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Zhang K, Han Y. Thermostable Bacterial Collagenolytic Proteases: A Review. J Microbiol Biotechnol 2024; 34:1385-1394. [PMID: 38934777 PMCID: PMC11294657 DOI: 10.4014/jmb.2404.04051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
Collagenolytic proteases are widely used in the food, medical, pharmaceutical, cosmetic, and textile industries. Mesophilic collagenases exhibit collagenolytic activity under physiological conditions, but have limitations in efficiently degrading collagen-rich wastes, such as collagen from fish scales, at high temperatures due to their poor thermostability. Bacterial collagenolytic proteases are members of various proteinase families, including the bacterial collagenolytic metalloproteinase M9 and the bacterial collagenolytic serine proteinase families S1, S8, and S53. Notably, the C-terminal domains of collagenolytic proteases, such as the pre-peptidase C-terminal domain, the polycystic kidney disease-like domain, the collagen-binding domain, the proprotein convertase domain, and the β-jelly roll domain, exhibit collagen-binding or -swelling activity. These activities can induce conformational changes in collagen or the enzyme active sites, thereby enhancing the collagen-degrading efficiency. In addition, thermostable bacterial collagenolytic proteases can function at high temperatures, which increases their degradation efficiency since heat-denatured collagen is more susceptible to proteolysis and minimizes the risk of microbial contamination. To date, only a few thermophile-derived collagenolytic proteases have been characterized. TSS, a thermostable and halotolerant subtilisin-like serine collagenolytic protease, exhibits high collagenolytic activity at 60°C. In this review, we present and summarize the current research on A) the classification and nomenclature of thermostable and mesophilic collagenolytic proteases derived from diverse microorganisms, and B) the functional roles of their C-terminal domains. Furthermore, we analyze the cleavage specificity of the thermostable collagenolytic proteases within each family and comprehensively discuss the thermostable collagenolytic protease TSS.
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Affiliation(s)
- Kui Zhang
- College of Life Sciences and Technology, Longdong University, Qingyang 745000, P.R. China
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Qingyang 745000, P.R. China
| | - Yapeng Han
- College of Life Sciences and Technology, Longdong University, Qingyang 745000, P.R. China
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Qingyang 745000, P.R. China
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2
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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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3
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Falkenberg F, Bott M, Bongaerts J, Siegert P. Phylogenetic survey of the subtilase family and a data-mining-based search for new subtilisins from Bacillaceae. Front Microbiol 2022; 13:1017978. [PMID: 36225363 PMCID: PMC9549277 DOI: 10.3389/fmicb.2022.1017978] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
The subtilase family (S8), a member of the clan SB of serine proteases are ubiquitous in all kingdoms of life and fulfil different physiological functions. Subtilases are divided in several groups and especially subtilisins are of interest as they are used in various industrial sectors. Therefore, we searched for new subtilisin sequences of the family Bacillaceae using a data mining approach. The obtained 1,400 sequences were phylogenetically classified in the context of the subtilase family. This required an updated comprehensive overview of the different groups within this family. To fill this gap, we conducted a phylogenetic survey of the S8 family with characterised holotypes derived from the MEROPS database. The analysis revealed the presence of eight previously uncharacterised groups and 13 subgroups within the S8 family. The sequences that emerged from the data mining with the set filter parameters were mainly assigned to the subtilisin subgroups of true subtilisins, high-alkaline subtilisins, and phylogenetically intermediate subtilisins and represent an excellent source for new subtilisin candidates.
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Affiliation(s)
- Fabian Falkenberg
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
- *Correspondence: Petra Siegert,
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4
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Alviz-Gazitua P, González A, Lee MR, Aranda CP. Molecular Relationships in Biofilm Formation and the Biosynthesis of Exoproducts in Pseudoalteromonas spp. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:431-447. [PMID: 35486299 DOI: 10.1007/s10126-022-10097-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Most members of the Pseudoalteromonas genus have been isolated from living surfaces as members of epiphytic and epizooic microbiomes on marine macroorganisms. Commonly Pseudoalteromonas isolates are reported as a source of bioactive exoproducts, i.e., secondary metabolites, such as exopolymeric substances and extracellular enzymes. The experimental conditions for the production of these agents are commonly associated with sessile metabolic states such as biofilms or liquid cultures in the stationary growth phase. Despite this, the molecular mechanisms that connect biofilm formation and the biosynthesis of exoproducts in Pseudoalteromonas isolates have rarely been mentioned in the literature. This review compiles empirical evidence about exoproduct biosynthesis conditions and molecular mechanisms that regulate sessile metabolic states in Pseudoalteromonas species, to provide a comprehensive perspective on the regulatory convergences that generate the recurrent coexistence of both phenomena in this bacterial genus. This synthesis aims to provide perspectives on the extent of this phenomenon for the optimization of bioprospection studies and biotechnology processes based on these bacteria.
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Affiliation(s)
- P Alviz-Gazitua
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile
| | - A González
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile
| | - M R Lee
- Centro i~mar, Universidad de Los Lagos, Camino a Chinquihue km 6, P. Box 5480000, Puerto Montt, Chile
| | - C P Aranda
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile.
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A Novel Gelatinase from Marine Flocculibacter collagenilyticus SM1988: Characterization and Potential Application in Collagen Oligopeptide-Rich Hydrolysate Preparation. Mar Drugs 2022; 20:md20010048. [PMID: 35049903 PMCID: PMC8780967 DOI: 10.3390/md20010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
Although the S8 family in the MEROPS database contains many peptidases, only a few S8 peptidases have been applied in the preparation of bioactive oligopeptides. Bovine bone collagen is a good source for preparing collagen oligopeptides, but has been so far rarely applied in collagen peptide preparation. Here, we characterized a novel S8 gelatinase, Aa2_1884, from marine bacterium Flocculibacter collagenilyticus SM1988T, and evaluated its potential application in the preparation of collagen oligopeptides from bovine bone collagen. Aa2_1884 is a multimodular S8 peptidase with a distinct domain architecture from other reported peptidases. The recombinant Aa2_1884 over-expressed in Escherichia coli showed high activity toward gelatin and denatured collagens, but no activity toward natural collagens, indicating that Aa2_1884 is a gelatinase. To evaluate the potential of Aa2_1884 in the preparation of collagen oligopeptides from bovine bone collagen, three enzymatic hydrolysis parameters, hydrolysis temperature, hydrolysis time and enzyme-substrate ratio (E/S), were optimized by single factor experiments, and the optimal hydrolysis conditions were determined to be reaction at 60 ℃ for 3 h with an E/S of 400 U/g. Under these conditions, the hydrolysis efficiency of bovine bone collagen by Aa2_1884 reached 95.3%. The resultant hydrolysate contained 97.8% peptides, in which peptides with a molecular weight lower than 1000 Da and 500 Da accounted for 55.1% and 39.5%, respectively, indicating that the hydrolysate was rich in oligopeptides. These results indicate that Aa2_1884 likely has a promising potential application in the preparation of collagen oligopeptide-rich hydrolysate from bovine bone collagen, which may provide a feasible way for the high-value utilization of bovine bone collagen.
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Maturation process and characterization of a novel thermostable and halotolerant subtilisin-like protease with high collagenolytic but low gelatinolytic activity. Appl Environ Microbiol 2021; 88:e0218421. [DOI: 10.1128/aem.02184-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enzymatic degradation of collagen is of great industrial and environmental significance; however, little is known about thermophile-derived collagenolytic proteases. Here, we report a novel collagenolytic protease (TSS) from thermophilic
Brevibacillus
sp. WF146. The TSS precursor comprises a signal peptide, an N-terminal propeptide, a subtilisin-like catalytic domain, a β-jelly roll (βJR) domain, and a prepeptidase C-terminal (PPC) domain. The maturation of TSS involves a stepwise autoprocessing of the N-terminal propeptide and the PPC domain, and the βJR rather than the PPC domain is necessary for correct folding of the enzyme. Purified mature TSS displayed optimal activity at 70°C and pH 9.0, a half-life of 1.5 h at 75°C, and an increased thermostability with rising salinity up to 4 M. TSS possesses an increased number of surface acidic residues and ion pairs, as well as four Ca
2+
-binding sites, which contribute to its high thermostability and halotolerance. At high temperatures, TSS exhibited high activity toward insoluble type I collagen and azocoll, but showed a low gelatinolytic activity, with a strong preference for Arg and Gly at the P1 and P1’ positions, respectively. Both the βJR and PPC domains could bind but not swell collagen, and thus facilitate TSS-mediated collagenolysis via improving the accessibility of the enzyme to the substrate. Additionally, TSS has the ability to efficiently degrade fish scale collagen at high temperatures.
IMPORTANCE
Proteolytic degradation of collagen at high temperatures has the advantages of increasing degradation efficiency and minimizing the risk of microbial contamination. Reports on thermostable collagenolytic proteases are limited, and their maturation and catalytic mechanisms remain to be elucidated. Our results demonstrate that the thermophile-derived TSS matures in an autocatalytic manner, and represents one of the most thermostable collagenolytic proteases reported so far. At elevated temperatures, TSS prefers hydrolyzing insoluble heat-denatured collagen rather than gelatin, providing new insight into the mechanism of collagen degradation by thermostable collagenolytic proteases. Moreover, TSS has the potential to be used in recycling collagen-rich wastes such as fish scales.
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7
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A Novel Thermostable Keratinase from Deinococcus geothermalis with Potential Application in Feather Degradation. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11073136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Keratinase can specifically attack disulfide bridges in keratin to convert them from complex to simplified forms. Keratinase thermal stability has drawn attention to various biotechnological industries. In this study, a keratinase DgeKer was identified from a slightly thermophilic species, D. geothermalis. The in silico analysis showed that DgeKer is composed of signal peptide, N-terminal propeptide, mature domain, and C-terminal extension. DgeKer and its C-terminal extension-truncated enzyme (DgeKer-C) were cloned and expressed in E. coli. The purified DgeKer and DgeKer-C showed maximum activity at 70 °C and pH 9–The thermal stability assay (60 °C) showed that the half-life value of DgeKer and DgeKer-C were 103.45 min and 169.10 min, respectively. DgeKer and DgeKer-C were stable at the range of pH from 9 to 11 and showed good tolerance to some metal ions, surfactants and organic solvent. Furthermore, DgeKer could degrade feathers at 70 °C for 60 min. However, the medium became turbid with obvious softening of barbules after being treated with DgeKer-C, which might be due to C-terminal extension. In summary, a thermostable keratinase DgeKer with high efficiency degradation of feathers may have great potential in industry.
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8
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Li J, Cheng JH, Teng ZJ, Sun ZZ, He XY, Wang P, Shi M, Song XY, Chen XL, Zhang YZ, Tian X, Zhang XY. Taxonomic and Enzymatic Characterization of Flocculibacter collagenilyticus gen. nov., sp. nov., a Novel Gammaproteobacterium With High Collagenase Production. Front Microbiol 2021; 12:621161. [PMID: 33786038 PMCID: PMC8005334 DOI: 10.3389/fmicb.2021.621161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
Collagens from marine animals are an important component of marine organic nitrogen. Collagenase-producing bacteria and their collagenases play important roles in collagen degradation and organic nitrogen recycling in the ocean. However, only a few collagenase-producing marine bacteria have been so far discovered. Here, we reported the isolation and characterization of a collagenase-secreting bacterium, designated strain SM1988T, isolated from a green alga Codium fragile sample. Strain SM1988T is a Gram-negative, aerobic, oxidase-, and catalase-positive, unipolar flagellated, and rod-shaped bacterium capable of hydrolyzing casein, gelatin and collagens. Phylogenetic analysis revealed that strain SM1988T formed a distinct phylogenetic lineage along with known genera within the family Pseudoalteromonadaceae, with 16S rRNA gene sequence similarity being less than 93.3% to all known species in the family. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data, strain SM1988T was considered to represent a novel species in a novel genus in the family Pseudoalteromonadaceae, for which the name Flocculibacter collagenilyticus gen. nov., sp. nov. is proposed, with the type strain being SM1988T (= MCCC 1K04279T = KCTC 72761T). Strain SM1988T showed a high production of extracellular collagenases, which had high activity against both bovine collagen and codfish collagen. Biochemical tests combined with genome and secretome analyses indicated that the collagenases secreted by strain SM1988T are serine proteases from the MEROPS S8 family. These data suggest that strain SM1988T acts as an important player in marine collagen degradation and recycling and may have a promising potential in collagen resource utilization.
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Affiliation(s)
- Jian Li
- College of Life Science and Technology, Xinjiang University, Urumqi, China.,State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Zhong-Zhi Sun
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Yan He
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Peng Wang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xinmin Tian
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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9
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Furhan J, Nissar J. Cold-Adapted Serine Metalloprotease from Serratia DLCP2: Purification, Characterization and Industrial Potential. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Tsutsuki H, Ogura K, Moss J, Yahiro K. Host response to the subtilase cytotoxin produced by locus of enterocyte effacement-negative Shiga-toxigenic Escherichia coli. Microbiol Immunol 2020; 64:657-665. [PMID: 32902863 DOI: 10.1111/1348-0421.12841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/05/2020] [Accepted: 09/07/2020] [Indexed: 12/26/2022]
Abstract
Shiga-toxigenic Escherichia coli (STEC) is a major bacterium responsible for disease resulting from foodborne infection, including bloody diarrhea and hemolytic uremic syndrome. STEC produces important virulence factors such as Shiga toxin (Stx) 1 and/or 2. In the STEC family, some locus of enterocyte effacement-negative STEC produce two different types of cytotoxins, namely, Stx2 and subtilase cytotoxin (SubAB). The Stx2 and SubAB cytotoxins are structurally similar and composed of one A subunit and pentamer of B subunits. The catalytically active A subunit of SubAB is a subtilase-like serine protease and specifically cleaves an endoplasmic reticulum (ER) chaperone 78-kDa glucose-regulated protein (GRP78/BiP), a monomeric ATPase that is crucial in protein folding and quality control. The B subunit binds to cell surface receptors. SubAB recognizes sialic carbohydrate-modified cell surface proteins as a receptor. After translocation into cells, SubAB is delivered to the ER, where it cleaves GRP78/BiP. SubAB-catalyzed BiP cleavage induces ER stress, which causes various cell events including inhibition of protein synthesis, suppression of nuclear factor-kappa B activation, apoptotic cell death, and stress granules formation. In this review, we describe SubAB, the SubAB receptor, and the mechanism of cell response to the toxin.
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Affiliation(s)
- Hiroyasu Tsutsuki
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kohei Ogura
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kinnosuke Yahiro
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba, Japan
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11
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Wang Y, Liu BX, Cheng JH, Su HN, Sun HM, Li CY, Yang L, Shen QT, Zhang YZ, Zhang X, Chen XL. Characterization of a New M4 Metalloprotease With Collagen-Swelling Ability From Marine Vibrio pomeroyi Strain 12613. Front Microbiol 2020; 11:1868. [PMID: 32849455 PMCID: PMC7426729 DOI: 10.3389/fmicb.2020.01868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/16/2020] [Indexed: 01/22/2023] Open
Abstract
The ocean harbors a variety of bacteria that contain huge protease resources and offer a great potential for industrial and biotechnological applications. Here, we isolated a protease-secreting bacterium Vibrio pomeroyi strain 12613 from Atlantic seawater and purified a protease VP9 from strain 12613. VP9 was identified as a metalloprotease of the M4 family. VP9 could hydrolyze casein and gelatin but not elastin and collagen. With gelatin as the substrate, VP9 showed the highest activity at 40°C and pH 6.0–8.0. It was stable at temperatures of 50°C and less and in the range of pH 5.0–11.0. VP9 also had good tolerance to NaCl, non-ionic detergents, and organic solvent methanol. Unlike other M4 metalloproteases, VP9 has distinct collagen-swelling ability, and its collagen-swelling effect was concentration dependent. The relative expansion volume of collagen increased by approximately eightfold after treatment with 10 μM VP9 at 37°C for 12 h. The collagen-swelling mechanism of VP9 on bovine-insoluble type I collagen was further studied. Atomic force microscopy observation and biochemical analyses showed that VP9 can degrade proteoglycans in collagen fibers, resulting in the release of collagen fibrils from collagen fibers and the swelling of the latter. In addition, VP9 can degrade glycoproteins, a non-collagenous constituent interacting with collagen in the skin. The characteristics of VP9, such as sufficient specificity toward proteoglycans and glycoproteins but no activity toward collagen, suggest its promising potential in the unhairing and fiber-opening processing in leather industry.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Bai-Xue Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - He-Min Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liuyan Yang
- School of Life Science and Technology, iHuman Institute, ShanghaiTech University, Shanghai, China.,Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Shanghai, China
| | - Qing-Tao Shen
- School of Life Science and Technology, iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xia Zhang
- Department of Molecular Biology, Qingdao Vland Biotech Inc., Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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12
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Amao JA, Barooah M, Omojasola PF. Comparative 16S rDNA metagenomics study of two samples of cassava peel heap from Nigeria and India. 3 Biotech 2019; 9:418. [PMID: 31696023 DOI: 10.1007/s13205-019-1941-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/10/2019] [Indexed: 11/28/2022] Open
Abstract
The microbiology of many cassava products and the wastes generated during the processing have been reported; however, majority of these reports used culture-dependent methods. This has resulted in a dearth of information on the bacterial diversity of cassava peels and peel heaps. Large amounts of cassava peels generated during the processing of cassava root are usually discharged on land or water as wastes and are allowed to rot in the open, especially in some developing countries. Culture-independent methods such as PCR-based amplification and sequencing of 16S rRNA genes, among others have been used in recent times to study the diversity of microbes in different environmental samples. In this study, bacterial isolates were screened for cellulase and xylanase enzyme activities on minimal agar and genomic DNA was isolated from cassava peel samples; metagenomics was carried out using MiSeq 2 × 300 with primers specific for V3-V4 bacterial region. Samples collected from Nigeria (AAG) had more species compared with samples from India (JHA) with 793 and 525 observed OTUs (operational taxonomic units), respectively. Five bacterial isolates from cassava peel-heap samples obtained from Ogbomoso, Nigeria showed no ability to produce cellulase enzyme, seven isolates from the Nigeria samples and three from Jorhat samples were positive for xylanase production; the highest amylase activity was shown by isolate AG18 (10,055 U/mL), while the lowest was recorded for isolate JA2 (2333 U/mL) with a significant difference observed in the amylase activities of isolates (p ≤ 0.05). Comparing the most abundant taxonomy for each of the samples at different taxonomic levels, the most abundant for sample AAG were phylum Firmicutes (42.11%), class Bacilli (41.27%), order Lactobacillales (33.11%), family Acetobacteraceae (31.30%), genus Acetobacter (30.02%) and unclassified species of Acetobacter (29.88%), while sample JHA had Actinobacteria (47.47%) as the highest phylum and class, order Actinomycetales (47.47%), family Brevibacteriaceae (46.97%), genus Brevibacterium (46.97%) and unclassified species of Brevibacterium (46.89%). This study provides an insight into the vast diversity of the bacteria associated with cassava peel heaps and the ability of some of the bacteria to produce selected extracellular enzymes.
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Affiliation(s)
- John Ayobami Amao
- 1Department of Microbiology, University of Ilorin, Ilorin, Nigeria
- 2Microbial Biotechnology Laboratory, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Madhumita Barooah
- 2Microbial Biotechnology Laboratory, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
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13
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Chen XL, Yang JY, Zheng XY, Sheng Q, Wang L, Zhang YZ, Qin QL, Zhang XY. Tripeptides From Casein Are Signal Molecules to Induce the Expression of the Extracellular Protease MCP-01 Gene in Marine Bacterium Pseudoalteromonas sp. SM9913. Front Microbiol 2019; 10:1354. [PMID: 31293532 PMCID: PMC6606773 DOI: 10.3389/fmicb.2019.01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 01/29/2023] Open
Abstract
Microbial extracellular proteases play crucial roles in marine protein degradation and nitrogen recycling. Although a large number of marine bacteria are found to produce extracellular proteases, it is still unknown how marine bacteria respond to environmental proteins to activate the expression of genes encoding extracellular proteases. The inducing signal molecule for marine bacterial extracellular proteases has never been identified. In this study, we identified tripeptides as the inducing signal molecules for the extracellular protease MCP-01 of the deep-sea bacterium Pseudoalteromonas sp. SM9913. We found that casein, but not casamino acids, can induce the gene expression and synthesis of MCP-01, suggesting that peptides rather than amino acids derived from casein induce the gene expression and synthesis of MCP-01 in SM9913. Then, casein was hydrolyzed by SM9913 extracellular proteases, and the peptides with inducing effect were isolated and characterized. Finally, four tripeptides, SPP, RYP, RQF and FRQ, were shown to have significant inducing effect on the expression of MCP-01 gene, indicating that they are likely the inducing signal molecules for the expression of protease MCP-01 gene in SM9913. This study sheds light on the induction mechanism for the gene expression and biosynthesis of marine microbial extracellular proteases, which is helpful in better understanding the adaptation of bacteria to deep-sea sedimental environment.
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Affiliation(s)
- Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jin-Yu Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Xiao-Yu Zheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi Sheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Lei Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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14
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Schultz-Johansen M, Cueff M, Hardouin K, Jam M, Larocque R, Glaring MA, Hervé C, Czjzek M, Stougaard P. Discovery and screening of novel metagenome-derived GH107 enzymes targeting sulfated fucans from brown algae. FEBS J 2018; 285:4281-4295. [PMID: 30230202 DOI: 10.1111/febs.14662] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/16/2018] [Accepted: 09/17/2018] [Indexed: 12/17/2023]
Abstract
Sulfated fucans, often denoted as fucoidans, are highly variable cell wall polysaccharides of brown algae, which possess a wide range of bioactive properties with potential pharmaceutical applications. Due to their complex architecture, the structures of algal fucans have until now only been partly determined. Enzymes capable of hydrolyzing sulfated fucans may allow specific release of defined bioactive oligosaccharides and may serve as a tool for structural elucidation of algal walls. Currently, such enzymes include only a few hydrolases belonging to the glycoside hydrolase family 107 (GH107), and little is known about their mechanistics and the substrates they degrade. In this study, we report the identification and recombinant production of three novel GH107 family proteins derived from a marine metagenome. Activity screening against a large substrate collection showed that all three enzymes degraded sulfated fucans from brown algae in the order Fucales. This is in accordance with a hydrolytic activity against α-1,4-fucosidic linkages in sulfated fucans as reported for previous GH107 members. Also, the activity screening gave new indications about the structural differences in brown algal cell walls. Finally, sequence analyses allowed identification of the proposed catalytic residues of the GH107 family. The findings presented here form a new basis for understanding the GH107 family of enzymes and investigating the complex sulfated fucans from brown algae. DATABASE: The assembled metagenome and raw sequence data is available at EMBL-EBI (Study number: PRJEB28480). Sequences of the GH107 fucanases (Fp273, Fp277, and Fp279) have been deposited in GenBank under accessions MH755451-MH755453.
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Affiliation(s)
| | - Marie Cueff
- UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universités, Roscoff, Bretagne, France
| | - Kévin Hardouin
- UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universités, Roscoff, Bretagne, France
| | - Murielle Jam
- UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universités, Roscoff, Bretagne, France
| | - Robert Larocque
- UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universités, Roscoff, Bretagne, France
| | - Mikkel A Glaring
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Cécile Hervé
- UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universités, Roscoff, Bretagne, France
| | - Mirjam Czjzek
- UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universités, Roscoff, Bretagne, France
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
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15
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Huang J, Xu Y, Zhang Y, Sun A, Hu Y. Utilization of one novel deep-sea microbial protease sin3406-1 in the preparation of ethyl (S)-3-hydroxybutyrate through kinetic resolution. World J Microbiol Biotechnol 2018; 34:124. [PMID: 30083971 DOI: 10.1007/s11274-018-2513-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/01/2018] [Indexed: 10/28/2022]
Abstract
One novel protease sin3406-1 was identified from Streptomyces niveus SCSIO 3406, which was isolated from the deep sea of the South China Sea, and heterologously expressed in E. coli BL21(DE3). Protease sin3406-1 was further used as a green biocatalyst in the kinetic resolution of racemic ethyl-3-hydroxybutyrate. After careful process optimization, chiral product ethyl (S)-3-hydroxybutyrate was generated with an enantiomeric excess of over 99% and a conversion rate of up to 50% through direct hydrolysis of inexpensive racemic ethyl-3-hydroxybutyrate catalyzed by sin3406-1. Interestingly, protease sin3406-1 exhibited the same enantio-preference as that of esterase PHE21 during the asymmetric hydrolysis of the ester bonds of racemic ethyl-3-hydroxybutyrate. Through mutation studies and molecular docking, we also demonstrated that the four residues close to the catalytic center, S85, A86, Q87 and Y254, played key roles in both the hydrolytic activity and the enantioselectivity of protease sin3406-1, possibly through forming hydrogen bonds between the enzyme and the substrates. Deep-sea microbial proteases represented by sin3406-1 are new contributions to the biocatalyst library for the preparation of valuable chiral drug intermediates and chemicals through enzymatic kinetic resolution.
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Affiliation(s)
- Jinlong Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,College of Life Science, Guangxi Normal University, Guilin, 541004, People's Republic of China
| | - Yongkai Xu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, People's Republic of China
| | - Yun Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Aijun Sun
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Yunfeng Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China. .,Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China. .,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, People's Republic of China.
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16
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Crystal structure of a cold-active protease (Pro21717) from the psychrophilic bacterium, Pseudoalteromonas arctica PAMC 21717, at 1.4 Å resolution: Structural adaptations to cold and functional analysis of a laundry detergent enzyme. PLoS One 2018; 13:e0191740. [PMID: 29466378 PMCID: PMC5821440 DOI: 10.1371/journal.pone.0191740] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 01/10/2018] [Indexed: 02/04/2023] Open
Abstract
Enzymes isolated from organisms found in cold habitats generally exhibit higher catalytic activity at low temperatures than their mesophilic homologs and are therefore known as cold-active enzymes. Cold-active proteases are very useful in a variety of biotechnological applications, particularly as active ingredients in laundry and dishwashing detergents, where they provide strong protein-degrading activity in cold water. We identified a cold-active protease (Pro21717) from a psychrophilic bacterium, Pseudoalteromonas arctica PAMC 21717, and determined the crystal structure of its catalytic domain (CD) at a resolution of 1.4 Å. The Pro21717-CD structure shows a conserved subtilisin-like fold with a typical catalytic triad (Asp185, His244, and Ser425) and contains four calcium ions and three disulfide bonds. Interestingly, we observed an unexpected electron density at the substrate-binding site from a co-purified peptide. Although the sequence of this peptide is unknown, analysis of the peptide-complexed structure nonetheless provides some indication of the substrate recognition and binding mode of Pro21717. Moreover, various parameters, including a wide substrate pocket size, an abundant active-site loop content, and a flexible structure provide potential explanations for the cold-adapted properties of Pro21717. In conclusion, this is first structural characterization of a cold-adapted subtilisin-like protease, and these findings provide a structural and functional basis for industrial applications of Pro21717 as a cold-active laundry or dishwashing detergent enzyme.
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17
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Guo Y, Hu D, Guo J, Wang T, Xiao Y, Wang X, Li S, Liu M, Li Z, Bi D, Zhou Z. Riemerella anatipestifer Type IX Secretion System Is Required for Virulence and Gelatinase Secretion. Front Microbiol 2017; 8:2553. [PMID: 29312236 PMCID: PMC5742166 DOI: 10.3389/fmicb.2017.02553] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 12/08/2017] [Indexed: 11/16/2022] Open
Abstract
Riemerella anatipestifer (RA), a major causative agent of septicemia anserum exsudativa in domesticated ducklings, has a protein secretion system known as the type IX secretion system (T9SS). It is unknown whether the T9SS contributes to the virulence of RA through secretion of factors associated with pathogenesis. To answer this question, we constructed an RA mutant deficient in sprT, which encodes a core protein of the T9SS. Deletion of sprT yielded cells that failed to digest gelatin, an effect that was rescued via complementation by a plasmid encoding wild-type sprT. Complement-mediated killing was significantly increased in the deletion mutant, suggesting that proteins secreted by the T9SS are necessary for complement evasion in RA. Liquid chromatography-tandem mass spectrometry analysis revealed that RAYM_01812 and RAYM_04099 proteins containing a subtilisin-like serine protease domain and exhibiting extracellular gelatinase activity were secreted by the T9SS. Animal experiments demonstrated that the virulence of mutant strain ΔsprT strain was attenuated by 42,000-fold relative to wild-type RA-YM. Immunization with the ΔsprT protected ducks from challenge with RA-YM, suggesting that the former can be used as a live attenuated vaccine. These results indicate that the T9SS is functional in RA and contributes to its virulence by exporting key proteins. In addition, subtilisin-like serine proteases which are important virulence factors that interact with complement proteins may enable RA to evade immune surveillance in the avian innate immune system.
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Affiliation(s)
- Yunqing Guo
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Di Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jie Guo
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Tao Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yuncai Xiao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Xiliang Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Shaowen Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Mei Liu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zili Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Dingren Bi
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zutao Zhou
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
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18
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Dynamics of the Bacterial Community Associated with Phaeodactylum tricornutum Cultures. Processes (Basel) 2017. [DOI: 10.3390/pr5040077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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19
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Salwan R, Sharma V, Pal M, Kasana RC, Yadav SK, Gulati A. Heterologous expression and structure-function relationship of low-temperature and alkaline active protease from Acinetobacter sp. IHB B 5011(MN12). Int J Biol Macromol 2017; 107:567-574. [PMID: 28916383 DOI: 10.1016/j.ijbiomac.2017.09.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 09/11/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022]
Abstract
The gene encoding protease from Acinetobacter sp. IHB B 5011(MN12) was cloned and expressed in Escherichia coli BL21(DE3). The nucleotide sequence revealed 1323bp ORF encoding 441 amino acids protein with molecular weight 47.2kDa. The phylogenetic analysis showed clustering of Alp protease with subtilisin-like serine proteases of S8 family. The amino acid sequence was comprised of N-terminal signal peptide 1-21 amino acids, pre-peptide 22-143 amino acids, peptidase S8 domain 144-434 amino acids, and pro-peptide 435-441 amino acids at C-terminus. Three constructs with signal peptide pET-Alp, without signal peptide pET-Alp1 and peptidase S8 domain pET-Alp2 were prepared for expression in E. coli BL21(DE3). The recombinant proteins Alp1 and Alp2 expressed as inclusion bodies showed ∼50kDa and ∼40kDa bands, respectively. The pre-propeptide ∼11kDa removed from Alp1 resulted in mature protein of ∼35kDa with 1738Umg-1 specific activity. The recombinant protease was optimally active at 40°C and pH 9, and stable over 10-70°C and 6-12pH. The activity at low-temperature and alkaline pH was supported by high R/(R+K) ratio, more glycine, less proline, negatively charged amino acids, less salt bridges and longer loops. These properties suggested the suitability of Alp as additive in the laundry.
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Affiliation(s)
- Richa Salwan
- Academy of Scientific and Innovative Research, New Delhi, India; CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
| | - Vivek Sharma
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
| | - Mohinder Pal
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
| | | | - Sudesh Kumar Yadav
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
| | - Arvind Gulati
- Academy of Scientific and Innovative Research, New Delhi, India; CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India.
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20
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Li HJ, Tang BL, Shao X, Liu BX, Zheng XY, Han XX, Li PY, Zhang XY, Song XY, Chen XL. Characterization of a New S8 serine Protease from Marine Sedimentary Photobacterium sp. A5-7 and the Function of Its Protease-Associated Domain. Front Microbiol 2016; 7:2016. [PMID: 28066343 PMCID: PMC5177683 DOI: 10.3389/fmicb.2016.02016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/01/2016] [Indexed: 11/13/2022] Open
Abstract
Bacterial extracellular proteases are important for bacterial nutrition and marine sedimentary organic nitrogen degradation. However, only a few proteases from marine sedimentary bacteria have been characterized. Some subtilases have a protease-associated (PA) domain inserted in the catalytic domain. Although structural analysis and deletion mutation suggests that the PA domain in subtilases is involved in substrate binding, direct evidence to support this function is still absent. Here, a protease, P57, secreted by Photobacterium sp. A5-7 isolated from marine sediment was characterized. P57 could hydrolyze casein, gelatin and collagen. It showed the highest activity at 40°C and pH 8.0. P57 is a new subtilase, with 63% sequence identity to the closest characterized protease. Mature P57 contains a catalytic domain and an inserted PA domain. The recombinant PA domain from P57 was shown to have collagen-binding ability, and Phe349 and Tyr432 were revealed to be key residues for collagen binding in the PA domain. This study first shows direct evidence that the PA domain of a subtilase can bind substrate, which provides a better understanding of the function of the PA domain of subtilases and bacterial extracellular proteases from marine sediment.
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Affiliation(s)
- Hui-Juan Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
- College of Chemical and Environmental Engineering, Shandong University of Science and TechnologyQingdao, China
| | - Bai-Lu Tang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xuan Shao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Bai-Xue Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiao-Yu Zheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiao-Xu Han
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
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21
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Yang J, Yu Y, Tang BL, Zhong S, Shi M, Xie BB, Zhang XY, Zhou BC, Zhang YZ, Chen XL. Pilot-Scale Production and Thermostability Improvement of the M23 Protease Pseudoalterin from the Deep Sea Bacterium Pseudoalteromonas sp. CF6-2. Molecules 2016; 21:molecules21111567. [PMID: 27869696 PMCID: PMC6273387 DOI: 10.3390/molecules21111567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/09/2016] [Accepted: 11/14/2016] [Indexed: 01/05/2023] Open
Abstract
Pseudoalterin is the most abundant protease secreted by the marine sedimental bacterium Pseudoalteromonas sp. CF6-2 and is a novel cold-adapted metalloprotease of the M23 family. Proteases of the M23 family have high activity towards peptidoglycan and elastin, suggesting their promising biomedical and biotechnological potentials. To lower the fermentive cost and improve the pseudoalterin production of CF6-2, we optimized the fermentation medium by using single factor experiments, added 0.5% sucrose as a carbon source, and lowered the usage of artery powder from 1.2% to 0.6%. In the optimized medium, pseudoalterin production reached 161.15 ± 3.08 U/mL, 61% greater than that before optimization. We further conducted a small-scale fermentation experiment in a 5-L fermenter and a pilot-scale fermentation experiment in a 50-L fermenter. Pseudoalterin production during pilot-scale fermentation reached 103.48 ± 8.64 U/mL, 77% greater than that before the medium was optimized. In addition, through single factor experiments and orthogonal tests, we developed a compound stabilizer for pseudoalterin, using medically safe sugars and polyols. This stabilizer showed a significant protective effect for pseudoalterin against enzymatic thermal denaturation. These results lay a solid foundation for the industrial production of pseudoalterin and the development of its biomedical and biotechnological potentials.
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Affiliation(s)
- Jie Yang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Yang Yu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Bai-Lu Tang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Shuai Zhong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China.
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
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22
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Huang J, Wu C, Liu D, Yang X, Wu R, Zhang J, Ma C, He H. C-terminal domains of bacterial proteases: structure, function and the biotechnological applications. J Appl Microbiol 2016; 122:12-22. [DOI: 10.1111/jam.13317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/21/2016] [Accepted: 10/03/2016] [Indexed: 12/28/2022]
Affiliation(s)
- J. Huang
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - C. Wu
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - D. Liu
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - X. Yang
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - R. Wu
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - J. Zhang
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - C. Ma
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - H. He
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
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23
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Varshney D, Jaiswar A, Adholeya A, Prasad P. Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales. BMC Evol Biol 2016; 16:220. [PMID: 27756202 PMCID: PMC5069783 DOI: 10.1186/s12862-016-0793-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 10/07/2016] [Indexed: 11/15/2022] Open
Abstract
Background Subtilisin-like serine proteases or Subtilases in fungi are important for penetration and colonization of host. In Hypocreales, these proteins share several properties with other fungal, bacterial, plant and mammalian homologs. However, adoption of specific roles in entomopathogenesis may be governed by attainment of unique biochemical and structural features during the evolutionary course. Due to such functional shifts Subtilases coded by different family members of Hypocreales acquire distinct features according to respective hosts and lifestyle. We conducted phylogenetic and DIVERGE analyses and identified important protein residues that putatively assign functional specificity to Subtilases in fungal families/species under the order Hypocreales. Results A total of 161 Subtilases coded by 10 species from five different families under the fungal order Hypocreales was included in the analysis. Based on the presence of conserved domains, the Subtilase genes were divided into three subfamilies, Subtilisin (S08.005), Proteinase K (S08.054) and Serine-carboxyl peptidases (S53.001). These subfamilies were investigated for phylogenetic associations, protein residues under positive selection and functional divergence among paralogous clades. The observations were co-related with the life-styles of the fungal families/species. Phylogenetic and Divergence analyses of Subtilisin (S08.005) and Proteinase K (S08.054) families of proteins revealed that the paralogous clades were clear-cut representation of familial origin of the protein sequences. We observed divergence between the paralogous clades of plant-pathogenic fungi (Nectriaceae), insect-pathogenic fungi (Cordycipitaceae/Clavicipitaceae) and nematophagous fungi (Ophiocordycipitaceae). In addition, Subtilase genes from the nematode-parasitic fungus Purpureocillium lilacinum made a unique cluster which putatively indicated that the fungus might have developed distinctive mechanisms for nematode-pathogenesis. Our evolutionary genetics analysis revealed evidence of positive selection on the Subtilisin (S08.005) and Proteinase K (S08.054) protein sequences of the entomopathogenic and nematophagous species belonging to Cordycipitaceae, Clavicipitaceae and Ophiocordycipitaceae families of Hypocreales. Conclusions Our study provided new insights into the evolution of Subtilisin like serine proteases in Hypocreales, a fungal order largely consisting of biological control species. Subtilisin (S08.005) and Proteinase K (S08.054) proteins seemed to play important roles during life style modifications among different families and species of Hypocreales. Protein residues found significant in functional divergence analysis in the present study may provide support for protein engineering in future. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0793-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deepti Varshney
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari, Faridabad Road, Gurgaon, Haryana, 122001, India
| | - Akanksha Jaiswar
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari, Faridabad Road, Gurgaon, Haryana, 122001, India
| | - Alok Adholeya
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari, Faridabad Road, Gurgaon, Haryana, 122001, India
| | - Pushplata Prasad
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari, Faridabad Road, Gurgaon, Haryana, 122001, India.
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Characterization of a salt-activated protease with temperature-dependent secretion in Stenotrophomonas maltophilia FF11 isolated from frozen Antarctic krill. ACTA ACUST UNITED AC 2016; 43:829-40. [DOI: 10.1007/s10295-016-1749-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/15/2016] [Indexed: 11/26/2022]
Abstract
Abstract
Seafood is sometimes wasted due to the growth of psychrotolerant microbes which secrete proteases and break down proteins. Stenotrophomonas maltophilia FF11, isolated from frozen Antarctic krill, grows at a wide range of temperatures and secretes more proteases at low temperatures. According to zymogram analysis, two kinds of proteases were produced from this strain. A major protease was produced largely at 15 °C, but not at 37 °C. The temperature-dependent secreted protease was purified to homogeneity. Its molecular mass was determined at 37.4 kDa and its amino acid sequence was also obtained. This protease is a member of the subtilase group according to the NCBI blast analysis. The enzyme was highly stable at high salt concentration (4 M). Interestingly, its activity increased about 1.6-fold under high salt condition. The enzyme remains active and stable in different organic solvents (50 %, v/v) such as dimethylsulfoxide, dimethyl formamide, dioxane and acetone. These properties may provide potential applications in quality control for sea foods, in protein degradation at high salt concentration, in biocatalysis and biotransformation within non-aqueous media, such as detergent and transesterification.
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25
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Wani AH, Sharma M, Salwan R, Singh G, Chahota R, Verma S. Cloning, Expression, and Functional Characterization of Serine Protease Aprv2 from Virulent Isolate Dichelobacter nodosus of Indian Origin. Appl Biochem Biotechnol 2016; 180:576-587. [PMID: 27168406 DOI: 10.1007/s12010-016-2117-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 05/05/2016] [Indexed: 10/21/2022]
Abstract
A gene encoding an extracellular protease from Dichelobacter nodosus was characterized and expressed in E. coli rosetta-gami (DE3). The nucleotide sequence analysis revealed an ORF of 1427 bp ecoding 475 amino acids long protein of calculated molecular weight 50.6 kDa and pI value 6.09. The phylogenetic analysis showed relatedness to subtilisin-like serine proteases of peptidase S8 family. The amino acid sequence analysis showed presence of N-terminal pre-peptide (1-23 aa), pro-peptide (24-160 aa), peptidase S8 domain (161-457 aa), and a C-terminal extension (458-475 aa). The gene harboring native signal peptide was expressed in pET-22b(+) for production of AprV2 recombinant protein. SDS-PAGE revealed the highest production of IPTG induced recombinant protein ∼37 kDa at 16 °C after 16 h. The purified protein after Ni-NTA affinity chromatography showed single protein band of ∼37 kDa which was also confirmed by the detection of blue coloured band of same size in Western blotting. The recombinant protein showed activity over broad temperature and pH range with optimum at 35 °C and pH 7.0. Similarly, the enzyme was stable over broad range 15-65 °C and 4-10 pH with maximum stability at 25 °C and pH 6. The activity of purified enzyme was also stimulated in the presence of Ca2+. The purified enzyme showed highest activity towards casein as compared to gelatin and BSA. These findings suggest AprV2 as an important candidate for industrial applications such as pharmaceuticals.
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Affiliation(s)
- Aasim Habib Wani
- Department of Veterinary Microbiology, Dr. G.C. Negi-College of Veterinary and Animal Sciences, CSK-Himachal Pradesh Agricultural University, Palampur, 176062, India
| | - Mandeep Sharma
- Department of Veterinary Microbiology, Dr. G.C. Negi-College of Veterinary and Animal Sciences, CSK-Himachal Pradesh Agricultural University, Palampur, 176062, India
| | - Richa Salwan
- Department of Veterinary Microbiology, Dr. G.C. Negi-College of Veterinary and Animal Sciences, CSK-Himachal Pradesh Agricultural University, Palampur, 176062, India
| | - Geetanjali Singh
- Department of Veterinary Physiology and Biochemistry, Dr. G.C. Negi-College of Veterinary and Animal Sciences, CSK-Himachal Pradesh Agricultural University, Palampur, 176062, India
| | - Rajesh Chahota
- Department of Veterinary Microbiology, Dr. G.C. Negi-College of Veterinary and Animal Sciences, CSK-Himachal Pradesh Agricultural University, Palampur, 176062, India
| | - Subhash Verma
- Department of Veterinary Microbiology, Dr. G.C. Negi-College of Veterinary and Animal Sciences, CSK-Himachal Pradesh Agricultural University, Palampur, 176062, India.
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26
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Pal GK, PV S. Microbial collagenases: challenges and prospects in production and potential applications in food and nutrition. RSC Adv 2016. [DOI: 10.1039/c5ra23316j] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Microbial collagenases are promising enzymes in view of their extensive industrial and biological applications.
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Affiliation(s)
- Gaurav Kumar Pal
- Academy of Scientific and Innovative Research
- Meat and Marine Sciences Department
- CSIR-Central Food Technological Research Institute
- Mysuru-570020
- India
| | - Suresh PV
- Academy of Scientific and Innovative Research
- Meat and Marine Sciences Department
- CSIR-Central Food Technological Research Institute
- Mysuru-570020
- India
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27
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Diversity, Structures, and Collagen-Degrading Mechanisms of Bacterial Collagenolytic Proteases. Appl Environ Microbiol 2015; 81:6098-107. [PMID: 26150451 DOI: 10.1128/aem.00883-15] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bacterial collagenolytic proteases are important because of their essential role in global collagen degradation and because of their virulence in some human bacterial infections. Bacterial collagenolytic proteases include some metalloproteases of the M9 family from Clostridium or Vibrio strains, some serine proteases distributed in the S1, S8, and S53 families, and members of the U32 family. In recent years, there has been remarkable progress in discovering new bacterial collagenolytic proteases and in investigating the collagen-degrading mechanisms of bacterial collagenolytic proteases. This review provides comprehensive insight into bacterial collagenolytic proteases, especially focusing on the structures and collagen-degrading mechanisms of representative bacterial collagenolytic proteases in each family. The roles of bacterial collagenolytic proteases in human diseases and global nitrogen cycling, together with the biotechnological and medical applications for these proteases, are also briefly discussed.
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Shao X, Ran LY, Liu C, Chen XL, Zhang XY, Qin QL, Zhou BC, Zhang YZ. Culture Condition Optimization and Pilot Scale Production of the M12 Metalloprotease Myroilysin Produced by the Deep-Sea Bacterium Myroides profundi D25. Molecules 2015; 20:11891-901. [PMID: 26132910 PMCID: PMC6331793 DOI: 10.3390/molecules200711891] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/19/2015] [Accepted: 06/23/2015] [Indexed: 11/16/2022] Open
Abstract
The protease myroilysin is the most abundant protease secreted by marine sedimental bacterium Myroides profundi D25. As a novel elastase of the M12 family, myroilysin has high elastin-degrading activity and strong collagen-swelling ability, suggesting its promising biotechnological potential. Because myroilysin cannot be maturely expressed in Escherichia coli, it is important to be able to improve the production of myroilysin in the wild strain D25. We optimized the culture conditions of strain D25 for protease production by using single factor experiments. Under the optimized conditions, the protease activity of strain D25 reached 1137 ± 53.29 U/mL, i.e., 174% of that before optimization (652 ± 23.78 U/mL). We then conducted small scale fermentations of D25 in a 7.5 L fermentor. The protease activity of strain D25 in small scale fermentations reached 1546.4 ± 82.65 U/mL after parameter optimization. Based on the small scale fermentation results, we further conducted pilot scale fermentations of D25 in a 200 L fermentor, in which the protease production of D25 reached approximately 1100 U/mL. These results indicate that we successfully set up the small and pilot scale fermentation processes of strain D25 for myroilysin production, which should be helpful for the industrial production of myroilysin and the development of its biotechnological potential.
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Affiliation(s)
- Xuan Shao
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
| | - Li-Yuan Ran
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
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29
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Cloning, heterologous expression and characterization of two keratinases from Stenotrophomonas maltophilia BBE11-1. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.01.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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Ran LY, Su HN, Zhou MY, Wang L, Chen XL, Xie BB, Song XY, Shi M, Qin QL, Pang X, Zhou BC, Zhang YZ, Zhang XY. Characterization of a novel subtilisin-like protease myroicolsin from deep sea bacterium Myroides profundi D25 and molecular insight into its collagenolytic mechanism. J Biol Chem 2014; 289:6041-53. [PMID: 24429289 DOI: 10.1074/jbc.m113.513861] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Collagen is an insoluble protein that widely distributes in the extracellular matrix of marine animals. Collagen degradation is an important step in the marine nitrogen cycle. However, the mechanism of marine collagen degradation is still largely unknown. Here, a novel subtilisin-like collagenolytic protease, myroicolsin, which is secreted by the deep sea bacterium Myroides profundi D25, was purified and characterized, and its collagenolytic mechanism was studied. Myroicolsin displays low identity (<30%) to previously characterized subtilisin-like proteases, and it contains a novel domain structure. Protein truncation indicated that the Pro secretion system C-terminal sorting domain in the precursor protein is involved in the cleavage of the N-propeptide, and the linker is required for protein folding during myroicolsin maturation. The C-terminal β-jelly roll domain did not bind insoluble collagen fiber, suggesting that myroicolsin may degrade collagen without the assistance of a collagen-binding domain. Myroicolsin had broad specificity for various collagens, especially fish-insoluble collagen. The favored residue at the P1 site was basic arginine. Scanning electron microscopy and atomic force microscopy, together with biochemical analyses, confirmed that collagen fiber degradation by myroicolsin begins with the hydrolysis of proteoglycans and telopeptides in collagen fibers and fibrils. Myroicolsin showed strikingly different cleavage patterns between native and denatured collagens. A collagen degradation model of myroicolsin was proposed based on our results. Our study provides molecular insight into the collagen degradation mechanism and structural characterization of a subtilisin-like collagenolytic protease secreted by a deep sea bacterium, shedding light on the degradation mechanism of deep sea sedimentary organic nitrogen.
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Affiliation(s)
- Li-Yuan Ran
- From the State Key Laboratory of Microbial Technology
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31
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Ran LY, Su HN, Zhao GY, Gao X, Zhou MY, Wang P, Zhao HL, Xie BB, Zhang XY, Chen XL, Zhou BC, Zhang YZ. Structural and mechanistic insights into collagen degradation by a bacterial collagenolytic serine protease in the subtilisin family. Mol Microbiol 2013; 90:997-1010. [DOI: 10.1111/mmi.12412] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2013] [Indexed: 01/22/2023]
Affiliation(s)
- Li-Yuan Ran
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Guo-Yan Zhao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Ming-Yang Zhou
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Peng Wang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Hui-Lin Zhao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
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32
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Joshi S, Satyanarayana T. Biotechnology of cold-active proteases. BIOLOGY 2013; 2:755-83. [PMID: 24832807 PMCID: PMC3960895 DOI: 10.3390/biology2020755] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/17/2013] [Accepted: 04/24/2013] [Indexed: 11/17/2022]
Abstract
The bulk of Earth's biosphere is cold (<5 °C) and inhabited by psychrophiles. Biocatalysts from psychrophilic organisms (psychrozymes) have attracted attention because of their application in the ongoing efforts to decrease energy consumption. Proteinases as a class represent the largest category of industrial enzymes. There has been an emphasis on employing cold-active proteases in detergents because this allows laundry operations at ambient temperatures. Proteases have been used in environmental bioremediation, food industry and molecular biology. In view of the present limited understanding and availability of cold-active proteases with diverse characteristics, it is essential to explore Earth's surface more in search of an ideal cold-active protease. The understanding of molecular and mechanistic details of these proteases will open up new avenues to tailor proteases with the desired properties. A detailed account of the developments in the production and applications of cold-active proteases is presented in this review.
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Affiliation(s)
- Swati Joshi
- Department of Microbiology, University of Delhi South Campus, New Delhi 110021, India.
| | - Tulasi Satyanarayana
- Department of Microbiology, University of Delhi South Campus, New Delhi 110021, India.
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33
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Draft genome sequence of Arctic marine Bacterium Pseudoalteromonas issachenkonii PAMC 22718. J Bacteriol 2012; 194:4140. [PMID: 22815453 DOI: 10.1128/jb.00744-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The psychrotolerant Pseudoalteromonas issachenkonii PAMC 22718 was isolated for its higher chitinase and protease activities from cold seawater in the Kara Sea, Arctic. Here, we present the draft genome sequence of PAMC 22718 to provide further information for the ecological function of the genus Pseudoalteromonas in a cold marine environment.
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34
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Tenderization effect of cold-adapted collagenolytic protease MCP-01 on beef meat at low temperature and its mechanism. Food Chem 2012; 134:1738-44. [DOI: 10.1016/j.foodchem.2012.03.118] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 01/17/2012] [Accepted: 03/14/2012] [Indexed: 11/19/2022]
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35
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Zhao HL, Chen XL, Xie BB, Zhou MY, Gao X, Zhang XY, Zhou BC, Weiss AS, Zhang YZ. Elastolytic mechanism of a novel M23 metalloprotease pseudoalterin from deep-sea Pseudoalteromonas sp. CF6-2: cleaving not only glycyl bonds in the hydrophobic regions but also peptide bonds in the hydrophilic regions involved in cross-linking. J Biol Chem 2012; 287:39710-20. [PMID: 23012370 DOI: 10.1074/jbc.m112.405076] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Elastin is a common insoluble protein that is abundant in marine vertebrates, and for this reason its degradation is important for the recycling of marine nitrogen. It is still unclear how marine elastin is degraded because of the limited study of marine elastases. Here, a novel protease belonging to the M23A subfamily, secreted by Pseudoalteromonas sp. CF6-2 from deep-sea sediment, was purified and characterized, and its elastolytic mechanism was studied. This protease, named pseudoalterin, has low identities (<40%) to the known M23 proteases. Pseudoalterin has a narrow specificity but high activity toward elastin. Analysis of the cleavage sites of pseudoalterin on elastin showed that pseudoalterin cleaves the glycyl bonds in hydrophobic regions and the peptide bonds Ala-Ala, Ala-Lys, and Lys-Ala involved in cross-linking. Two peptic derivatives of desmosine, desmosine-Ala-Ala and desmosine-Ala-Ala-Ala, were detected in the elastin hydrolysate, indicating that pseudoalterin can dissociate cross-linked elastin. These results reveal a new elastolytic mechanism of the M23 protease pseudoalterin, which is different from the reported mechanism where the M23 proteases only cleave glycyl bonds in elastin. Genome analysis suggests that M23 proteases may be popular in deep-sea sediments, implying their important role in elastin degradation. An elastin degradation model of pseudoalterin was proposed, based on these results and scanning electron microscopic analysis of the degradation by pseudoalterin of bovine elastin and cross-linked recombinant tropoelastin. Our results shed light on the mechanism of elastin degradation in deep-sea sediment.
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Affiliation(s)
- Hui-Lin Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
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Ramli ANM, Mahadi NM, Shamsir MS, Rabu A, Joyce-Tan KH, Murad AMA, Illias RM. Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function. J Comput Aided Mol Des 2012; 26:947-61. [DOI: 10.1007/s10822-012-9585-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 06/04/2012] [Indexed: 12/29/2022]
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37
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He HL, Guo J, Chen XL, Xie BB, Zhang XY, Yu Y, Chen B, Zhou BC, Zhang YZ. Structural and functional characterization of mature forms of metalloprotease E495 from Arctic sea-ice bacterium Pseudoalteromonas sp. SM495. PLoS One 2012; 7:e35442. [PMID: 22523598 PMCID: PMC3327674 DOI: 10.1371/journal.pone.0035442] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 03/16/2012] [Indexed: 11/19/2022] Open
Abstract
E495 is the most abundant protease secreted by the Arctic sea-ice bacterium Pseudoalteromonas sp. SM495. As a thermolysin family metalloprotease, E495 was found to have multiple active forms in the culture of strain SM495. E495-M (containing only the catalytic domain) and E495-M-C1 (containing the catalytic domain and one PPC domain) were two stable mature forms, and E495-M-C1-C2 (containing the catalytic domain and two PPC domains) might be an intermediate. Compared to E495-M, E495-M-C1 had similar affinity and catalytic efficiency to oligopeptides, but higher affinity and catalytic efficiency to proteins. The PPC domains from E495 were expressed as GST-fused proteins. Both of the recombinant PPC domains were shown to have binding ability to proteins C-phycocyanin and casein, and domain PPC1 had higher affinity to C-phycocyanin than domain PPC2. These results indicated that the domain PPC1 in E495-M-C1 could be helpful in binding protein substrate, and therefore, improving the catalytic efficiency. Site-directed mutagenesis on the PPC domains showed that the conserved polar and aromatic residues, D26, D28, Y30, Y/W65, in the PPC domains played key roles in protein binding. Our study may shed light on the mechanism of organic nitrogen degradation in the Arctic sea ice.
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Affiliation(s)
- Hai-Lun He
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Jun Guo
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Bai-Cheng Zhou
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
- * E-mail:
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Zhao DL, Yu ZC, Li PY, Wu ZY, Chen XL, Shi M, Yu Y, Chen B, Zhou BC, Zhang YZ. Characterization of a cryptic plasmid pSM429 and its application for heterologous expression in psychrophilic Pseudoalteromonas. Microb Cell Fact 2011; 10:30. [PMID: 21542941 PMCID: PMC3112385 DOI: 10.1186/1475-2859-10-30] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/05/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pseudoalteromonas is an important genus widespread in marine environment, and a lot of psychrophilic Pseudoalteromonas strains thrive in deep sea and polar sea. By now, there are only a few genetic systems for Pseudoalteromonas reported and no commercial Pseudoalteromonas genetic system is available, which impedes the study of Pseudoalteromonas, especially for psychrophilic strains. The aim of this study is to develop a heterologous expression system for psychrophilic Pseudoalteromonas. RESULTS A cryptic plasmid pSM429 isolated from psychrophilic Pseudoalteromonas sp. BSi20429 from the Arctic sea ice, was sequenced and characterized. The plasmid pSM429 is 3874 bp in length, with a G+C content of 28%. Four putative open reading frames (ORFs) were identified on pSM429. Based on homology, the ORF4 was predicted to encode a replication initiation (Rep) protein. A shuttle vector (Escherichia coli, Pseudoalteromonas), pWD, was constructed by ligating pSM429 and pUC19 and inserting a chloramphenicol acetyl transferase (CAT) cassette conferring chloramphenicol resistance. To determine the minimal replicon of pSM429 and to check the functionality of identified ORFs, various pWD derivatives were constructed. All derivatives except the two smallest ones were shown to allow replication in Pseudoalteromonas sp. SM20429, a plasmid-cured strain of Pseudoalteromonas sp. BSi20429, suggesting that the orf4 and its flanking intergenic regions are essential for plasmid replication. Although not essential, the sequence including some repeats between orf1 and orf2 plays important roles in segregational stability of the plasmid. With the aid of pWD-derived plasmid pWD2, the erythromycin resistance gene and the cd gene encoding the catalytic domain of a cold-adapted cellulase were successfully expressed in Pseudoalteromonas sp. SM20429. CONCLUSIONS Plasmid pSM429 was isolated and characterized, and the regions essential for plasmid replication and stability were determined, helping the development of pSM429-based shuttle vectors. The shuttle vectors pWD and its derivatives could be used as cloning vectors for Pseudoalteromonas, offering new perspectives in the genetic manipulation of Pseudoalteromonas strains. With the aid of pWD-derived vector and its host, the erythromycin resistance gene and the cd gene of a cold-adapted protein were successfully expressed, indicating that the potential use of this system for recombinant protein production, especially for cold-adapted proteins.
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Affiliation(s)
- Dian-Li Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
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Affiliation(s)
- Roland J Siezen
- Kluyver Centre for Genomics of Industrial Fermentation; TI Food and Nutrition, 6700AN Wageningen, the Netherlands.
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Subtilase genes diversity in the biogas digester microbiota. Curr Microbiol 2011; 62:1542-7. [PMID: 21327889 DOI: 10.1007/s00284-011-9876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 01/08/2011] [Indexed: 10/18/2022]
Abstract
Biogas digesters contain microbial assemblages that process a mass of extracellular polymeric substances from animal manure and domestic wastewater; however, due to the limitation of available technology in cultivation of majority of the micro-organisms in biogas digesters, the enzymatic potential of these microbial communities remains largely unexplored. In this study, to evaluate subtilase gene diversity in a biogas digester, the partial sequences of the gene were directly amplified from the metagenomic DNA by using consensus-degenerate primers. The desired PCR products were cloned into pGEM-T Easy vector, and thirty positive clones were chose for Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, from which thirteen distinguished patterns were obtained and then sequenced. Phylogenetic analysis showed that ten out of the thirteen sequences were related to the subtilase genes in GenBank and were grouped into three families of the subtilases superfamily. The nucleotide sequences analysis through BLAST search revealed that none of the partial genes the authors isolated showed significant similarity against the non-redundant Nucleotide database of NCBI. Meanwhile, the deduced amino acid sequences of ten partial subtilase genes showed moderate identities to the previously identified sequences in GenBank, with a range from 39 to 61%. Collectively, the data indicate that there is a great diversity of subtilase genes in the biogas digester; and may be a rich reservoir for novel subtilase genes.
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Domains III and I-2{alpha}, at the entrance of the binding cleft, play an important role in cold adaptation of the periplasmic dipeptide-binding protein (DppA) from the deep-sea psychrophilic bacterium Pseudoalteromonas sp. strain SM9913. Appl Environ Microbiol 2010; 76:4354-61. [PMID: 20453143 DOI: 10.1128/aem.02884-09] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The peptide transporter from a cold-adapted bacterium has never been reported. In the present study, the dpp operon from the psychrophilic bacterium Pseudoalteromonas sp. strain SM9913 was cloned and analyzed. The dipeptide binding protein DppA of SM9913 was overexpressed in Escherichia coli, and its cold adaptation characteristics were studied. The recombinant DppA of SM9913 (PsDppA) displayed the highest ligand-binding affinity at 15 degrees C, whereas the recombinant DppA of E. coli (EcDppA) displayed the highest ligand-binding affinity at 35 degrees C. Thermal and guanidium hydrochloride unfolding analyses indicated that PsDppA has more structural instability than EcDppA. Six domain-exchanged mutants of PsDppA were expressed and purified. Analyses of these mutants indicated that domains III, I-2, and I-3 of PsDppA were less stable than those from EcDppA and that domains III and I-2 made a significant contribution to the high binding affinity of PsDppA at low temperatures. Structural and sequence analyses suggested that the state transition-involved regions in domain III and the alpha part of domain I-2 are the hot spots of optimization during cold adaptation and that decreasing the side-chain size in these regions is an important strategy for the cold adaptation of PsDppA.
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Wang YK, Zhao GY, Li Y, Chen XL, Xie BB, Su HN, Lv YH, He HL, Liu H, Hu J, Zhou BC, Zhang YZ. Mechanistic insight into the function of the C-terminal PKD domain of the collagenolytic serine protease deseasin MCP-01 from deep sea Pseudoalteromonas sp. SM9913: binding of the PKD domain to collagen results in collagen swelling but does not unwind the collagen triple helix. J Biol Chem 2010; 285:14285-91. [PMID: 20207733 DOI: 10.1074/jbc.m109.087023] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deseasin MCP-01 is a bacterial collagenolytic serine protease. Its catalytic domain alone can degrade collagen, and its C-terminal PKD domain is a collagen-binding domain (CBD) that can improve the collagenolytic efficiency of the catalytic domain by an unknown mechanism. Here, scanning electron microscopy (SEM), atomic force microscopy (AFM), zeta potential, and circular dichroism spectroscopy were used to clarify the functional mechanism of the PKD domain in MCP-01 collagenolysis. The PKD domain observably swelled insoluble collagen. Its collagen-swelling ability and its improvement to the collagenolysis of the catalytic domain are both temperature-dependent. SEM observation showed the PKD domain swelled collagen fascicles with an increase of their diameter from 5.3 mum to 8.8 mum after 1 h of treatment, and the fibrils forming the fascicles were dispersed. AFM observation directly showed that the PKD domain bound collagen, swelled the microfibrils, and exposed the monomers. The PKD mutant W36A neither bound collagen nor disturbed its structure. Zeta potential results demonstrated that PKD treatment increased the net positive charges of the collagen surface. PKD treatment caused no change in the content or the thermostability of the collagen triple helix. Furthermore, the PKD-treated collagen could not be degraded by gelatinase. Therefore, though the triple helix monomers were exposed, the PKD domain could not unwind the collagen triple helix. Our study reveals the functional mechanism of the PKD domain of the collagenolytic serine protease MCP-01 in collagen degradation, which is distinct from that of the CBDs of mammalian matrix metalloproteases.
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Affiliation(s)
- Yu-Kai Wang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
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Zhou MY, Chen XL, Zhao HL, Dang HY, Luan XW, Zhang XY, He HL, Zhou BC, Zhang YZ. Diversity of both the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the South China sea. MICROBIAL ECOLOGY 2009; 58:582-590. [PMID: 19301066 DOI: 10.1007/s00248-009-9506-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 02/22/2009] [Indexed: 05/27/2023]
Abstract
Protease-producing bacteria are known to play an important role in degrading sedimentary particular organic nitrogen, and yet, their diversity and extracellular proteases remain largely unknown. In this paper, the diversity of the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the South China Sea was investigated. The richness of the cultivable protease-producing bacteria reached 10(6) cells/g in all sediment samples. Analysis of the 16S rRNA gene sequences revealed that the predominant cultivated protease-producing bacteria are Gammaproteobacteria affiliated with the genera Pseudoalteromonas, Alteromonas, Marinobacter, Idiomarina, Halomonas, Vibrio, Shewanella, Pseudomonas, and Rheinheimera, with Alteromonas (34.6%) and Pseudoalteromonas (28.2%) as the predominant groups. Inhibitor analysis showed that nearly all the extracellular proteases from the bacteria are serine proteases or metalloproteases. Moreover, these proteases have different hydrolytic ability to different proteins, reflecting they may belong to different kinds of serine proteases or metalloproteases. To our knowledge, this study represents the first report of the diversity of bacterial proteases in deep-sea sediments.
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Affiliation(s)
- Ming-Yang Zhou
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, People's Republic of China
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Yan BQ, Chen XL, Hou XY, He H, Zhou BC, Zhang YZ. Molecular analysis of the gene encoding a cold-adapted halophilic subtilase from deep-sea psychrotolerant bacterium Pseudoalteromonas sp. SM9913: cloning, expression, characterization and function analysis of the C-terminal PPC domains. Extremophiles 2009; 13:725-33. [PMID: 19544039 DOI: 10.1007/s00792-009-0263-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 06/04/2009] [Indexed: 10/20/2022]
Abstract
Only a few cold-adapted halophilic proteases have been reported. Here, the gene mcp03 encoding a cold-adapted halophilic protease MCP-03 was cloned from deep-sea psychrotolerant bacterium Pseudoalteromonas sp. SM9913, which contains a 2,130-bp ORF encoding a novel subtilase precursor. The recombinant MCP-03, expressed in Escherichia coli BL21 and purified from fermented broth, is a multi-domain protein with a catalytic domain and two PPC domains. Compared to mesophilic subtilisin Carlsberg, MCP-03 had characteristics of a typical cold-adapted enzyme (e.g., higher activity at low temperatures, lower optimum temperature and higher thermolability). MCP-03 also exhibited good halophilic ability with maximal activity at 3 M NaCl/KCl and good stability in 3 M NaCl. Deletion mutagenesis showed that the C-terminal PPC domains were unnecessary for enzyme secretion but had an inhibitory effect on MCP-03 catalytic efficiency and were essential for keeping MCP-03 thermostable.
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Affiliation(s)
- Bing-Qiang Yan
- Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
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Iijima S, Washio K, Okahara R, Morikawa M. Biofilm formation and proteolytic activities of Pseudoalteromonas bacteria that were isolated from fish farm sediments. Microb Biotechnol 2009; 2:361-9. [PMID: 21261930 PMCID: PMC3815756 DOI: 10.1111/j.1751-7915.2009.00097.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In order to save natural resources and supply good fishes, it is important to improve fish‐farming techniques. The survival rate of fish fry appears to become higher when powders of foraminifer limestone are submerged at the bottom of fish‐farming fields, where bacterial biofilms often grow. The observations suggest that forming biofilms can benefit to keep health status of breeding fishes. We employed culture‐based methods for the identification and characterization of biofilm‐forming bacteria and assessed the application of their properties for fish farming. Fifteen bacterial strains were isolated from the biofilm samples collected from fish farm sediments. The 16S rRNA gene sequences indicated that these bacteria belonged to the genera, Pseudoalteromonas (seven strains), Vibrio (seven strains) and Halomonas (one strain). It was found that Pseudoalteromonas strains generally formed robust biofilms in a laboratory condition and produced extracellular proteases in a biofilm‐dependent manner. The results suggest that Pseudoalteromonas bacteria, living in the biofilm community, contribute in part to remove excess proteineous matters from the sediment sludge of fish farms.
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Affiliation(s)
- Saori Iijima
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
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Zhao GY, Chen XL, Zhao HL, Xie BB, Zhou BC, Zhang YZ. Hydrolysis of insoluble collagen by deseasin MCP-01 from deep-sea Pseudoalteromonas sp. SM9913: collagenolytic characters, collagen-binding ability of C-terminal polycystic kidney disease domain, and implication for its novel role in deep-sea sedimentary particulate organic nitrogen degradation. J Biol Chem 2008; 283:36100-7. [PMID: 18977758 DOI: 10.1074/jbc.m804438200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Collagens are the most abundant proteins in marine animals and their degradation is important for the recycling of marine nitrogen. However, it is rather unclear how marine collagens are degraded because few marine collagenolytic proteases are studied in detail. Deseasins are a new type of multidomain subtilases. Here, the collagenolytic activity of deseasin MCP-01, the type example of deseasins, was studied. MCP-01 had broad substrate specificity to various type collagens from terrestrial and marine animals. It completely decomposed insoluble collagen into soluble peptides and amino acids, and was more prone to degrade marine collagen than terrestrial collagen. Thirty-seven cleavage sites of MCP-01 on bovine collagen chains were elucidated, showing the cleavage is various but specific. As the main extracellular cold-adapted protease from deep-sea bacterium Pseudoalteromonas sp. SM9913, MCP-01 displayed high activity at low temperature and alkaline range. Our data also showed that the C-terminal polycystic kidney disease (PKD) domain of MCP-01 was able to bind insoluble collagen and facilitate the insoluble collagen digestion by MCP-01. Site-directed mutagenesis demonstrated that Trp-36 of the PKD domain played a key role in its binding to insoluble collagen. It is the first time that the structure and function of a marine collagenolytic protease, deseasin MCP-01, has been studied in detail. Moreover, the PKD domain was experimentally proven to bind to insoluble protein for the first time. These results imply that MCP-01 would play an important role in the degradation of deep-sea sedimentary particulate organic nitrogen.
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Affiliation(s)
- Guo-Yan Zhao
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
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