bacillaceae sp. strain IKA-2 is a bacterium isolated from the permanently cold and alkaline ikaite columns in the Ikka Fjord in SW Greenland (61°12'05″N; 48°00'50″W). The bacterium grows well at 10°C in a substrate buffered to pH 10. It has a genome size of 4,424,890 bp and a guanine-cytosine (GC) content of 36.2%. The genome harbors genes involved in hydrolysis of long carbohydrates and in protection against cold shock.
Collapse
Affiliation(s)
- A. Zervas
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - P. Stougaard
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - M. S. Thøgersen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| |
Collapse
|
3
|
Ashok PP, Dasgupta D, Ray A, Suman SK. Challenges and prospects of microbial α-amylases for industrial application: a review. World J Microbiol Biotechnol 2023; 40:44. [PMID: 38114825 DOI: 10.1007/s11274-023-03821-y] [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: 08/29/2023] [Accepted: 10/27/2023] [Indexed: 12/21/2023]
Abstract
α-Amylases are essential biocatalysts representing a billion-dollar market with significant long-term global demand. They have varied applications ranging from detergent, textile, and food sectors such as bakery to, more recently, biofuel industries. Microbial α-amylases have distinct advantages over their plant and animal counterparts owing to generally good activities and better stability at temperature and pH extremes. With the scope of applications expanding, the need for new and improved α-amylases is ever-growing. However, scaling up microbial α-amylase technology from the laboratory to industry for practical applications is impeded by several issues, ranging from mass transfer limitations, low enzyme yields, and energy-intensive product recovery that adds to high production costs. This review highlights the major challenges and prospects for the production of microbial α-amylases, considering the various avenues of industrial bioprocessing such as culture-independent approaches, nutrient optimization, bioreactor operations with design improvements, and product down-streaming approaches towards developing efficient α-amylases with high activity and recyclability. Since the sequence and structure of the enzyme play a crucial role in modulating its functional properties, we have also tried to analyze the structural composition of microbial α-amylase as a guide to its thermodynamic properties to identify the areas that can be targeted for enhancing the catalytic activity and thermostability of the enzyme through varied immobilization or selective enzyme engineering approaches. Also, the utilization of inexpensive and renewable substrates for enzyme production to isolate α-amylases with non-conventional applications has been briefly discussed.
Collapse
Affiliation(s)
- Patel Pratima Ashok
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Dehradun, 248005, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Diptarka Dasgupta
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Dehradun, 248005, India.
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Anjan Ray
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Dehradun, 248005, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sunil K Suman
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Dehradun, 248005, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| |
Collapse
|
4
|
Zhang Y, Liu F, Liang H, Gao D. Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline-Alkaline Wetland: a Metagenomic Analysis. MICROBIAL ECOLOGY 2023; 86:985-996. [PMID: 36585489 DOI: 10.1007/s00248-022-02165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61-80.71 mg/(m2‧h), the average CH4 flux decreased from 10.72 to 1.96-3.94 mg/(m2‧h), and the average N2O flux decreased from 56.17 to - 27.14 to - 20.70 μg/(m2‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.
Collapse
Affiliation(s)
- Yupeng Zhang
- Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
- College of Resources and Environmental Sciences, Henan Agricultural University, No.63 Agricultural Road, Zhengzhou, 450002, China
| | - Fengqin Liu
- College of Life Sciences, Henan Agricultural University, No.63 Agricultural Road, Zhengzhou, 450002, China
| | - Hong Liang
- Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China.
- Centre for Urban Environmental Remedeation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China.
| | - Dawen Gao
- Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China.
- Centre for Urban Environmental Remedeation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China.
| |
Collapse
|
5
|
Bharwad K, Shekh S, Singh NK, Patel A, Joshi C. Heterologous expression and biochemical characterization of novel multifunctional thermostable α-amylase from hot-spring metagenome. Int J Biol Macromol 2023; 242:124810. [PMID: 37182622 DOI: 10.1016/j.ijbiomac.2023.124810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/24/2023] [Accepted: 05/07/2023] [Indexed: 05/16/2023]
Abstract
Hot-springs are regarded as the best source of industrially significant biocules and one of the unique locations for extremophiles. The α-amylase is one of the most important enzymes used in starch consuming industries, where the need of thermostability is paramount. In this study, the full metagenome sequences obtained from the soil of Tuwa hot-spring (Gujarat, India) were examined for the presence of several thermostable enzymes using bioinformatic techniques. The whole gene sequence for α-amylase was found from the metagenome. The α-amylase gene was amplified, cloned, and expressed in Escherichia coli and further characterized in vitro. The rm-α-amylase was found optimally active at 60 °C and at pH 6.0 and showed significantly high activity in 0.1 mM Co2+ as well as in other heavy metal ions without any effect on its thermostability. Apart from α-amylase activity the purified rm-α-amylase was also shown to hydrolyse agar, xylan, pectin, alginate and cellulose. To our knowledge, this is the first report of a new, multifunctional, thermostable amylase that was discovered from the hot-spring metagenomes. Owing to their multifunctionality, resilience towards high temperature and heavy metal ions, stability with solvents, additives and inhibitors, rm-α-amylase can be exploited for a variety of biotechnological applications.
Collapse
Affiliation(s)
- Krishna Bharwad
- Gujarat Biotechnology Research Centre, Gandhinagar 382011, India
| | - Satyamitra Shekh
- Gujarat Biotechnology Research Centre, Gandhinagar 382011, India
| | | | - Amrutlal Patel
- Gujarat Biotechnology Research Centre, Gandhinagar 382011, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar 382011, India.
| |
Collapse
|
6
|
BADASS: BActeriocin-Diversity ASsessment Software. BMC Bioinformatics 2023; 24:24. [PMID: 36670373 PMCID: PMC9854158 DOI: 10.1186/s12859-022-05106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/07/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Bacteriocins are defined as thermolabile peptides produced by bacteria with biological activity against taxonomically related species. These antimicrobial peptides have a wide application including disease treatment, food conservation, and probiotics. However, even with a large industrial and biotechnological application potential, these peptides are still poorly studied and explored. BADASS is software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data. RESULTS The search for bacteriocin sequences is performed with tools such as BLAST or DIAMOND using the BAGEL4 database as a reference. The putative bacteriocin sequences identified are used to determine the abundance and richness of the three classes of bacteriocins. Abundance is calculated by comparing the reads identified as bacteriocins to the reads identified as 16S rRNA gene using SILVA database as a reference. BADASS has a complete pipeline that starts with the quality assessment of the raw data. At the end of the analysis, BADASS generates several plots of richness and abundance automatically as well as tabular files containing information about the main bacteriocins detected. The user is able to change the main parameters of the analysis in the graphical interface. To demonstrate how the software works, we used four datasets from WMS studies using default parameters. Lantibiotics were the most abundant bacteriocins in the four datasets. This class of bacteriocin is commonly produced by Streptomyces sp. CONCLUSIONS With a user-friendly graphical interface and a complete pipeline, BADASS proved to be a powerful tool for prospecting bacteriocin sequences in Whole-Metagenome Shotgun Sequencing (WMS) data. This tool is publicly available at https://sourceforge.net/projects/badass/ .
Collapse
|
7
|
Jeilu O, Simachew A, Alexandersson E, Johansson E, Gessesse A. Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics. Front Microbiol 2022; 13:1059061. [PMID: 36569080 PMCID: PMC9768486 DOI: 10.3389/fmicb.2022.1059061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.
Collapse
Affiliation(s)
- Oliyad Jeilu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden,*Correspondence: Oliyad Jeilu,
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| |
Collapse
|
8
|
Cakmak U, Tuncay FO, Kolcuoğlu Y. Cold active α-amylase obtained from Cladophora hutchinsiae-Purification, biochemical characterization and some potential applications. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Kim SY, Kim H, Kim YJ, Jung DH, Seo DH, Jung JH, Park CS. Enzymatic analysis of truncation mutants of a type II pullulanase from Bifidobacterium adolescentis P2P3, a resistant starch-degrading gut bacterium. Int J Biol Macromol 2021; 193:1340-1349. [PMID: 34740684 DOI: 10.1016/j.ijbiomac.2021.10.193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/28/2022]
Abstract
A putative type II pullulanase gene, pulP, was identified in Bifidobacterium adolescentis P2P3. PulP possesses an α-amylase domain at the N-terminus and a pullulanase type I domain at the C-terminus, as well as three carbohydrate-binding modules (one CBM25 and two CBM41s) between them. The native PulP and four truncated mutant recombinant proteins (PulPΔCΔP, PulPΔP, PulPΔAΔC, and PulPΔA), in which each of the two catalytic domains and/or the CBMs were deleted, were produced in Escherichia coli and their specific properties were characterized. The removal of either catalytic domain abolished the corresponding catalytic activity of the wild-type enzyme. Deletion of the C-terminal domain resulted in a drastic decrease in the optimal temperature and thermostability, indicating that the pullulanase domain might be related to the temperature dependency of the enzyme. In addition, the elimination of the CBMs in the mutant proteins led to a loss of binding affinity toward raw substrates as well as the loss of their hydrolysis activities compared to the wild-type enzyme. HPAEC and TLC analyses proved that PulP and its mutants could hydrolyze α-glucans into maltotriose as their main product. These results suggest that PulP may play an important role in α-glucan metabolism in B. adolescentis P2P3.
Collapse
Affiliation(s)
- Sun-Young Kim
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hyeran Kim
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Ye-Jin Kim
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Dong-Hyun Jung
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Dong-Ho Seo
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Cheon-Seok Park
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea.
| |
Collapse
|
11
|
Kumar A, Mukhia S, Kumar R. Industrial applications of cold-adapted enzymes: challenges, innovations and future perspective. 3 Biotech 2021; 11:426. [PMID: 34567931 DOI: 10.1007/s13205-021-02929-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Extreme cold environments are potential reservoirs of microorganisms producing unique and novel enzymes in response to environmental stress conditions. Such cold-adapted enzymes prove to be valuable tools in industrial biotechnology to meet the increasing demand for efficient biocatalysts. The inherent properties like high catalytic activity at low temperature, high specific activity and low activation energy make the cold-adapted enzymes well suited for application in various industries. The interest in this group of enzymes is expanding as they are the preferred alternatives to harsh chemical synthesis owing to their biodegradable and non-toxic nature. Irrespective of the multitude of applications, the use of cold-adapted enzymes at the industrial level is still limited. The current review presents the unique adaptive features and the role of cold-adapted enzymes in major industries like food, detergents, molecular biology and bioremediation. The review highlights the significance of omics technology i.e., metagenomics, metatranscriptomics and metaproteomics in enzyme bioprospection from extreme environments. It further points out the challenges in using cold-adapted enzymes at the industrial level and the innovations associated with novel enzyme prospection strategies. Documentations on cold-adapted enzymes and their applications are abundant; however, reports on the role of omics tools in exploring cold-adapted enzymes are still scarce. So, the review covers the aspect concerning the novel techniques for enzyme discovery from nature.
Collapse
Affiliation(s)
- Anil Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201 002 India
| | - Srijana Mukhia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
| |
Collapse
|
12
|
Ariaeenejad S, Zolfaghari B, Sadeghian Motahar SF, Kavousi K, Maleki M, Roy S, Hosseini Salekdeh G. Highly Efficient Computationally Derived Novel Metagenome α-Amylase With Robust Stability Under Extreme Denaturing Conditions. Front Microbiol 2021; 12:713125. [PMID: 34526977 PMCID: PMC8437397 DOI: 10.3389/fmicb.2021.713125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
α-Amylases are among the very critical enzymes used for different industrial purposes. Most α-amylases cannot accomplish the requirement of industrial conditions and easily lose their activity in harsh environments. In this study, a novel α-amylase named PersiAmy1 has been identified through the multistage in silico screening pipeline from the rumen metagenomic data. The long-term storage of PersiAmy1 in low and high temperatures demonstrated 82.13 and 71.01% activities after 36 days of incubation at 4 and 50°C, respectively. The stable α-amylase retained 61.09% of its activity after 180 min of incubation at 90°C and was highly stable in a broad pH range, showing 60.48 and 86.05% activities at pH 4.0 and pH 9.0 after 180 min of incubation, respectively. Also, the enzyme could resist the high-salinity condition and demonstrated 88.81% activity in the presence of 5 M NaCl. PersiAmy1 showed more than 74% activity in the presence of various metal ions. The addition of the detergents, surfactants, and organic solvents did not affect the α-amylase activity considerably. Substrate spectrum analysis showed that PersiAmy1 could act on a wide array of substrates. PersiAmy1 showed high stability in inhibitors and superb activity in downstream conditions, thus useful in detergent and baking industries. Investigating the applicability in detergent formulation, PersiAmy1 showed more than 69% activity after incubation with commercial detergents at different temperatures (30–50°C) and retained more than 56% activity after incubation with commercial detergents for 3 h at 10°C. Furthermore, the results of the wash performance analysis exhibited a good stain removal at 10°C. The power of PersiAmy1 in the bread industry revealed soft, chewable crumbs with improved volume and porosity compared with control. This study highlights the intense power of robust novel PersiAmy1 as a functional bio-additive in many industrial applications.
Collapse
Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Behrouz Zolfaghari
- Department of Computer Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Seyedeh Fatemeh Sadeghian Motahar
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics, Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Morteza Maleki
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Swapnoneel Roy
- School of Computing, University of North Florida, Jacksonville, FL, United States
| | - Ghasem Hosseini Salekdeh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization, Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
13
|
Chen L, Yi Z, Fang Y, Jin Y, He K, Xiao Y, Zhao D, Luo H, He H, Sun Q, Zhao H. Biochemical and synergistic properties of a novel alpha-amylase from Chinese nong-flavor Daqu. Microb Cell Fact 2021; 20:80. [PMID: 33827572 PMCID: PMC8028695 DOI: 10.1186/s12934-021-01571-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Daqu is the most important fermentation starter for Chinese liquor, with large number of microbes and enzymes being openly enriched in the Daqu system over thousands of years. However, only a few enzymes have been analyzed with crude protein for total liquefying power and saccharifying power of Daqu. Therefore, the complex enzymatic system present in Daqu has not been completely characterized. Moreover, their pivotal and complicated functions in Daqu are completely unknown. Results
In this study, a novel α-amylase NFAmy13B, from GH13_5 subfamily (according to the Carbohydrate-Active enZYmes Database, CAZy) was successfully heterologous expressed by Escherichia coli from Chinese Nong-flavor (NF) Daqu. It exhibited high stability ranging from pH 5.5 to 12.5, and higher specific activity, compared to other GH13_5 fungal α-amylases. Moreover, NFAmy13B did not show activity loss and retained 96% residual activity after pre-incubation at pH 11 for 21 h and pH 12 for 10 h, respectively. Additionally, 1.25 mM Ca2+ significantly improved its thermostability. NFAmy13B showed a synergistic effect on degrading wheat starch with NFAmy13A (GH13_1), another α-amylase from Daqu. Both enzymes could cleave maltotetraose and maltopentaose in same degradation pattern, and only NFAmy13A could efficiently degrade maltotriose. Moreover, NFAmy13B showed higher catalytic efficiency on long-chain starch, while NFAmy13A had higher catalytic efficiency on short-chain maltooligosaccharides. Their different catalytic efficiencies on starch and maltooligosaccharides may be caused by their discrepant substrate-binding region. Conclusions This study mined a novel GH13_5 fungal α-amylase (NFAmy13B) with outstanding alkali resistance from Nong-flavor (NF) Daqu. Furthermore, its synergistic effect with NFAmy13A (GH13_1) on hydrolyzing wheat starch was confirmed, and their possible contribution in NF Daqu was also speculated. Thus, we not only provide a candidate α-amylase for industry, but also a useful strategy for further studying the interactions in the complex enzyme system of Daqu. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01571-w.
Collapse
Affiliation(s)
- Lanchai Chen
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, People's Republic of China
| | - Zhuolin Yi
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yang Fang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yanling Jin
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Kaize He
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yao Xiao
- Analytical and Testing Center, Sichuan University of Science and Engineering, Zigong, 643000, China
| | - Dong Zhao
- Wuliangye Group, Yibin, 644007, China
| | - Huibo Luo
- Liquor Making Bio-Technology and Application of Key Laboratory of Sichuan Province, Bioengineering College, Sichuan University of Science and Engineering, Zigong, 643000, China
| | - Hui He
- Department of Liquor Making Engineering, Moutai College, Renhuai, 564501, China
| | - Qun Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, People's Republic of China.
| | - Hai Zhao
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China.
| |
Collapse
|
14
|
Molecular strategies to enhance stability and catalysis of extremophile-derived α-amylase using computational biology. Extremophiles 2021; 25:221-233. [PMID: 33754213 DOI: 10.1007/s00792-021-01223-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/10/2021] [Indexed: 12/29/2022]
Abstract
α-Amylase is the most significant glycoside hydrolase having applications in various industries. It cleaves the α,1-4 glucosidic linkages of polysaccharides like starch, glycogen to yield a small polymer of glucose in α-anomeric configuration. α-Amylase is produced by all the three domains of life but microorganisms are preferred sources for industrial-scale production due to several advantages. Enormous studies and research have been done in this field in the past few decades. Still, it is requisite to work on enzyme stability and catalysis, as it loses its functionality in extreme. As the enzyme loses its structural and catalytic property under extreme environmental conditions, it is mandatory to confer some potential strategies for enhancing enzyme behaviour in such conditions. This limitation of an enzyme can be overcome up to some extent by extremophiles. They serve as an excellent source of α-amylase with outstanding features. This review is an attempt to encapsulate some structure-based strategies for improving enzyme behaviour thereby enabling researchers to selectively amend any of the strategies as per requirement during upstream and downstream processing for higher enzyme yield and stability. Thus, it will provide some cutting-edge strategies for tailoring α-amylase producing organism and enzyme with the help of several computational biology tools.
Collapse
|
15
|
Effect of Barium Addition on Hydrolytic Enzymatic Activities in Food Waste Degradation under Anaerobic Conditions. Processes (Basel) 2020. [DOI: 10.3390/pr8111371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Enzymatic hydrolysis of complex components of residual materials, such as food waste, is a rate-limiting step that conditionates the production rate of biofuels. Research into the anaerobic degradation of cellulose and starch, which are abundant components in organic waste, could contribute to optimize biofuels production processes. In this work, a lab-scale anaerobic semi-continuous hydrolytic reactor was operated for 171 days using food waste as feedstock; the effect of Ba2+ dosage over the activity of five hydrolytic enzymes was also evaluated. No significant effects were observed on the global performance of the hydrolytic process during the steady-state of the operation of the reactor, nevertheless, it was detected that Ba2+ promoted β-amylases activity by 76%, inhibited endoglucanases and α-amylases activity by 39 and 20%, respectively, and had no effect on β-glucosidases and glucoamylases activity. The mechanisms that rule the observed enzymatic activity changes remain unknown; however, the discussion in this paper provides hypothetical explanations for further research.
Collapse
|
16
|
|
17
|
Ojha SK, Singh PK, Mishra S, Pattnaik R, Dixit S, Verma SK. Response surface methodology based optimization and scale-up production of amylase from a novel bacterial strain, Bacillus aryabhattai KIIT BE-1. ACTA ACUST UNITED AC 2020; 27:e00506. [PMID: 32742945 PMCID: PMC7388185 DOI: 10.1016/j.btre.2020.e00506] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/16/2020] [Accepted: 07/13/2020] [Indexed: 12/31/2022]
Abstract
A novel strain KIIT BE-1 isolated from a specialized environment, screened through starch iodine test from a set of eighty-five biodigestate isolates, produced amylase maximally when cultured for 48 h at 37 °C. The molecular and biochemical characterization confirmed it as a strain of Bacillus aryabhattai. It exhibited optimal amylase activity (3.20 U/ml) at 36 h post incubation with a media combination of starch and yeast extract for C-N source respectively. Statistical optimisation by response surface modeling showed R2 values of 0.9645 for biomass and 0.9831 for amylase activity, suggesting the significance of the model. The optimised medium (10.25 % starch, 5.0 % peptone, 5.18 % yeast extract, pH 7.3) enhanced the enzyme activity to 4.16 U/ml (1.39-fold) from 3.20 U/ml of un-optimised medium. Further, the biomass yield and the enzymatic activity in optimized medium and process conditions increased by 1.14 and 1.21 folds subjected to a 5 l scaled-up operation in a lab-scale bioreactor.
Collapse
Affiliation(s)
- Sanjay Kumar Ojha
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed-to-be-University, Bhubaneswar, 751 024, India.,Pandorum Technologies Pvt. Ltd., Bangalore Bioinnovation Centre, Helix Biotech Park, Electronic City Phase 1, Bengaluru, 560 100, India
| | - Puneet Kumar Singh
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed-to-be-University, Bhubaneswar, 751 024, India
| | - Snehasish Mishra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed-to-be-University, Bhubaneswar, 751 024, India
| | - Ritesh Pattnaik
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed-to-be-University, Bhubaneswar, 751 024, India
| | - Shubha Dixit
- School of Pharmacy, Lloyd Institute of Management and Technology, PlotNo.11, Knowledge Park II, Greater Noida, 201310, India
| | - Suresh K Verma
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed-to-be-University, Bhubaneswar, 751 024, India
| |
Collapse
|
18
|
Pinto ÉSM, Dorn M, Feltes BC. The tale of a versatile enzyme: Alpha-amylase evolution, structure, and potential biotechnological applications for the bioremediation of n-alkanes. CHEMOSPHERE 2020; 250:126202. [PMID: 32092569 DOI: 10.1016/j.chemosphere.2020.126202] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/10/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
As the primary source of a wide range of industrial products, the study of petroleum-derived compounds is of pivotal importance. However, the process of oil extraction and refinement is among the most environmentally hazardous practices, impacting almost all levels of the ecological chain. So far, the most appropriate strategy to overcome such an issue is through bioremediation, which revolves around the employment of different microorganisms to degrade hazardous compounds, generating less environmental impact and lower monetary costs. In this sense, a myriad of organisms and enzymes are considered possible candidates for the bioremediation process. Amidst the potential candidates is α-amylase, an evolutionary conserved starch-degrading enzyme. Notably, α-amylase was not only seen to degrade n-alkanes, a subclass of alkanes considered the most abundant petroleum-derived compounds but also low-density polyethylene, a dangerous pollutant produced from petroleum. Thus, due to its high conservation in both eukaryotic and prokaryotic lineages, in addition to the capability to degrade different types of hazardous compounds, the study of α-amylase becomes a rising interest. Nevertheless, there are no studies that review all biotechnological applications of α-amylase for bioremediation. In this work, we critically review the potential biotechnological applications of α-amylase, focusing on the biodegradation of petroleum-derived compounds. Evolutionary aspects are discussed, as well for all structural information and all features that could impact on the employment of this protein in the biotechnological industry, such as pH, temperature, and medium conditions. New perspectives and critical assessments are conducted regarding the application of α-amylase in the bioremediation of n-alkanes.
Collapse
Affiliation(s)
- Éderson Sales Moreira Pinto
- Laboratory of Structural Bioinformatics and Computational Biology, Center for Biotechnology, Federal University of Rio Grande do Sul, Brazil
| | - Márcio Dorn
- Laboratory of Structural Bioinformatics and Computational Biology, Institute of Informatics, Federal University of Rio Grande do Sul, Brazil; Laboratory of Structural Bioinformatics and Computational Biology, Center for Biotechnology, Federal University of Rio Grande do Sul, Brazil
| | - Bruno César Feltes
- Laboratory of Structural Bioinformatics and Computational Biology, Institute of Informatics, Federal University of Rio Grande do Sul, Brazil.
| |
Collapse
|
19
|
Cold survival strategies for bacteria, recent advancement and potential industrial applications. Arch Microbiol 2018; 201:1-16. [PMID: 30478730 DOI: 10.1007/s00203-018-1602-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/04/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022]
Abstract
Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.
Collapse
|
20
|
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.
Collapse
|
21
|
Arabacı N, Arıkan B. Isolation and characterization of a cold-active, alkaline, detergent stable α-amylase from a novel bacterium Bacillus subtilis N8. Prep Biochem Biotechnol 2018; 48:419-426. [PMID: 29561221 DOI: 10.1080/10826068.2018.1452256] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A cold-active alkaline amylase producer Bacillus subtilis N8 was isolated from soil samples. Amylase synthesis optimally occurred at 15°C and pH 10.0 on agar plates containing starch. The molecular weight of the enzyme was found to be 205 kDa by performing SDS-PAGE. While the enzyme exhibited the highest activity at 25°C and pH 8.0, it was highly stable in alkaline media (pH 8.0-12.0) and retained 96% of its original activity at low temperatures (10-40°C) for 24 hr. While the amylase activity increased in the presence of β-mercaptoethanol (103%); Ba2+, Ca2+, Na+, Zn2+, Mn2+, H2O2, and Triton X-100 slightly inhibited the activity. The enzyme showed resistance to some denaturants: such as SDS, EDTA, and urea (52, 65, and 42%, respectively). N8 α-amylase displayed the maximum remaining activity of 56% with 3% NaCl. The major final products of starch were glucose, maltose, and maltose-derived oligosaccharides. This novel cold-active α-amylase has the potential to be used in the industries of detergent and food, bioremediation process and production of prebiotics.
Collapse
Affiliation(s)
- Nihan Arabacı
- a Department of Biology , Çukurova University , Adana , Turkey
| | - Burhan Arıkan
- a Department of Biology , Çukurova University , Adana , Turkey
| |
Collapse
|
22
|
Sindhu R, Binod P, Madhavan A, Beevi US, Mathew AK, Abraham A, Pandey A, Kumar V. Molecular improvements in microbial α-amylases for enhanced stability and catalytic efficiency. BIORESOURCE TECHNOLOGY 2017; 245:1740-1748. [PMID: 28478894 DOI: 10.1016/j.biortech.2017.04.098] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
α-Amylases is one of the most important industrial enzyme which contributes to 25% of the industrial enzyme market. Though it is produced by plant, animals and microbial source, those from microbial source seems to have potential applications due to their stability and economic viability. However a large number of α-amylases from different sources have been detailed in the literature, only few numbers of them could withstand the harsh industrial conditions. Thermo-stability, pH tolerance, calcium independency and oxidant stability and starch hydrolyzing efficiency are the crucial qualities for α-amylase in starch based industries. Microbes can be genetically modified and fine tuning can be done for the production of enzymes with desired characteristics for specific applications. This review focuses on the native and recombinant α-amylases from microorganisms, their heterologous production and the recent molecular strategies which help to improve the properties of this industrial enzyme.
Collapse
Affiliation(s)
- Raveendran Sindhu
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India.
| | - Parameswaran Binod
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Aravind Madhavan
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India
| | - Ummalyma Sabeela Beevi
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Institute of Bioresources and Sustainable Development, Takyelpat, Imphal 795 001, India
| | - Anil Kuruvilla Mathew
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Amith Abraham
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Ashok Pandey
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
| | - Vinod Kumar
- Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
| |
Collapse
|
23
|
Gupta P, Mishra AK, Vakhlu J. Cloning and characterization of thermo-alkalistable and surfactant stable endoglucanase from Puga hot spring metagenome of Ladakh (J&K). Int J Biol Macromol 2017; 103:870-877. [DOI: 10.1016/j.ijbiomac.2017.05.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 11/28/2022]
|
24
|
Wu YR, Mao A, Sun C, Shanmugam S, Li J, Zhong M, Hu Z. Catalytic hydrolysis of starch for biohydrogen production by using a newly identified amylase from a marine bacterium Catenovulum sp. X3. Int J Biol Macromol 2017. [PMID: 28647525 DOI: 10.1016/j.ijbiomac.2017.06.084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
An identified cold-adaptive, organic solvents-tolerant alkaline α-amylase (HP664) from Catenovulum sp. strain X3 was heterologously expressed and characterized in E. coli, and it was further applied to starch saccharification for biohydrogen production. The recombinant HP664 belongs to a member of glycoside hydrolase family 13 (GH13), with a molecular weight of 69.6kDa without signal peptides, and also shares a relatively low similarity (49%) to other reported amylases. Biochemical characterization demonstrated that the maximal enzymatic activity of HP664 was observed at 35°C and pH 9.0. Most metal ions inhibited its activity; however, low polar organic solvents (e.g., benzene and n-hexane) could enhance the activity by 35-50%. Additionally, HP664 also exhibited the catalytic capability on various polysaccharides, including potato starch, amylopectin, dextrin and agar. In order to increase the bioavailability of starch for H2 production, HP664 was utilized to elevate fermentable oligosaccharide level, and the results revealed that the maximal hydrolytic percentage of starch was up to 44% with 12h of hydrolysis using 5.63U of HP664. Biohydrogen fermentation of the starch hydrolysate by Clostridium sp. strain G1 yielded 297.7mL of H2 after 84h of fermentation, which is 3.73-fold higher than the control without enzymatic treatment of HP664.
Collapse
Affiliation(s)
- Yi-Rui Wu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China
| | - Aihua Mao
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China
| | - Chongran Sun
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China
| | | | - Jin Li
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China
| | - Mingqi Zhong
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China.
| |
Collapse
|
25
|
Towards a sustainable biobased industry - Highlighting the impact of extremophiles. N Biotechnol 2017; 40:144-153. [PMID: 28512003 DOI: 10.1016/j.nbt.2017.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/28/2017] [Accepted: 05/03/2017] [Indexed: 11/21/2022]
Abstract
The transition of the oil-based economy towards a sustainable economy completely relying on biomass as renewable feedstock requires the concerted action of academia, industry, politics and civil society. An interdisciplinary approach of various fields such as microbiology, molecular biology, chemistry, genetics, chemical engineering and agriculture in addition to cross-sectional technologies such as economy, logistics and digitalization is necessary to meet the future global challenges. The genomic era has contributed significantly to the exploitation of naturés biodiversity also from extreme habitats. By applying modern technologies it is now feasible to deliver robust enzymes (extremozymes) and robust microbial systems that are active at temperatures up to 120°C, at pH 0 and 12 and at 1000bar. In the post-genomic era, different sophisticated "omics" analyses will allow the identification of countless novel enzymes regardless of the lack of cultivability of most microorganisms. Furthermore, elaborate protein-engineering methods are clearing the way towards tailor-made robust biocatalysts. Applying environmentally friendly and efficient biological processes, terrestrial and marine biomass can be converted to high value products e.g. chemicals, building blocks, biomaterials, pharmaceuticals, food, feed and biofuels. Thus, further application of extremophiles has the potential to improve sustainability of existing biotechnological processes towards a greener biobased industry.
Collapse
|
26
|
Molecular cloning and characterization of a halotolerant α-amylase from marine metagenomic library derived from Arabian Sea sediments. 3 Biotech 2017; 7:65. [PMID: 28452011 DOI: 10.1007/s13205-017-0674-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/27/2017] [Indexed: 10/19/2022] Open
Abstract
Functional screening of a metagenomic library of marine sediment revealed an amylolytic clone BTM109. This report states the purification and characterization of a moderately halotolerant α-amylase, with more than 51% activity in 2.5 M NaCl. The molecular mass of purified protein was determined to be 55.7 kDa by MALDI-TOF MS. The optimum pH for enzyme activity was pH 7 and temperature for maximal activity was 40 °C. At 5 mM concentration, Ca2+ enhanced the enzyme activity indicating that the enzyme is a Ca2+ dependent α-amylase which was confirmed by the starch hydrolysis pattern using TLC. These physico-chemical properties support the suitability of this enzyme for various industrial applications.
Collapse
|
27
|
Dos Santos DFK, Istvan P, Quirino BF, Kruger RH. Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments. MICROBIAL ECOLOGY 2017; 73:479-491. [PMID: 27709246 DOI: 10.1007/s00248-016-0866-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 09/19/2016] [Indexed: 05/26/2023]
Abstract
Antibiotic resistance has become a major concern for human and animal health, as therapeutic alternatives to treat multidrug-resistant microorganisms are rapidly dwindling. The problem is compounded by low investment in antibiotic research and lack of new effective antimicrobial drugs on the market. Exploring environmental antibiotic resistance genes (ARGs) will help us to better understand bacterial resistance mechanisms, which may be the key to identifying new drug targets. Because most environment-associated microorganisms are not yet cultivable, culture-independent techniques are essential to determine which organisms are present in a given environmental sample and allow the assessment and utilization of the genetic wealth they represent. Metagenomics represents a powerful tool to achieve these goals using sequence-based and functional-based approaches. Functional metagenomic approaches are particularly well suited to the identification new ARGs from natural environments because, unlike sequence-based approaches, they do not require previous knowledge of these genes. This review discusses functional metagenomics-based ARG research and describes new possibilities for surveying the resistome in environmental samples.
Collapse
Affiliation(s)
| | - Paula Istvan
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | - Betania Ferraz Quirino
- Embrapa-Agroenergia, Brasília, DF, Brazil
- Universidade Católica de Brasília, Genomic Sciences and Biotechnology Program, Brasília, DF, Brazil
| | | |
Collapse
|
28
|
Ma Y, Shen W, Chen X, Liu L, Zhou Z, Xu F, Yang H. Significantly enhancing recombinant alkaline amylase production in Bacillus subtilis by integration of a novel mutagenesis-screening strategy with systems-level fermentation optimization. J Biol Eng 2016; 10:13. [PMID: 27777616 PMCID: PMC5067897 DOI: 10.1186/s13036-016-0035-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/03/2016] [Indexed: 11/13/2022] Open
Abstract
Background Alkaline amylase has significant potential for applications in the textile, paper and detergent industries, however, low yield of which cannot meet the requirement of industrial application. In this work, a novel ARTP mutagenesis-screening method and fermentation optimization strategies were used to significantly improve the expression level of recombinant alkaline amylase in B. subtilis 168. Results The activity of alkaline amylase in mutant B. subtilis 168 mut-16# strain was 1.34-fold greater than that in the wild-type, and the highest specific production rate was improved from 1.31 U/(mg·h) in the wild-type strain to 1.57 U/(mg·h) in the mutant strain. Meanwhile, the growth of B. subtilis was significantly enhanced by ARTP mutagenesis. When the agitation speed was 550 rpm, the highest activity of recombinant alkaline amylase was 1.16- and 1.25-fold of the activities at 450 and 650 rpm, respectively. When the concentration of soluble starch and soy peptone in the initial fermentation medium was doubled, alkaline amylase activity was increased 1.29-fold. Feeding hydrolyzed starch and soy peptone mixture or glucose significantly improved cell growth, but inhibited the alkaline amylase production in B. subtilis 168 mut-16#. The highest alkaline amylase activity by feeding hydrolyzed starch reached 591.4 U/mL, which was 1.51-fold the activity by feeding hydrolyzed starch and soy peptone mixture. Single pulse feeding-based batch feeding at 10 h favored the production of alkaline amylase in B. subtilis 168 mut-16#. Conclusion The results indicated that this novel ARTP mutagenesis-screening method could significantly improve the yield of recombinant proteins in B. subtilis. Meanwhile, fermentation optimization strategies efficiently promoted expression of recombinant alkaline amylase in B. subtilis 168 mut-16#. These findings have great potential for facilitating the industrial-scale production of alkaline amylase and other enzymes, using B. subtilis cultures as microbial cell factories.
Collapse
Affiliation(s)
- Yingfang Ma
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Wei Shen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xianzhong Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Long Liu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122 China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Fei Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| |
Collapse
|
29
|
Apolinar-Hernández MM, Peña-Ramírez YJ, Pérez-Rueda E, Canto-Canché BB, De Los Santos-Briones C, O'Connor-Sánchez A. Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatán underground water. Gene 2016; 593:154-161. [PMID: 27522038 DOI: 10.1016/j.gene.2016.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/19/2016] [Accepted: 08/04/2016] [Indexed: 01/19/2023]
Abstract
Metagenomics is a culture-independent technology that allows access to novel and potentially useful genetic resources from a wide range of unknown microorganisms. In this study, a fosmid metagenomic library of tropical underground water was constructed, and clones were functionally screened for extracellular proteolytic activity. One of the positive clones, containing a 41,614-bp insert, had two genes with 60% and 68% identity respectively with a peptidase S8 of Chitinimonas koreensis. When these genes were individually sub-cloned, in both cases their sub-clones showed proteolytic phenotype, confirming that they both encode functional proteases. These genes -named PrAY5 and PrAY6- are next to each other. They are similar in size (1845bp and 1824bp respectively) and share 66.5% identity. An extensive in silico characterization showed that their ORFs encode complex zymogens having a signal peptide at their 5' end, followed by a pro-peptide, a catalytic region, and a PPC domain at their 3' end. Their translated sequences were classified as peptidases S8A by sequence comparisons against the non-redundant database and corroborated by Pfam and MEROPS. Phylogenetic analysis of the catalytic region showed that they encode novel proteases that clustered with the sub-family S8_13, which according to the CDD database at NCBI, is an uncharacterized subfamily. They clustered in a clade different from the other three proteases S8 found so far by functional metagenomics, and also different from proteases S8 found in sequenced environmental samples, thereby expanding the range of potentially useful proteases that have been identified by metagenomics. I-TASSER modeling corroborated that they may be subtilases, thus possibly they participate in the hydrolysis of proteins with broad specificity for peptide bonds, and have a preference for a large uncharged residue in P1.
Collapse
Affiliation(s)
- Max M Apolinar-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Chuburná de Hidalgo, Mérida, Yucatán CP 97200, Mexico
| | - Yuri J Peña-Ramírez
- El Colegio de la Frontera Sur (ECOSUR) Unidad Campeche, Avenida Rancho Polígono 2A, Ciudad Industrial Lerma, Campeche, Campeche CP 24500, Mexico
| | - Ernesto Pérez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos CP 62210, Mexico
| | - Blondy B Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Chuburná de Hidalgo, Mérida, Yucatán CP 97200, Mexico
| | - César De Los Santos-Briones
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Chuburná de Hidalgo, Mérida, Yucatán CP 97200, Mexico
| | - Aileen O'Connor-Sánchez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Chuburná de Hidalgo, Mérida, Yucatán CP 97200, Mexico.
| |
Collapse
|
30
|
Mehta D, Satyanarayana T. Bacterial and Archaeal α-Amylases: Diversity and Amelioration of the Desirable Characteristics for Industrial Applications. Front Microbiol 2016; 7:1129. [PMID: 27516755 PMCID: PMC4963412 DOI: 10.3389/fmicb.2016.01129] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/06/2016] [Indexed: 11/13/2022] Open
Abstract
Industrial enzyme market has been projected to reach US$ 6.2 billion by 2020. Major reasons for continuous rise in the global sales of microbial enzymes are because of increase in the demand for consumer goods and biofuels. Among major industrial enzymes that find applications in baking, alcohol, detergent, and textile industries are α-amylases. These are produced by a variety of microbes, which randomly cleave α-1,4-glycosidic linkages in starch leading to the formation of limit dextrins. α-Amylases from different microbial sources vary in their properties, thus, suit specific applications. This review focuses on the native and recombinant α-amylases from bacteria and archaea, their production and the advancements in the molecular biology, protein engineering and structural studies, which aid in ameliorating their properties to suit the targeted industrial applications.
Collapse
Affiliation(s)
- Deepika Mehta
- Department of Microbiology, University of Delhi New Delhi, India
| | | |
Collapse
|
31
|
Song Q, Wang Y, Yin C, Zhang XH. LaaA, a novel high-active alkalophilic alpha-amylase from deep-sea bacterium Luteimonas abyssi XH031(T). Enzyme Microb Technol 2016; 90:83-92. [PMID: 27241296 DOI: 10.1016/j.enzmictec.2016.05.003] [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: 01/08/2016] [Revised: 04/30/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
Abstract
Alpha-amylase is a kind of broadly used industrial enzymes, most of which have been exploited from terrestrial organism. Comparatively, alpha-amylase from marine environment was largely undeveloped. In this study, a novel alkalophilic alpha-amylase with high activity, Luteimonas abyssi alpha-amylase (LaaA), was cloned from deep-sea bacterium L. abyssi XH031(T) and expressed in Escherichia coli BL21. The gene has a length of 1428bp and encodes 475 amino acids with a 35-residue signal peptide. The specific activity of LaaA reached 8881U/mg at the optimum pH 9.0, which is obvious higher than other reported alpha-amylase. This enzyme can remain active at pH levels ranging from 6.0 to 11.0 and temperatures below 45°C, retaining high activity even at low temperatures (almost 38% residual activity at 10°C). In addition, 1mM Na(+), K(+), and Mn(2+) enhanced the activity of LaaA. To investigate the function of potential active sites, R227G, D229K, E256Q/H, H327V and D328V mutants were generated, and the results suggested that Arg227, Asp229, Glu256 and Asp328 were total conserved and essential for the activity of alpha-amylase LaaA. This study shows that the alpha-amylase LaaA is an alkali-tolerant and high-active amylase with strong potential for use in detergent industry.
Collapse
Affiliation(s)
- Qinghao Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yan Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Chong Yin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| |
Collapse
|
32
|
Lee HW, Jeon HY, Choi HJ, Kim NR, Choung WJ, Koo YS, Ko DS, You S, Shim JH. Characterization and Application of BiLA, a Psychrophilic α-Amylase from Bifidobacterium longum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:2709-2718. [PMID: 26979859 DOI: 10.1021/acs.jafc.5b05904] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this study, a novel α-amylase was cloned from Bifidobacterium longum and named BiLA. The enzyme exhibited optimal activity at 20 °C and a pH value of 5.0. Kinetic analysis using various carbohydrate substrates revealed that BiLA had the highest k(cat/)K(m) value for amylose. Interestingly, analysis of the enzymatic reaction products demonstrated that BiLA specifically catalyzed the hydrolysis of oligosaccharides and starches up to G5 from the nonreducing ends. To determine whether BiLA can be used to generate slowly digestible starch (SDS), starch was treated with BiLA, and the kinetic parameters were analyzed using porcine pancreatic α-amylase (PPA) and amyloglucosidase (AMG). Compared to normal starch, BiLA-treated starch showed lower k(cat)/K(m) values with PPA and AMG, suggesting that BiLA is a potential candidate for the production of SDS.
Collapse
Affiliation(s)
- Hye-Won Lee
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Hye-Yeon Jeon
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Hye-Jeong Choi
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Na-Ri Kim
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Woo-Jae Choung
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Ye-Seul Koo
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Dam-Seul Ko
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - SangGuan You
- Department of Marine Food Science and Technology, Gangneung-Wonju National University , 120 Gangneung Daehangno, Gangneung, Gangwon 210-702, South Korea
| | - Jae-Hoon Shim
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| |
Collapse
|
33
|
Lylloff JE, Hansen LBS, Jepsen M, Sanggaard KW, Vester JK, Enghild JJ, Sørensen SJ, Stougaard P, Glaring MA. Genomic and exoproteomic analyses of cold- and alkaline-adapted bacteria reveal an abundance of secreted subtilisin-like proteases. Microb Biotechnol 2016; 9:245-56. [PMID: 26834075 PMCID: PMC4767292 DOI: 10.1111/1751-7915.12343] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Proteases active at low temperature or high pH are used in many commercial applications, including the detergent, food and feed industries, and bacteria specifically adapted to these conditions are a potential source of novel proteases. Environments combining these two extremes are very rare, but offer the promise of proteases ideally suited to work at both high pH and low temperature. In this report, bacteria from two cold and alkaline environments, the ikaite columns in Greenland and alkaline ponds in the McMurdo Dry Valley region, Antarctica, were screened for extracellular protease activity. Two isolates, Arsukibacterium ikkense from Greenland and a related strain, Arsukibacterium sp. MJ3, from Antarctica, were further characterized with respect to protease production. Genome sequencing identified a range of potential extracellular proteases including a number of putative secreted subtilisins. An extensive liquid chromatography–tandem mass spectrometry analysis of proteins secreted by A. ikkense identified six subtilisin‐like proteases as abundant components of the exoproteome in addition to other peptidases potentially involved in complete degradation of extracellular protein. Screening of Arsukibacterium genome libraries in Escherichia coli identified two orthologous secreted subtilisins active at pH 10 and 20°C, which were also present in the A. ikkense exoproteome. Recombinant production of both proteases confirmed the observed activity.
Collapse
Affiliation(s)
- Jeanette E Lylloff
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Lea B S Hansen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Morten Jepsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Kristian W Sanggaard
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan K Vester
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Jan J Enghild
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Mikkel A Glaring
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| |
Collapse
|
34
|
Identification of a novel alkaline amylopullulanase from a gut metagenome of Hermetia illucens. Int J Biol Macromol 2016; 82:514-21. [DOI: 10.1016/j.ijbiomac.2015.10.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/19/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
|
35
|
Draft genome sequences of two protease-producing strains of arsukibacterium, isolated from two cold and alkaline environments. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00585-15. [PMID: 26044431 PMCID: PMC4457068 DOI: 10.1128/genomea.00585-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Arsukibacterium ikkense GCM72(T) and a close relative, Arsukibacterium sp. MJ3, were isolated from two cold and alkaline environments as producers of extracellular proteolytic enzymes active at high pH and low temperature. This report describes the two draft genome sequences, which may serve as sources of future industrial enzymes.
Collapse
|
36
|
Glaring MA, Vester JK, Lylloff JE, Abu Al-Soud W, Sørensen SJ, Stougaard P. Microbial diversity in a permanently cold and alkaline environment in Greenland. PLoS One 2015; 10:e0124863. [PMID: 25915866 PMCID: PMC4411134 DOI: 10.1371/journal.pone.0124863] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/09/2015] [Indexed: 02/01/2023] Open
Abstract
The submarine ikaite columns located in the Ikka Fjord in Southern Greenland represent a unique, permanently cold (less than 6°C) and alkaline (above pH 10) environment and are home to a microbial community adapted to these extreme conditions. The bacterial and archaeal community inhabiting the ikaite columns and surrounding fjord was characterised by high-throughput pyrosequencing of 16S rRNA genes. Analysis of the ikaite community structure revealed the presence of a diverse bacterial community, both in the column interior and at the surface, and very few archaea. A clear difference in overall taxonomic composition was observed between column interior and surface. Whereas the surface, and in particular newly formed ikaite material, was primarily dominated by Cyanobacteria and phototrophic Proteobacteria, the column interior was dominated by Proteobacteria and putative anaerobic representatives of the Firmicutes and Bacteroidetes. The results suggest a stratification of the ikaite columns similar to that of classical soda lakes, with a light-exposed surface inhabited by primary producers and an anoxic subsurface. This was further supported by identification of major taxonomic groups with close relatives in soda lake environments, including members of the genera Rhodobaca, Dethiobacter, Thioalkalivibrio and Tindallia, as well as very abundant groups related to uncharacterised environmental sequences originally isolated from Mono Lake in California.
Collapse
Affiliation(s)
- Mikkel A. Glaring
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jan K. Vester
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jeanette E. Lylloff
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Søren J. Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
37
|
Gu X, Wang S, Wang S, Zhao LX, Cao M, Feng Z. Identification and Characterization of Two Novel Esterases from a Metagenomic Library. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2015. [DOI: 10.3136/fstr.21.649] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Xinqi Gu
- College of Food Science and Technology, Nanjing Agricultural University
| | - Shilin Wang
- College of Food Science and Technology, Nanjing Agricultural University
| | - Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University
| | - Li-Xing Zhao
- Key Laboratory of Medicinal chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University
| | - Mingming Cao
- College of Food Science and Technology, Nanjing Agricultural University
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University
| |
Collapse
|
38
|
Vester JK, Glaring MA, Stougaard P. Improved cultivation and metagenomics as new tools for bioprospecting in cold environments. Extremophiles 2014; 19:17-29. [PMID: 25399309 PMCID: PMC4272415 DOI: 10.1007/s00792-014-0704-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/28/2014] [Indexed: 11/28/2022]
Abstract
Only a small minority of microorganisms from an environmental sample can be cultured in the laboratory leaving the enormous bioprospecting potential of the uncultured diversity unexplored. This resource can be accessed by improved cultivation methods in which the natural environment is brought into the laboratory or through metagenomic approaches where culture-independent DNA sequence information can be combined with functional screening. The coupling of these two approaches circumvents the need for pure, cultured isolates and can be used to generate targeted information on communities enriched for specific activities or properties. Bioprospecting in extreme environments is often associated with additional challenges such as low biomass, slow cell growth, complex sample matrices, restricted access, and problematic in situ analyses. In addition, the choice of vector system and expression host may be limited as few hosts are available for expression of genes with extremophilic properties. This review summarizes the methods developed for improved cultivation as well as the metagenomic approaches for bioprospecting with focus on the challenges faced by bioprospecting in cold environments.
Collapse
Affiliation(s)
- Jan Kjølhede Vester
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark,
| | | | | |
Collapse
|