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Li X, Wang Y, Sun H, Wang Y, Han X, Yu J, Zhao X, Liu B. Differences in ingestion and biodegradation of the melamine formaldehyde plastic by yellow mealworms Tenebrio molitor and superworms Zophobas atratus, and the prediction of functional gut microbes. CHEMOSPHERE 2024; 352:141499. [PMID: 38373446 DOI: 10.1016/j.chemosphere.2024.141499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 01/11/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Plastics biodegradation by insect larvae is considered as a new strategy for plastic wastes treatment. To uncover the biodegradation of a more complex chemical polymer of melamine formaldehyde (MF) by insect larvae, two worm species of yellow mealworm Tenebrio molitor and superworm Zophobas atratus were fed on MF foam as sole diet for 45 days with sole bran diet as control. Although the MF foam consumption by yellow mealworms of 0.38 mg/d/g-larvae was almost 40% higher than that by superworms of 0.28 mg/d/g-larvae, a similar decrease of survival rates in both species were obtained at about 58%, indicating the adverse effects on their growth. Depolymerization and biodegradation of MF foam occurred in both larval guts, but was more extensive in yellow mealworms. MF foam sole diet influenced gut bacterial and fungal microbiomes of both larvae species, which were assessed by Illumina MiSeq on day 45. Compared to the bran-fed group, both gut bacterial and fungal communities significantly changed in MF-fed groups, but differed in the two larvae species. The results demonstrated a strong association between the distinctive gut microbiome and MF foam degradation, such as unclassified Enterobacteriaceae, Hyphopichia and Issatchenkia. However, sole MF foam diet negatively influenced worms, like lower survival rates and gut abnormalities. In summary, MF foam could be degraded by both yellow mealworms and superworms, albeit with adverse effects. Gut microbes were strongly associated to MF foam degradation, especially the gut fungi.
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Affiliation(s)
- Xin Li
- Department of Environmental Engineering, School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, PR China
| | - Yijing Wang
- Department of Environmental Engineering, School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, PR China
| | - Huayang Sun
- Department of Environmental Engineering, School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, PR China
| | - Yumeng Wang
- Department of Environmental Engineering, School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, PR China
| | - Xiaoyu Han
- Department of Environmental Engineering, School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, PR China
| | - Jingli Yu
- College of Ecology and Environment, Inner Mongolia University, Huhhot, 010021, PR China
| | - Xin Zhao
- Department of Environmental Engineering, School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, PR China.
| | - Baoqin Liu
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, 110122, PR China.
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2
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Nnaji PT, Adukwu E, Morse HR, Chidugu-Ogborigbo RU. Amylase production from marine sponge Hymeniacidon perlevis; potentials sustainability benefits. PLoS One 2023; 18:e0294931. [PMID: 38127953 PMCID: PMC10734944 DOI: 10.1371/journal.pone.0294931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/11/2023] [Indexed: 12/23/2023] Open
Abstract
The marine sponge Hymeniacidon perlevis is a globally distributed and invasive species with extensive filter-feeding characteristics. The symbiotic relationship fostered between the sea sponge and the inhabiting microorganism is key in the production of metabolic enzymes which is the focus of this study. Sponge bacterial symbionts were grown on starch agar for 48hrs. Colourimetric analyses of amylase were conducted at 540nm using a spectrophotometric plate reader. Using an X-Bridge column (3.5μM, 4.6x150mm), 80/20 acetonitrile/water in 0.1% ammonium were the conditions used for the liquid chromatography-mass spectrometry (LC-MS) analyses. Seven reducing sugars were used to optimise LC-MS to determine the presence of the crude enzyme formed. Not all the bacterial symbionts isolated from H perlevis produced alpha and beta amylases to break down starch. From the statistical mean of crude enzyme concentrations from the hydrolysis of starch by amylase, isolate seven had the highest optical density (OD) at 0.43475 while isolate twelve had the lowest OD at 0.141417. From the LC-MS analysis, out of the seven sugars, Glucose and maltose constituted > 65% of the reducing sugars formed from the hydrolysis of starch by the amylases. Isolates 3,6 and 7 produced 6.906 mg/l, 12.309 mg/l, and 5.909 mg/l of glucose, while isolates 3,4,5,6 and 7 produced 203.391 mg/l, 176.238 mg/l, 139.938 mg/l, 39.030 mg/l, and 18.809 mg/l of maltose, respectively. Isolate two had the highest amount of maltose at a concentration of 267.237 mg/l while isolate four had the highest amount of glucose concentration of 53.084 mg/l. Enzymes from marine sponge bacteria offer greater potential for a green and sustainable production process. Amylase extraction from bacterial symbionts in H perlevis is sustainable and should be supported. They can serve as reliable sources of revenue for enzyme industries, and applications in food industries and biotechnological processes.
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Affiliation(s)
- Praise Tochukwu Nnaji
- School of Applied Sciences, College of Health, and Applied Sciences, The University of the West of England, Bristol, United Kingdom
| | - Emmanuel Adukwu
- Centre for Biosciences Research, School of Applied Sciences, The University of the West of England, Bristol, United Kingdom
| | - H. Ruth Morse
- Centre for Biosciences Research, School of Applied Sciences, The University of the West of England, Bristol, United Kingdom
| | - Rachael U. Chidugu-Ogborigbo
- School of Applied Sciences, College of Health, and Applied Sciences, The University of the West of England, Bristol, United Kingdom
- Centre for Biosciences Research, School of Applied Sciences, The University of the West of England, Bristol, United Kingdom
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3
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Saleena SK, Johnson JI, Joseph JK, Padinchati KK, Abdulla MHA. Production and optimization of l-asparaginase by Streptomyces koyangensis SK4 isolated from Arctic sediment. J Basic Microbiol 2023; 63:417-426. [PMID: 35462434 DOI: 10.1002/jobm.202200116] [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: 02/24/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 11/06/2022]
Abstract
Actinomycetes isolated from the Arctic sediment were evaluated for the production of the enzyme l-asparaginase, an enzyme used to treat acute lymphoblastic leukemia. The most potent strain Streptomyces koyangensis SK4 was selected for l-asparaginase enzyme production by submerged fermentation. The effect of various fermentation parameters on enzyme production was analyzed statistically using the Plackett-Burman design and response surface method. Effects of eight parameters including temperature, pH, incubation time, inoculum size, agitation speed, the concentration of starch, l-asparagine, and yeast extract were studied on l-asparaginase production by the Arctic isolate S. koyangensis SK4. Factors such as temperature, pH, incubation time, agitation speed, and l-asparagine concentration were found to be important factors influencing l-asparaginase production. Maximum enzyme activity of 136 IU/ml was obtained at 20°C on the seventh day of incubation in the asparagine dextrose broth maintained at pH 7.5, agitation speed 125 rpm, and l-asparagine concentration of 7.5 g/L. The statistical optimization method described in this study proved effective for increasing the l-asparaginase production by Arctic actinomycetes.
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Affiliation(s)
- Shahana K Saleena
- Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Jeslin I Johnson
- Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Joseph K Joseph
- Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology, Kochi, Kerala, India
| | | | - Mohamed H A Abdulla
- Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology, Kochi, Kerala, India
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4
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Ghattavi S, Homaei A. Marine enzymes: Classification and application in various industries. Int J Biol Macromol 2023; 230:123136. [PMID: 36621739 DOI: 10.1016/j.ijbiomac.2023.123136] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/23/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.
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Affiliation(s)
- Saba Ghattavi
- Fisheries Department, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
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Isolation and Molecular Identification of Xylanase-Producing Bacteria from Ulva flexuosa of the Persian Gulf. Processes (Basel) 2022. [DOI: 10.3390/pr10091834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The marine ecosystem is one of the richest sources of biologically active compounds, such as enzymes, among which seaweed is one of the most diverse marine species and has a rich diversity of bacteria that produce different enzymes. Among these, the bacteria-derived xylanase enzyme has many applications in the fruit juice, paper, and baking industries; so, to consider the economic value of the xylanase enzyme and the isolation and identification of xylanase-producing bacteria is of particular importance. In this study, specimens of the alga Ulva flexuosa species were collected from the coasts of Bandar Abbas and Qeshm Island. The bacteria coexisting with the algae were isolated using a nutrient agar medium. The bacteria producing the xylanase enzyme were then screened by a specific solid culture medium containing xylan, and the activity of the xylanase enzyme isolated from the bacteria was measured using a xylan substrate. The bacteria with the highest enzymatic activity were selected and identified by 16S rRNA gene sequence analysis, and the culture medium conditions for the enzyme production by the selected bacterial strains were optimized. Among the bacterial community, two strains with the highest xylanase activity, which belonged to the genera Bacillus and Shewanella, were identified as Bacillus subtilis strain HR05 and Shewanella algae strain HR06, respectively. The two selected bacteria were registered in the NCBI gene database. The results demonstrated that the two selected strains had different optimal growing conditions in terms of pH and temperature, as well as the sources of carbon and nitrogen for enzyme production. It seems that the xylanase enzyme isolated from the bacterial strains HR05 and HR06, which coexist with alga Ulva flexousa, could be potential candidates for biotechnology and various industries, such as pulp production, paper, and food manufacture, due to their high activity and optimal alkaline pH.
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Sponge–Microbial Symbiosis and Marine Extremozymes: Current Issues and Prospects. SUSTAINABILITY 2022. [DOI: 10.3390/su14126984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Marine microorganisms have great potential for producing extremozymes. They enter useful relationships like many other organisms in the marine habitat. Sponge–microbial symbiosis enables both sponges and microorganisms to mutually benefit each other while performing their activities within the ecosystem. Sponges, because of their nature as marine cosmopolitan benthic epifaunas and filter feeders, serve as a host for many extremophilic marine microorganisms. Potential extremozymes from microbial symbionts are largely dependent on their successful relationship. Extremozymes have found relevance in food processing, bioremediation, detergent, and drug production. Species diversity approach, industrial-scale bioremediation, integrative bioremediation software, government and industrial support are considered. The high cost of sampling, limited research outcomes, low species growth in synthetic media, laborious nature of metagenomics projects, difficulty in the development of synthetic medium, limited number of available experts, and technological knowhow are current challenges. The unique properties of marine extremozymes underpin their application in industry and biotechnological processes. There is therefore an urgent need for the development of cost-effective methods with government and industry support.
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7
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Antarctic Porifera homogenates as a source of enzymes and antibacterial substances: first results. Polar Biol 2022. [DOI: 10.1007/s00300-022-03042-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractMarine Porifera (sponges) are known to produce several bioactive metabolites having a biotechnological potential, mostly derived from their bacterial symbionts; however, current knowledge on the production of metabolites such as enzymes and antibacterial molecules in sponges living in Antarctic environments is not fully exhaustive and needs further deepened investigation. The interest in discovering the broad spectrum of natural products potentially derived from species adapted to colonize extreme environments stimulates the research toward Antarctic sponge bioprospection. In this study, whole homogenates of Antarctic Demospongiae, belonging to five different species [Haliclona (Rhizoniera) sp., Haliclona (Rhizoniera) dancoi, Microxina sarai, Dendrilla antarctica, and Mycale acerata] were collected from Terra Nova Bay (Ross Sea) and examined for presence and activity of enzymes, including lysozyme, and antibacterial substances. Enzyme activities (leucine aminopeptidase, beta-glucosidase, and alkaline phosphatase) were measured using fluorogenic substrates; lysozyme content was determined on plates containing lyophilized Micrococcus lysodeikticus cell walls as a substrate. Homogenates were screened in microtiter plates for their antibacterial activity against Antarctic bacterial isolates, and the absorbance reduction was measured with a microplate reader. All homogenates exhibited proteolytic, glycolytic, and phosphatasic activities, lysozyme and antibacterial activities at near “in situ” temperature (5 °C), with some differences among the examined species. Results confirmed that Antarctic sponge homogenates are interesting sources of different bioactive substances, likely produced from associated bacterial symbionts, and that could have great potential to be used in medicine or industrial applications.
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Hennigan JN, Lynch MD. The past, present, and future of enzyme-based therapies. Drug Discov Today 2022; 27:117-133. [PMID: 34537332 PMCID: PMC8714691 DOI: 10.1016/j.drudis.2021.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/15/2021] [Accepted: 09/10/2021] [Indexed: 01/03/2023]
Abstract
Enzyme-based therapeutics (EBTs) have the potential to tap into an almost unmeasurable amount of enzyme biodiversity and treat myriad conditions. Although EBTs were some of the first biologics used clinically, the rate of development of newer EBTs has lagged behind that of other biologics. Here, we review the history of EBTs, and discuss the state of each class of EBT, their potential clinical advantages, and the unique challenges to their development. Additionally, we discuss key remaining technical barriers that, if addressed, could increase the diversity and rate of the development of EBTs.
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Affiliation(s)
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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9
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Exploring the Diversity and Biotechnological Potential of Cultured and Uncultured Coral-Associated Bacteria. Microorganisms 2021; 9:microorganisms9112235. [PMID: 34835361 PMCID: PMC8622030 DOI: 10.3390/microorganisms9112235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/20/2021] [Accepted: 10/24/2021] [Indexed: 11/17/2022] Open
Abstract
Coral-associated microbes are crucial for the biology of their hosts, contributing to nutrient cycling, adaptation, mitigation of toxic compounds, and biological control of pathogens. Natural products from coral-associated micro-organisms (CAM) may possess unique traits. Despite this, the use of CAM for biotechnological purposes has not yet been adequately explored. Here, we investigated the production of commercially important enzymes by 37 strains of bacteria isolated from the coral species Mussismilia braziliensis, Millepora alcicornis, and Porites astreoides. In-vitro enzymatic assays showed that up to 56% of the isolates produced at least one of the seven enzymes screened (lipase, caseinase, keratinase, cellulase, chitinase, amylase, and gelatinase); one strain, identified as Bacillus amyloliquefaciens produced all these enzymes. Additionally, coral species-specific cultured and uncultured microbial communities were identified. The phylum Firmicutes predominated among the isolates, including the genera Exiguobacterium, Bacillus, and Halomonas, among others. Next-generation sequencing and bacteria culturing produced similar but also complementary data, with certain genera detected only by one or the other method. Our results demonstrate the importance of exploring different coral species as sources of specific micro-organisms of biotechnological and industrial interest, at the same time reinforcing the economic and ecological importance of coral reefs as reservoirs of such diversity.
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10
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Chitin Degradation Machinery and Secondary Metabolite Profiles in the Marine Bacterium Pseudoalteromonas rubra S4059. Mar Drugs 2021; 19:md19020108. [PMID: 33673118 PMCID: PMC7917724 DOI: 10.3390/md19020108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
Genome mining of pigmented Pseudoalteromonas has revealed a large potential for the production of bioactive compounds and hydrolytic enzymes. The purpose of the present study was to explore this bioactivity potential in a potent antibiotic and enzyme producer, Pseudoalteromonas rubra strain S4059. Proteomic analyses (data are available via ProteomeXchange with identifier PXD023249) indicated that a highly efficient chitin degradation machinery was present in the red-pigmented P. rubra S4059 when grown on chitin. Four GH18 chitinases and two GH20 hexosaminidases were significantly upregulated under these conditions. GH19 chitinases, which are not common in bacteria, are consistently found in pigmented Pseudoalteromonas, and in S4059, GH19 was only detected when the bacterium was grown on chitin. To explore the possible role of GH19 in pigmented Pseudoalteromonas, we developed a protocol for genetic manipulation of S4059 and deleted the GH19 chitinase, and compared phenotypes of the mutant and wild type. However, none of the chitin degrading ability, secondary metabolite profile, or biofilm-forming capacity was affected by GH19 deletion. In conclusion, we developed a genetic manipulation protocol that can be used to unravel the bioactive potential of pigmented pseudoalteromonads. An efficient chitinolytic enzyme cocktail was identified in S4059, suggesting that this strain could be a candidate with industrial potential.
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11
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Bioprospecting for Biomolecules from Different Fungal Communities: An Introduction. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Barzkar N, Khan Z, Tamadoni Jahromi S, Pourmozaffar S, Gozari M, Nahavandi R. A critical review on marine serine protease and its inhibitors: A new wave of drugs? Int J Biol Macromol 2020; 170:674-687. [PMID: 33387547 DOI: 10.1016/j.ijbiomac.2020.12.134] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/10/2020] [Accepted: 12/17/2020] [Indexed: 01/04/2023]
Abstract
Marine organisms are rich sources of enzymes and their inhibitors having enormous therapeutic potential. Among different proteolytic enzymes, serine proteases, which can be obtained from various marine organisms show a potential to biomedical application as thrombolytic agents. Although this type of proteases plays a crucial role in almost all biological processes, their uncontrolled activity often leads to several diseases. Accordingly, the actions of these types of proteases are regulated by serine protease inhibitors (SPIs). Marine SPIs control complement activation and various other physiological functions, such as inflammation, immune function, fibrinolysis, blood clotting, and cancer metastasis. This review highlights the potential use of serine proteases and their inhibitors as the new wave of promising drugs.
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Affiliation(s)
- Noora Barzkar
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
| | - Zahoor Khan
- Department of Microbiology, University of Karachi, Karachi 75270, Pakistan
| | - Saeid Tamadoni Jahromi
- Persian Gulf and Oman Sea Ecological Research Center, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research, Education and Extension Organization (AREEO), Bandar 'Abbas, Iran
| | - Sajjad Pourmozaffar
- Persian Gulf Mollusks Research Station, Persian Gulf and Oman Sea Ecological Research Center, Agricultural Research Education and Extension Organization (AREEO), Iranian Fisheries Sciences Research Institute, Bandar-e-Lengeh, Iran
| | - Mohsen Gozari
- Persian Gulf and Oman Sea Ecological Research Center, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research, Education and Extension Organization (AREEO), Bandar 'Abbas, Iran
| | - Reza Nahavandi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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Hossain TJ, Chowdhury SI, Mozumder HA, Chowdhury MNA, Ali F, Rahman N, Dey S. Hydrolytic Exoenzymes Produced by Bacteria Isolated and Identified From the Gastrointestinal Tract of Bombay Duck. Front Microbiol 2020; 11:2097. [PMID: 32983064 PMCID: PMC7479992 DOI: 10.3389/fmicb.2020.02097] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
Bacteria producing hydrolytic exoenzymes are of great importance considering their contribution to the host metabolism as well as for their various applications in industrial bioprocesses. In this work hydrolytic capacity of bacteria isolated from the gastrointestinal tract of Bombay duck (Harpadon nehereus) was analyzed and the enzyme-producing bacteria were genetically characterized. A total of twenty gut-associated bacteria, classified into seventeen different species, were isolated and screened for the production of protease, lipase, pectinase, cellulase and amylase enzymes. It was found that thirteen of the isolates could produce at least one of these hydrolytic enzymes among which protease was the most common enzyme detected in ten isolates; lipase in nine, pectinase in four, and cellulase and amylase in one isolate each. This enzymatic array strongly correlated to the previously reported eating behavior of Bombay duck. 16S rRNA gene sequence-based taxonomic classification of the enzyme-producing isolates revealed that the thirteen isolates were grouped into three different classes of bacteria consisting of eight different genera. Staphylococcus, representing ∼46% of the isolates, was the most dominant genus. Measurement of enzyme-production via agar diffusion technique revealed that one of the isolates which belonged to the genus Exiguobacterium, secreted the highest amount of lipolytic and pectinolytic enzymes, whereas a Staphylococcus species produced highest proteolytic activity. The Exiguobacterium sp. expressing a maximum of four hydrolases, appeared to be the most promising isolate of all.
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Affiliation(s)
- Tanim J. Hossain
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Sumaiya I. Chowdhury
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Halima A. Mozumder
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Mohammad N. A. Chowdhury
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Ferdausi Ali
- Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| | - Nabila Rahman
- Department of Biology, Chittagong Sunshine College, Chattogram, Bangladesh
| | - Sujan Dey
- Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
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Al Khawli F, Martí-Quijal FJ, Ferrer E, Ruiz MJ, Berrada H, Gavahian M, Barba FJ, de la Fuente B. Aquaculture and its by-products as a source of nutrients and bioactive compounds. ADVANCES IN FOOD AND NUTRITION RESEARCH 2020; 92:1-33. [PMID: 32402442 DOI: 10.1016/bs.afnr.2020.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Underutilized marine resources (e.g., algae, fish, and shellfish processing by-products), as sustainable alternatives to livestock protein and interesting sources of bioactive compounds, have attracted the attention of the researchers. Aquatic products processing industries are growing globally and producing huge amounts of by-products that often discarded as waste. However, recent studies pointed out that marine waste contains several valuable components including high-quality proteins, lipids, minerals, vitamins, enzymes, and bioactive compounds that can be used against cancer and some cardiovascular disorders. Besides, previously conducted studies on algae have shown the presence of some unique biologically active compounds and valuable proteins. Hence, this chapter points out recent advances in this area of research and discusses the importance of aquaculture and fish processing by-products as alternative sources of proteins and bioactive compounds.
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Affiliation(s)
- Fadila Al Khawli
- Nutrition, Food Science and Toxicology Department, Faculty of Pharmacy, Universitat de València, Burjassot, València, Spain
| | - Francisco J Martí-Quijal
- Nutrition, Food Science and Toxicology Department, Faculty of Pharmacy, Universitat de València, Burjassot, València, Spain.
| | - Emilia Ferrer
- Nutrition, Food Science and Toxicology Department, Faculty of Pharmacy, Universitat de València, Burjassot, València, Spain
| | - María-José Ruiz
- Nutrition, Food Science and Toxicology Department, Faculty of Pharmacy, Universitat de València, Burjassot, València, Spain
| | - Houda Berrada
- Nutrition, Food Science and Toxicology Department, Faculty of Pharmacy, Universitat de València, Burjassot, València, Spain
| | - Mohsen Gavahian
- Product and Process Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC.
| | - Francisco J Barba
- Nutrition and Food Science Area, Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine Department, Faculty of Pharmacy, Universitat de València, Burjassot, València, Spain
| | - Beatriz de la Fuente
- Nutrition, Food Science and Toxicology Department, Faculty of Pharmacy, Universitat de València, Burjassot, València, Spain
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15
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Xylanases from marine microorganisms: A brief overview on scope, sources, features and potential applications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140312. [DOI: 10.1016/j.bbapap.2019.140312] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 01/10/2023]
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16
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Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
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Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida. Int J Mol Sci 2019; 20:ijms20123020. [PMID: 31226841 PMCID: PMC6627142 DOI: 10.3390/ijms20123020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 11/17/2022] Open
Abstract
Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the Bangiophyceae-Florideophyceae clade (BV) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria.
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18
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Dumorné K, Severe R. Marine enzymes and their industrial and biotechnological applications. MINERVA BIOTECNOL 2018. [DOI: 10.23736/s1120-4826.18.02442-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Trincone A. Update on Marine Carbohydrate Hydrolyzing Enzymes: Biotechnological Applications. Molecules 2018; 23:E901. [PMID: 29652849 PMCID: PMC6017418 DOI: 10.3390/molecules23040901] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/05/2018] [Accepted: 04/10/2018] [Indexed: 12/20/2022] Open
Abstract
After generating much interest in the past as an aid in solving structural problems for complex molecules such as polysaccharides, carbohydrate-hydrolyzing enzymes of marine origin still appear as interesting biocatalysts for a range of useful applications in strong interdisciplinary fields such as green chemistry and similar domains. The multifaceted fields in which these enzymes are of interest and the scarce number of original articles in literature prompted us to provide the specialized analysis here reported. General considerations from modern (2016-2017 interval time) review articles are at start of this manuscript; then it is subsequently organized in sections according to particular biopolymers and original research articles are discussed. Literature sources like the Science Direct database with an optimized W/in search, and the Espacenet patent database were used.
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Affiliation(s)
- Antonio Trincone
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078 Pozzuoli, Naples, Italy.
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20
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Valdehuesa KNG, Ramos KRM, Moron LS, Lee I, Nisola GM, Lee WK, Chung WJ. Draft Genome Sequence of Newly Isolated Agarolytic Bacteria Cellulophaga omnivescoria sp. nov. W5C Carrying Several Gene Loci for Marine Polysaccharide Degradation. Curr Microbiol 2018. [PMID: 29536113 DOI: 10.1007/s00284-018-1467-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The continued research in the isolation of novel bacterial strains is inspired by the fact that native microorganisms possess certain desired phenotypes necessary for recombinant microorganisms in the biotech industry. Most studies have focused on the isolation and characterization of strains from marine ecosystems as they present a higher microbial diversity than other sources. In this study, a marine bacterium, W5C, was isolated from red seaweed collected from Yeosu, South Korea. The isolate can utilize several natural polysaccharides such as agar, alginate, carrageenan, and chitin. Genome sequence and comparative genomics analyses suggest that strain W5C belongs to a novel species of the Cellulophaga genus, from which the name Cellulophaga omnivescoria sp. nov. is proposed. Its genome harbors 3,083 coding sequences and 146 carbohydrate-active enzymes (CAZymes). Compared to other reported Cellulophaga species, the genome of W5C contained a higher proportion of CAZymes (4.7%). Polysaccharide utilization loci (PUL) for agar, alginate, and carrageenan were identified in the genome, along with other several putative PULs. These PULs are excellent sources for discovering novel hydrolytic enzymes and pathways with unique characteristics required for biorefinery applications, particularly in the utilization of marine renewable biomass. The type strain is JCM 32108T (= KCTC 13157BPT).
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Affiliation(s)
- Kris Niño G Valdehuesa
- Department of Energy Science and Technology, Energy and Environment Fusion Technology Center, Myongji University, Yongin, Gyeonggi-do, South Korea
| | - Kristine Rose M Ramos
- Department of Energy Science and Technology, Energy and Environment Fusion Technology Center, Myongji University, Yongin, Gyeonggi-do, South Korea
| | - Llewelyn S Moron
- Department of Energy Science and Technology, Energy and Environment Fusion Technology Center, Myongji University, Yongin, Gyeonggi-do, South Korea
- Biology Department, College of Science, De La Salle University, Manila, Philippines
| | - Imchang Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Grace M Nisola
- Department of Energy Science and Technology, Energy and Environment Fusion Technology Center, Myongji University, Yongin, Gyeonggi-do, South Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggi-do, South Korea
| | - Wook-Jin Chung
- Department of Energy Science and Technology, Energy and Environment Fusion Technology Center, Myongji University, Yongin, Gyeonggi-do, South Korea.
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Izadpanah Qeshmi F, Homaei A, Fernandes P, Javadpour S. Marine microbial L-asparaginase: Biochemistry, molecular approaches and applications in tumor therapy and in food industry. Microbiol Res 2018; 208:99-112. [PMID: 29551216 DOI: 10.1016/j.micres.2018.01.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/23/2018] [Accepted: 01/28/2018] [Indexed: 10/18/2022]
Abstract
The marine environment is a rich source of biological and chemical diversity. It covers more than 70% of the Earth's surface and features a wide diversity of habitats, often displaying extreme conditions, where marine organisms thrive, offering a vast pool for microorganisms and enzymes. Given the dissimilarity between marine and terrestrial habitats, enzymes and microorganisms, either novel or with different and appealing features as compared to terrestrial counterparts, may be identified and isolated. L-asparaginase (E.C. 3.5.1.1), is among the relevant enzymes that can be obtained from marine sources. This amidohydrolase acts on L-asparagine and produce L-aspartate and ammonia, accordingly it has an acknowledged chemotherapeutic application, namely in acute lymphoblastic leukemia. Moreover, L-asparaginase is also of interest in the food industry as it prevents acrylamide formation. Terrestrial organisms have been largely tapped for L-asparaginases, but most failed to comply with criteria for practical applications, whereas marine sources have only been marginally screened. This work provides an overview on the relevant features of this enzyme and the framework for its application, with a clear emphasis on the use of L-asparaginase from marine sources. The review envisages to highlight the unique properties of marine L-asparaginases that could make them good candidates for medical applications and industries, especially in food safety.
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Affiliation(s)
| | - Ahmad Homaei
- Department of Biology, Faculty of Sciences, University of Hormozgan, Bandar Abbas, Iran.
| | - Pedro Fernandes
- Department of Bioengineering and IBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Faculty of Engineering, Universidade Lusófona de Humanidades e Tecnologias, Av. Campo Grande 376, 1749-024 Lisboa, Portugal
| | - Sedigheh Javadpour
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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22
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de Souza C, Lopes MD, De Oliveira FM, Passos MJF, Ferreira LCG, Faria BF, Villar JAFP, Junior MC, Taranto AG, Dos Santos LL, Fonseca CT, de Oliveira Lopes D. Rational selection of immunodominant and preserved epitope Sm043300e from Schistosoma mansoni and design of a chimeric molecule for biotechnological purposes. Mol Immunol 2017; 93:133-143. [PMID: 29175593 DOI: 10.1016/j.molimm.2017.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/12/2017] [Accepted: 11/19/2017] [Indexed: 12/18/2022]
Abstract
Human schistosomiasis is a neglected tropical disease of great importance in public health. A large number of people are infected with schistosomiasis, making vaccine development and effective diagnosis important control strategies. A rational epitope prediction workflow using Schistosoma mansoni hypothetical proteins was previously presented by our group, and an improvement to that approach is presented here. Briefly, immunodominant epitopes from parasite membrane proteins were predicted by reverse vaccinology strategy with additional in silico analysis. Furthermore, epitope recognition was evaluated using sera of individuals infected with S. mansoni. The epitope that stood out in both in silico and in vitro assays was used to compose a rational chimeric molecule to improve immune response activation. Out of 2185 transmembrane proteins, four epitopes with high binding affinities for human and mouse MHCII molecules were selected through computational screening. These epitopes were synthesized to evaluate their ability to induce TCD4+ lymphocyte proliferation in mice. Sm204830e and Sm043300e induced significant TCD4+ proliferation. Both epitopes were submitted to enzyme-linked immunosorbent assay to evaluate their recognition by IgG antibodies from the sera of infected individuals, and epitope Sm043300 was significantly recognized in most sera samples. Epitope Sm043300 also showed good affinity for human MHCII molecules in molecular docking, and its sequence is curiously highly conserved in four S. mansoni proteins, all of which are described as G-protein-coupled receptors. In addition, we have demonstrated the feasibility of incorporating this epitope, which showed low similarity to human sequences, into a chimeric molecule. The stability of the molecule was evaluated by molecular modeling aimed at future molecule production for use in diagnosis and vaccination trials.
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Affiliation(s)
- Cláudia de Souza
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil; Laboratório de Síntese Orgânica e Nanoestruturas, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | - Marcelo Donizete Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil; Laboratório de Síntese Orgânica e Nanoestruturas, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | - Flávio Martins De Oliveira
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil
| | - Maria Juliana Ferreira Passos
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil; Laboratório de Síntese Orgânica e Nanoestruturas, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | - Laís Cunha Grossi Ferreira
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil
| | - Bruna Franciele Faria
- Laboratório de Modelagem Molecular, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | | | - Moacyr Comar Junior
- Laboratório de Modelagem Molecular, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | - Alex Guterres Taranto
- Laboratório de Modelagem Molecular, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brazil, Brazil
| | - Luciana Lara Dos Santos
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil
| | - Cristina Toscano Fonseca
- Grupo de Pesquisa em Biologia e Imunologia de doenças Infeciosas e Parasitária, Centro de Pesquisas René Rachou-Fundação Oswaldo Cruz, Av. Augusto de Lima, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Débora de Oliveira Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, Minas Gerais, 35501-296, Brazil.
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Huo YY, Rong Z, Jian SL, Xu CD, Li J, Xu XW. A Novel Halotolerant Thermoalkaliphilic Esterase from Marine Bacterium Erythrobacter seohaensis SW-135. Front Microbiol 2017; 8:2315. [PMID: 29213264 PMCID: PMC5702849 DOI: 10.3389/fmicb.2017.02315] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/09/2017] [Indexed: 01/08/2023] Open
Abstract
A novel esterase gene, e69, was cloned from Erythrobacter seohaensis SW-135, which was isolated from a tidal flat sediment of the Yellow Sea in Korea. This gene is 825 bp in length and codes for a 29.54 kDa protein containing 274 amino acids. Phylogenetic analysis showed that E69 is a new member of the bacterial lipolytic enzyme family IV. This enzyme exhibited the highest level of activity toward p-nitrophenyl (NP) butyrate but little or no activity toward the other p-NP esters tested. The optimum temperature and pH of the catalytic activity of E69 were 60°C and pH 10.5, respectively. The enzyme exhibited stable activity over a wide range of alkaline pH values (7.5-9.5). In addition, E69 was found to be a halotolerant esterase as it exhibited the highest hydrolytic activity in the presence of 0.5 M NaCl and was still active in the presence of 3 M NaCl. Moreover, it possessed some degree of tolerance to Triton X-100 and several organic solvents. Through homology modeling and comparison with other esterases, it was suggested that the absence of the cap domain and its narrow substrate-binding pocket might be responsible for its narrow substrate specificity. Sequence and structural analysis results suggested that its high ratio of negatively to positively charged residues, large hydrophobic surface area, and negative electrostatic potential on the surface may be responsible for its alkaline adaptation. The results of this study provide insight into marine alkaliphilic esterases, and the unique properties of E69 make it a promising candidate as a biocatalyst for industrial applications.
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Affiliation(s)
- Ying-Yi Huo
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Zhen Rong
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Shu-Ling Jian
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Cao-Di Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
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