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Zhang H, Wang Z, Yu X, Cao J, Bao T, Liu J, Sun C, Wang J, Fang J. The Phylogeny and Metabolic Potentials of a Lignocellulosic Material-Degrading Aliiglaciecola Bacterium Isolated from Intertidal Seawater in East China Sea. Microorganisms 2024; 12:144. [PMID: 38257972 PMCID: PMC10821302 DOI: 10.3390/microorganisms12010144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Lignocellulosic materials are composed of cellulose, hemicellulose and lignin and are one of the most abundant biopolymers in marine environments. The extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, a novel lignin-degrading bacterial strain, LCG003, was isolated from intertidal seawater in Lu Chao Harbor, East China Sea. Phylogenetically, strain LCG003 was affiliated with the genus Aliiglaciecola within the family Alteromonadaceae. Metabolically, strain LCG003 contains various extracellular (signal-fused) glycoside hydrolase genes and carbohydrate transporter genes and can grow with various carbohydrates as the sole carbon source, including glucose, fructose, sucrose, rhamnose, maltose, stachyose and cellulose. Moreover, strain LCG003 contains many genes of amino acid and oligopeptide transporters and extracellular peptidases and can grow with peptone as the sole carbon and nitrogen source, indicating a proteolytic lifestyle. Notably, strain LCG003 contains a gene of dyp-type peroxidase and strain-specific genes involved in the degradation of 4-hydroxy-benzoate and vanillate. We further confirmed that it can decolorize aniline blue and grow with lignin as the sole carbon source. Our results indicate that the Aliiglaciecola species can depolymerize and mineralize lignocellulosic materials and potentially play an important role in the marine carbon cycle.
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Affiliation(s)
- Hongcai Zhang
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (H.Z.); (Z.W.); (X.Y.); (J.C.); (T.B.); (J.L.); (C.S.)
| | - Zekai Wang
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (H.Z.); (Z.W.); (X.Y.); (J.C.); (T.B.); (J.L.); (C.S.)
| | - Xi Yu
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (H.Z.); (Z.W.); (X.Y.); (J.C.); (T.B.); (J.L.); (C.S.)
| | - Junwei Cao
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (H.Z.); (Z.W.); (X.Y.); (J.C.); (T.B.); (J.L.); (C.S.)
| | - Tianqiang Bao
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (H.Z.); (Z.W.); (X.Y.); (J.C.); (T.B.); (J.L.); (C.S.)
| | - Jie Liu
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (H.Z.); (Z.W.); (X.Y.); (J.C.); (T.B.); (J.L.); (C.S.)
| | - Chengwen Sun
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (H.Z.); (Z.W.); (X.Y.); (J.C.); (T.B.); (J.L.); (C.S.)
| | - Jiahua Wang
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (H.Z.); (Z.W.); (X.Y.); (J.C.); (T.B.); (J.L.); (C.S.)
| | - Jiasong Fang
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (H.Z.); (Z.W.); (X.Y.); (J.C.); (T.B.); (J.L.); (C.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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2
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Mechanistic Insight into the Fragmentation of Type I Collagen Fibers into Peptides and Amino Acids by a Vibrio Collagenase. Appl Environ Microbiol 2022; 88:e0167721. [PMID: 35285716 DOI: 10.1128/aem.01677-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio collagenases of the M9A subfamily are closely related to Vibrio pathogenesis for their role in collagen degradation during host invasion. Although some Vibrio collagenases have been characterized, the collagen degradation mechanism of Vibrio collagenase is still largely unknown. Here, an M9A collagenase, VP397, from marine Vibrio pomeroyi strain 12613 was characterized, and its fragmentation pattern on insoluble type I collagen fibers was studied. VP397 is a typical Vibrio collagenase composed of a catalytic module featuring a peptidase M9N domain and a peptidase M9 domain and two accessory bacterial prepeptidase C-terminal domains (PPC domains). It can hydrolyze various collagenous substrates, including fish collagen, mammalian collagens of types I to V, triple-helical peptide [(POG)10]3, gelatin, and 4-phenylazobenzyloxycarbonyl-Pro-Leu-Gly-Pro-o-Arg (Pz-peptide). Atomic force microscopy (AFM) observation and biochemical analyses revealed that VP397 first assaults the C-telopeptide region to dismantle the compact structure of collagen and dissociate tropocollagen fragments, which are further digested into peptides and amino acids by VP397 mainly at the Y-Gly bonds in the repeating Gly-X-Y triplets. In addition, domain deletion mutagenesis showed that the catalytic module of VP397 alone is capable of hydrolyzing type I collagen fibers and that its C-terminal PPC2 domain functions as a collagen-binding domain during collagenolysis. Based on our results, a model for the collagenolytic mechanism of VP397 is proposed. This study sheds light on the mechanism of collagen degradation by Vibrio collagenase, offering a better understanding of the pathogenesis of Vibrio and helping in developing the potential applications of Vibrio collagenase in industrial and medical areas. IMPORTANCE Many Vibrio species are pathogens and cause serious diseases in humans and aquatic animals. The collagenases produced by pathogenic Vibrio species have been regarded as important virulence factors, which occasionally exhibit direct pathogenicity to the infected host or facilitate other toxins' diffusion through the digestion of host collagen. However, our knowledge concerning the collagen degradation mechanism of Vibrio collagenase is still limited. This study reveals the degradation strategy of Vibrio collagenase VP397 on type I collagen. VP397 binds on collagen fibrils via its C-terminal PPC2 domain, and its catalytic module first assaults the C-telopeptide region and then attacks the Y-Gly bonds in the dissociated tropocollagen fragments to release peptides and amino acids. This study offers new knowledge regarding the collagenolytic mechanism of Vibrio collagenase, which is helpful for better understanding the role of collagenase in Vibrio pathogenesis and for developing its industrial and medical applications.
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Structure of Vibrio collagenase VhaC provides insight into the mechanism of bacterial collagenolysis. Nat Commun 2022; 13:566. [PMID: 35091565 PMCID: PMC8799719 DOI: 10.1038/s41467-022-28264-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/10/2022] [Indexed: 02/06/2023] Open
Abstract
The collagenases of Vibrio species, many of which are pathogens, have been regarded as an important virulence factor. However, there is little information on the structure and collagenolytic mechanism of Vibrio collagenase. Here, we report the crystal structure of the collagenase module (CM) of Vibrio collagenase VhaC and the conformation of VhaC in solution. Structural and biochemical analyses and molecular dynamics studies reveal that triple-helical collagen is initially recognized by the activator domain, followed by subsequent cleavage by the peptidase domain along with the closing movement of CM. This is different from the peptidolytic mode or the proposed collagenolysis of Clostridium collagenase. We propose a model for the integrated collagenolytic mechanism of VhaC, integrating the functions of VhaC accessory domains and its collagen degradation pattern. This study provides insight into the mechanism of bacterial collagenolysis and helps in structure-based drug design targeting of the Vibrio collagenase. The collagenolytic mechanism of Vibrio collagenase, a virulence factor, remains unclear. Here, the authors report the structure of Vibrio collagenase VhaC and propose the mechanism for collagen recognition and degradation, providing new insight into bacterial collagenolysis.
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4
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Khan K, Tareen AK, Iqbal M, Mahmood A, Mahmood N, Shi Z, Yin J, Qing D, Ma C, Zhang H. Recent development in graphdiyne and its derivative materials for novel biomedical applications. J Mater Chem B 2021; 9:9461-9484. [PMID: 34762090 DOI: 10.1039/d1tb01794b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Graphdiyne (GDY), which possess sp- and sp2-hybridized carbon and Dirac cones, offers unique physical and chemical properties, including an adjustable intrinsic bandgap, excellent charge carrier transfer efficiency, and superior conductivity compared to other carbon allotropes. These exceptional qualities of GDY and its derivatives have been successfully used in a variety of fields, including catalysis, energy, environmental protection, and biological applications. Herein, we focus on the potential application of GDY and its derivatives in the biomedical domain, including biosensing, biological protection, cancer therapy, and antibacterial agents, demonstrating how the biomimetic behavior of these materials can be a step forward in bridging the gap between nature and applications. Considering the excellent biocompatibility, solubility and selectivity of GDY and its derived materials, they have shown great potential as biosensing and bio-imaging materials. The unusual combination of properties in GDY has been used in biological applications such as "OFF-ON" DNA detection and enzymatic sensing, where GDY has a greater adsorption capacity than graphene and other 2D materials, resulting in increased sensitivity. GDY and its derivatives have also been used in cancer treatment due to their high doxorubicin (DOX) loading capacity (using-stacking) and photothermal conversion ability, and radiation protection since their initial biological use. The poor biodegradation rate of graphene demands the search for new nanomaterials. Accordingly, GDY has better biocompatibility and bio-safety than other 2D nanomaterials, especially graphene and its oxide, due to its absence of aggregation in the physiological environment. Thus, GDY-based nanomaterials have become promising candidates as bio-delivery carriers. Besides, GDY and GDY-based materials have also shown interesting applications in the fields of cell-culture, cell-growth and tissue engineering. Herein, we present a comprehensive review on the applications of GDY and its derivatives as biomedical materials, followed by their future perspectives. This review will provide an outlook for the application of graphene and its derivatives and may open up new horizons to inspire broader interests across various disciplines. Finally, the future prospects for GDY-based materials are examined for their potential biological use.
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Affiliation(s)
- Karim Khan
- School of Electrical Engineering & Intelligentization, Dongguan University of Technology, Dongguan, 523808, China. .,Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Ayesha Khan Tareen
- Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Engineering, Shenzhen University, Shenzhen, 518060, China. .,College of Materials Science and Engineering, Guangdong Research Center for Interfacial Engineering of Functional Materials, Shenzhen University, 3688 Nanhai Ave, Shenzhen, 518060, P. R. China.,School of Mechanical Engineering, Dongguan University of Technology, Dongguan, 523808, P. R. China
| | - Muhammad Iqbal
- Department of Bio-Chemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa (K.P.K.), 23200, Islamic Republic of Pakistan
| | - Asif Mahmood
- School of Chemical and Bio-molecular Engineering, The University of Sydney, 2006, Sydney, Australia
| | - Nasir Mahmood
- School of Engineering, The Royal Melbourne Institute of Technology (RMIT) University, Melbourne, Victoria, Australia
| | - Zhe Shi
- Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Jinde Yin
- Shenzhen Nuoan Environmental & Safety Inc., Shenzhen 518107, P. R. China.,College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, P. R. China
| | - Duan Qing
- Shenzhen Nuoan Environmental & Safety Inc., Shenzhen 518107, P. R. China
| | - Chunyang Ma
- Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Han Zhang
- Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Engineering, Shenzhen University, Shenzhen, 518060, China.
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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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6
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Biochemical characterisation of a collagenase from Bacillus cereus strain Q1. Sci Rep 2021; 11:4187. [PMID: 33603127 PMCID: PMC7893005 DOI: 10.1038/s41598-021-83744-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/04/2021] [Indexed: 12/01/2022] Open
Abstract
Collagen is the most abundant protein in higher animals and as such it is a valuable source of amino acids and carbon for saprophytic bacteria. Due to its unique amino acid composition and triple-helical tertiary structure it can however only be cleaved by specialized proteases like the collagenases secreted by some bacteria. Among the best described bacterial collagenases are ColG and ColH from Clostridium histolyticum. Many Bacillus species contain homologues of clostridial collagenases, which play a role in some infections caused by B. cereus. Detailed biochemical and enzymatic characterizations of bacillial collagenases are however lacking at this time. In an effort to close this gap in knowledge we expressed ColQ1 from B. cereus strain Q1 recombinantly, investigated its metal dependency and performed peptide, gelatin and collagen degradation assays. Our results show that ColQ1 is a true collagenase, cleaving natively folded collagen six times more efficiently than ColG while at the same time being a similarly effective peptidase as ColH. In both ColQ1 and ColG the rate-limiting step in collagenolysis is the unwinding of the triple-helix. The data suggest an orchestrated multi-domain mechanism for efficient helicase activity.
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7
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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: 3] [Impact Index Per Article: 0.8] [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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Santra M, Sharma M, Katoch D, Jain S, Saikia UN, Dogra MR, Luthra-Guptasarma M. Induction of posterior vitreous detachment (PVD) by non-enzymatic reagents targeting vitreous collagen liquefaction as well as vitreoretinal adhesion. Sci Rep 2020; 10:8250. [PMID: 32427865 PMCID: PMC7237681 DOI: 10.1038/s41598-020-64931-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/26/2020] [Indexed: 11/20/2022] Open
Abstract
Induction of posterior vitreous detachment (PVD) by pharmacologic vitreolysis has been largely attempted through the use of enzymatic reagents. Ocriplasmin has been the only FDA-approved clinical reagent so far. Several adverse effects of ocriplasmin have emerged, however, and the search for alternative PVD-inducing reagents continues. Since i) collagen forms an important structural component of the vitreous, and ii) strong vitreo-retinal adhesions exist between the cortical vitreous and the internal limiting membrane (ILM) of the retina, an effective PVD-inducing reagent would require both, vitreous liquefaction, and concurrent dehiscence of vitreoretinal adhesion, without being toxic to retinal cells. We designed a combination of two reagents to achieve these two objectives; a triple helix-destabilizing collagen binding domain (CBD), and a fusion of RGD (integrin-binding) tripeptide with CBD (RCBD) to facilitate separation of posterior cortical vitreous from retinal surface. Based on in vitro, ex-vivo, and in vivo experiments, we show that a combination of CBD and RCBD displays potential for safe pharmacologic vitreolysis. Our findings assume significance in light of the fact that synthetic RGD-containing peptides have already been used for inhibition of tumor cell invasion. Proteins such as variants of collagen binding domains could have extended therapeutic uses in the future.
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Affiliation(s)
- Mithun Santra
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Maryada Sharma
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India.,Department of Otolaryngology and Head & Neck surgery, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Deeksha Katoch
- Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Sahil Jain
- Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Uma Nahar Saikia
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Mangat R Dogra
- Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Manni Luthra-Guptasarma
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India.
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9
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Mechanistic Insight into the Binding and Swelling Functions of Prepeptidase C-Terminal (PPC) Domains from Various Bacterial Proteases. Appl Environ Microbiol 2019; 85:AEM.00611-19. [PMID: 31076429 DOI: 10.1128/aem.00611-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/29/2019] [Indexed: 02/03/2023] Open
Abstract
The bacterial prepeptidase C-terminal (PPC) domain can be found in the C termini of a wide variety of proteases that are secreted by marine bacteria. However, the functions of these PPC domains remain unknown due to a lack of systematic research. Here, the binding and swelling abilities of eight PPC domains from six different proteases were compared systematically via scanning electron microscopy (SEM), enzyme assays, and fluorescence spectroscopy. These PPC domains all possess the ability to bind and swell insoluble collagen. PPC domains can expose collagen monomers but cannot disrupt the pyridinoline cross-links or unwind the collagen triple helix. This ability can play a synergistic role alongside collagenase in collagen hydrolysis. Site-directed mutagenesis of the PPC domain from Vibrio anguillarum showed that the conserved polar and aromatic residues Y6, D26, D28, Y30, W42, E53, C55, and Y65 and the hydrophobic residues V10, V18, and I57 played key roles in substrate binding. Molecular dynamic simulations were conducted to investigate the interactions between PPC domains and collagen. Most PPC domains have a similar mechanism for binding collagen, and the hydrophobic binding pocket of PPC domains may play an important role in collagen binding. This study sheds light on the substrate binding mechanisms of PPC domains and reveals a new function for the PPC domains of bacterial proteases in substrate degradation.IMPORTANCE Prepeptidase C-terminal (PPC) domains commonly exist in the C termini of marine bacterial proteases. Reports examining PPC have been limited, and its functions remain unclear. In this study, eight PPCs from six different bacteria were examined. Most of the PPCs possessed the ability to bind collagen, feathers, and chitin, and all PPCs could significantly swell insoluble collagen. PPCs can expose collagen monomers but cannot disrupt pyridinoline cross-links or unwind the collagen triple helix. This swelling ability may also play synergistic roles in collagen hydrolysis. Comparative structural analyses and the examination of PPC mutants revealed that the hydrophobic binding pockets of PPCs may play important roles in collagen binding. This study provides new insights into the functions and ecological significance of PPCs, and the molecular mechanism of the collagen binding of PPCs was clarified, which is beneficial for the protein engineering of highly active PPCs and collagenase in the pharmaceutical industry and of artificial biological materials.
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10
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Fujimaki H, Uchida K, Inoue G, Matsushita O, Nemoto N, Miyagi M, Inage K, Takano S, Orita S, Ohtori S, Tanaka K, Sekiguchi H, Takaso M. Polyglycolic acid-collagen tube combined with collagen-binding basic fibroblast growth factor accelerates gait recovery in a rat sciatic nerve critical-size defect model. J Biomed Mater Res B Appl Biomater 2019; 108:326-332. [PMID: 31016841 DOI: 10.1002/jbm.b.34391] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/24/2019] [Accepted: 04/04/2019] [Indexed: 02/03/2023]
Abstract
Several nerve conduits have been investigated for their potential as alternative sources of autografts for bridging neural gaps. However, autologous nerve transplants remain the most effective for nerve repair. We examined clinically approved nerve conduits containing collagen and polyglycolic acid (PGA-c) combined with collagen-binding basic fibroblast growth factor (bFGF) containing a polycystic kidney disease (PKD) domain and collagen binding domain (CBD) (bFGF-PKD-CBD) in a rat 15-mm sciatic nerve critical-size defect model. The treatment groups were: PGA-c immersed in phosphate-buffered saline (PBS) (PGA-c/PBS group), bFGF (PGA-c/bFGF group), or bFGF-PKD-CBD (PGA-c/bFGF-PKD-CBD group), and no treatment (Defect group). Gait and histological analyses were performed. Four weeks after treatment, the recovery rate of the paw print area was significantly greater in the PGA-c/bFGFPKD-CBD group than the PGA-c/PBS and PGA-c/bFGF groups. Mean intensity of paw prints was significantly greater in the PGA-c/bFGF-PKD-CBD group than the PGA-c/PBS and Defect groups. Swing time was significantly greater in the PGA-c/PBS, PGA-c/bFGF, and PGA-c/bFGF-PKD-CBD groups than the Defect group. At 8 weeks, all three parameters were significantly greater in the PGA-c/PBS, PGA-c/bFGF, and PGA-c/bFGF-PKD-CBD groups than the Defect group. Regenerated myelinated fibers were observed in 7/8 (87.5%) rats in the PGA-c/bFGF-PKD-CBD group after 8 weeks, and in 1/8 (12.5%) and 3/8 (37.5%) rats in the PGA-c/PBS and PGA-c/bFGF groups, respectively. PGA-c/bFGF-PKD-CBD composites may be promising biomaterials for promoting functional recovery of long-distance peripheral nerve defects in clinical practice.
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Affiliation(s)
- Hisako Fujimaki
- Department of Orthopedic Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Kentaro Uchida
- Department of Orthopedic Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Gen Inoue
- Department of Orthopedic Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Osamu Matsushita
- Research Center for Biological Imaging, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Noriko Nemoto
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Masayuki Miyagi
- Department of Orthopedic Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Kazuhide Inage
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shotaro Takano
- Department of Orthopedic Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Sumihisa Orita
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Seiji Ohtori
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Tanaka
- Nippi Research Institute of Biomatrix and Protein Engineering Project, 520-11, Toride, Japan
| | - Hiroyuki Sekiguchi
- Shonan University of Medical Sciences Research Institute, Chigasaki City, Kanagawa, Japan
| | - Masashi Takaso
- Department of Orthopedic Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
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11
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New method of detecting hydrophobic interaction between C-terminal binding domain and biomacromolecules. J Biotechnol 2018; 265:101-108. [DOI: 10.1016/j.jbiotec.2017.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 10/16/2017] [Accepted: 11/17/2017] [Indexed: 01/29/2023]
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12
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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: 21] [Impact Index Per Article: 3.0] [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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13
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Schönauer E, Kany AM, Haupenthal J, Hüsecken K, Hoppe IJ, Voos K, Yahiaoui S, Elsässer B, Ducho C, Brandstetter H, Hartmann RW. Discovery of a Potent Inhibitor Class with High Selectivity toward Clostridial Collagenases. J Am Chem Soc 2017; 139:12696-12703. [PMID: 28820255 PMCID: PMC5607459 DOI: 10.1021/jacs.7b06935] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Secreted virulence
factors like bacterial collagenases are conceptually
attractive targets for fighting microbial infections. However, previous
attempts to develop potent compounds against these metalloproteases
failed to achieve selectivity against human matrix metalloproteinases
(MMPs). Using a surface plasmon resonance-based screening complemented
with enzyme inhibition assays, we discovered an N-aryl mercaptoacetamide-based inhibitor scaffold that showed
sub-micromolar affinities toward collagenase H (ColH) from the human
pathogen Clostridium histolyticum. Moreover, these
inhibitors also efficiently blocked the homologous bacterial collagenases,
ColG from C. histolyticum, ColT from C. tetani, and ColQ1 from the Bacillus cereus strain Q1,
while showing negligible activity toward human MMPs-1, -2, -3, -7,
-8, and -14. The most active compound displayed a more than 1000-fold
selectivity over human MMPs. This selectivity can be rationalized
by the crystal structure of ColH with this compound, revealing a distinct
non-primed binding mode to the active site. The non-primed binding
mode presented here paves the way for the development of selective
broad-spectrum bacterial collagenase inhibitors with potential therapeutic
application in humans.
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Affiliation(s)
- Esther Schönauer
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Andreas M Kany
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Jörg Haupenthal
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Kristina Hüsecken
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Isabel J Hoppe
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Katrin Voos
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
| | - Samir Yahiaoui
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Brigitta Elsässer
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
| | - Hans Brandstetter
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Rolf W Hartmann
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
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14
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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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15
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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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16
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Schönauer E, Brandstetter H. Inhibition and Activity Regulation of Bacterial Collagenases. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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17
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Bathige SDNK, Umasuthan N, Godahewa GI, Jayasinghe JDHE, Whang I, Noh JK, Lee J. A homolog of Kunitz-type serine protease inhibitor from rock bream, Oplegnathus fasciatus: Molecular insights and transcriptional modulation in response to microbial and PAMP stimulation, and tissue injury. FISH & SHELLFISH IMMUNOLOGY 2015; 46:285-291. [PMID: 26162478 DOI: 10.1016/j.fsi.2015.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/16/2015] [Accepted: 07/02/2015] [Indexed: 06/04/2023]
Abstract
Serine proteases and their inhibitors play vital roles in diverse biological processes. In this study, we identified and characterized cDNA coding for a Kunitz-type serine protease inhibitor (SPI), which we designated as RbKSPI, in a commercially important species, rock bream. The full-length cDNA sequence of RbKSPI consisted of 2452 bp with an open reading frame (ORF) of 1521 bp encoding a polypeptide of 507 amino acid (aa) residues. In the RbKSPI protein, MANEC, PKD, LDLa, and two Kunitz domains responsible for various functions were identified as characteristic features. Homology analysis revealed that RbKSPI shared the highest identity with the Kunitz homolog in Takifugu rubripes (77.6%). Phylogenetic analysis indicated that RbKSPI clusters with other teleostean KSPIs. In tissue-specific expression analysis, RbKSPI transcripts were detected in all the tested tissues, with the highest expression in gill tissue, followed by kidney and intestine. The mRNA expression of RbKSPI significantly increased in blood cells upon stimulation with two strains of bacteria (Edwardsiella tarda and Streptococcus iniae) and two pathogen-associated molecular patterns (PAMPs; LPS and poly I:C). Meanwhile, down-regulated expression of RbKSPI was observed in response to tissue injury. Collectively, these results suggest that the RbKSPI may be involved in essential immune defense against microbial pathogens and in the wound-healing process.
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Affiliation(s)
- S D N K Bathige
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea
| | - Navaneethaiyer Umasuthan
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea
| | - G I Godahewa
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea
| | - J D H E Jayasinghe
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea
| | - Ilson Whang
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea
| | - Jae Koo Noh
- Genetics & Breeding Research Center, National Fisheries Research & Development Institute, Geoje 656-842, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea.
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18
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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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19
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Yang J, Zhao HL, Ran LY, Li CY, Zhang XY, Su HN, Shi M, Zhou BC, Chen XL, Zhang YZ. Mechanistic insights into elastin degradation by pseudolysin, the major virulence factor of the opportunistic pathogen Pseudomonas aeruginosa. Sci Rep 2015; 5:9936. [PMID: 25905792 PMCID: PMC4407726 DOI: 10.1038/srep09936] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/12/2015] [Indexed: 01/01/2023] Open
Abstract
Pseudolysin is the most abundant protease secreted by Pseudomonas aeruginosa and is the major extracellular virulence factor of this opportunistic human pathogen. Pseudolysin destroys human tissues by solubilizing elastin. However, the mechanisms by which pseudolysin binds to and degrades elastin remain elusive. In this study, we investigated the mechanism of action of pseudolysin on elastin binding and degradation by biochemical assay, microscopy and site-directed mutagenesis. Pseudolysin bound to bovine elastin fibers and preferred to attack peptide bonds with hydrophobic residues at the P1 and P1’ positions in the hydrophobic domains of elastin. The time-course degradation processes of both bovine elastin fibers and cross-linked human tropoelastin by pseudolysin were further investigated by microscopy. Altogether, the results indicate that elastin degradation by pseudolysin began with the hydrophobic domains on the fiber surface, followed by the progressive disassembly of macroscopic elastin fibers into primary structural elements. Moreover, our site-directed mutational results indicate that five hydrophobic residues in the S1-S1’ sub-sites played key roles in the binding of pseudolysin to elastin. This study sheds lights on the pathogenesis of P. aeruginosa infection.
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Affiliation(s)
- Jie Yang
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China [2] Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Hui-Lin Zhao
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China [2] Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Li-Yuan Ran
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China [2] Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Chun-Yang Li
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China [2] Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Xi-Ying Zhang
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China [2] Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Hai-Nan Su
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China [2] Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Mei Shi
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China [2] Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Bai-Cheng Zhou
- Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Xiu-Lan Chen
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China [2] Biotechnology Research Center, Shandong University, Jinan 250100, China [3] Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan 250100, China
| | - Yu-Zhong Zhang
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China [2] Biotechnology Research Center, Shandong University, Jinan 250100, China [3] Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan 250100, China
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20
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Uchida K, Matsushita O, Nishi N, Inoue G, Horikawa K, Takaso M. Enhancement of periosteal bone formation by basic fibroblast-derived growth factor containing polycystic kidney disease and collagen-binding domains fromClostridium histolyticumcollagenase. J Tissue Eng Regen Med 2015; 11:1165-1172. [DOI: 10.1002/term.2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 01/08/2015] [Accepted: 01/23/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Kentaro Uchida
- Department of Orthopaedic Surgery; Kitasato University School of Medicine; 1-15-1 Minami-ku Kitasato Sagamihara Kanagawa Japan
| | - Osamu Matsushita
- Department of Bacteriology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Okayama University; 2-5-1 Shikata-cho Kita-ku Okayama Japan
| | - Nozomu Nishi
- Life Science Research Centre; Kagawa University; 1750-1 Kita-gun Miki-cho Kagawa Japan
| | - Gen Inoue
- Department of Orthopaedic Surgery; Kitasato University School of Medicine; 1-15-1 Minami-ku Kitasato Sagamihara Kanagawa Japan
| | - Kyosuke Horikawa
- Okayama University Medical School; 2-5-1 Shikata-cho Kita-ku Okayama Japan
| | - Masashi Takaso
- Department of Orthopaedic Surgery; Kitasato University School of Medicine; 1-15-1 Minami-ku Kitasato Sagamihara Kanagawa Japan
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21
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Bauer R, Janowska K, Taylor K, Jordan B, Gann S, Janowski T, Latimer EC, Matsushita O, Sakon J. Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH. ACTA ACUST UNITED AC 2015; 71:565-77. [PMID: 25760606 PMCID: PMC4356367 DOI: 10.1107/s1399004714027722] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 12/19/2014] [Indexed: 11/25/2022]
Abstract
The surface properties and dynamics of PKD-like domains from ColG and ColH differ. Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca2+-triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable number of polycystic kidney disease-like (PKD-like) domains (s2a and s2b in ColH and s2 in ColG) and a variable number of collagen-binding domains (s3 in ColH and s3a and s3b in ColG). The X-ray crystal structures of Ca2+-bound holo s2b (1.4 Å resolution, R = 15.0%, Rfree = 19.1%) and holo s2a (1.9 Å resolution, R = 16.3%, Rfree = 20.7%), as well as of Ca2+-free apo s2a (1.8 Å resolution, R = 20.7%, Rfree = 27.2%) and two new forms of N-terminally truncated apo s2 (1.4 Å resolution, R = 16.9%, Rfree = 21.2%; 1.6 Å resolution, R = 16.2%, Rfree = 19.2%), are reported. The structurally similar PKD-like domains resemble the V-set Ig fold. In addition to a conserved β-bulge, the PKD-like domains feature a second bulge that also changes the allegiance of the subsequent β-strand. This β-bulge and the genesis of a Ca2+ pocket in the archaeal PKD-like domain suggest a close kinship between bacterial and archaeal PKD-like domains. Different surface properties and indications of different dynamics suggest unique roles for the PKD-like domains in ColG and in ColH. Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3. B-factor analyses suggest that in the presence of Ca2+ the midsection of s2 becomes more flexible but the midsections of s2a and s2b stay rigid. The different surface properties and dynamics of the domains suggest that the PKD-like domains of M9B bacterial collagenase can be grouped into either a ColG subset or a ColH subset. The conserved properties of PKD-like domains in ColG and in ColH include Ca2+ binding. Conserved residues not only interact with Ca2+, but also position the Ca2+-interacting water molecule. Ca2+ aligns the N-terminal linker approximately parallel to the major axis of the domain. Ca2+ binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix. The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.
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Affiliation(s)
- Ryan Bauer
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Katarzyna Janowska
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Kelly Taylor
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Brad Jordan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Steve Gann
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Tomasz Janowski
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ethan C Latimer
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Osamu Matsushita
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Joshua Sakon
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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22
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Wang P, Yu Z, Li B, Cai X, Zeng Z, Chen X, Wang X. Development of an efficient conjugation-based genetic manipulation system for Pseudoalteromonas. Microb Cell Fact 2015; 14:11. [PMID: 25612661 PMCID: PMC4318363 DOI: 10.1186/s12934-015-0194-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/10/2015] [Indexed: 11/10/2022] Open
Abstract
Pseudoalteromonas is commonly found throughout the world's oceans, and has gained increased attention due to the ecological and biological significance. Although over fifty Pseudoalteromonas genomes have been sequenced with an aim to explore the adaptive strategies in different habitats, in vivo studies are hampered by the lack of effective genetic manipulation systems for most strains in this genus. Here, nine Pseudoalteromonas strains isolated from different habitats were selected and used as representative strains to develop a universal genetic manipulation system. Erythromycin and chloramphenicol resistance were chosen as selection markers based on antibiotics resistance test of the nine strains. A conjugation protocol based on the RP4 conjugative machinery in E. coli WM3064 was developed to overcome current limitations of genetic manipulation in Pseudoalteromonas. Two mobilizable gene expression shuttle vectors (pWD2-oriT and pWD2Ery-oriT) were constructed, and conjugation efficiency of pWD2-oriT from E. coli to the nine Pseudoalteromonas strains ranged from 10(-6) to 10(-3) transconjugants per recipient cells. Two suicide vectors, pK18mobsacB-Cm and pK18mobsacB-Ery (with sacB for counter-selection), were constructed for gene knockout. To verify the feasibility of this system, we selected gene or operon that may lead to phenotypic change once disrupted as targets to facilitate in vivo functional confirmation. Successful deletions of two genes related to prodigiosin biosynthesis (pigMK) in P. rubra DSM 6842, one biofilm related gene (bsmA) in P. sp. SM9913, one gene related to melanin hyperproduction (hmgA) in P. lipolytica SCSIO 04301 and two flagella-related genes (fliF and fliG) in P. sp. SCSIO 11900 were verified, respectively. In addition, complementation of hmgA using shuttle vector pWD2-oriT was rescued the phenotype caused by deletion of chromosomal copy of hmgA in P. lipolytica SCSIO 04301. Taken together, we demonstrate that the vectors and the conjugative protocol developed here have potential to use in various Pseudoalteromonas strains.
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Affiliation(s)
- Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Zichao Yu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.
| | - Baiyuan Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xingsheng Cai
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Zhenshun Zeng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiulan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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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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24
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Labourel A, Jam M, Jeudy A, Hehemann JH, Czjzek M, Michel G. The β-glucanase ZgLamA from Zobellia galactanivorans evolved a bent active site adapted for efficient degradation of algal laminarin. J Biol Chem 2013; 289:2027-42. [PMID: 24337571 DOI: 10.1074/jbc.m113.538843] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Laminarinase is commonly used to describe β-1,3-glucanases widespread throughout Archaea, bacteria, and several eukaryotic lineages. Some β-1,3-glucanases have already been structurally and biochemically characterized, but very few from organisms that are in contact with genuine laminarin, the storage polysaccharide of brown algae. Here we report the heterologous expression and subsequent biochemical and structural characterization of ZgLamAGH16 from Zobellia galactanivorans, the first GH16 laminarinase from a marine bacterium associated with seaweeds. ZgLamAGH16 contains a unique additional loop, compared with other GH16 laminarinases, which is composed of 17 amino acids and gives a bent shape to the active site cleft of the enzyme. This particular topology is perfectly adapted to the U-shaped conformation of laminarin chains in solution and thus explains the predominant specificity of ZgLamAGH16 for this substrate. The three-dimensional structure of the enzyme and two enzyme-substrate complexes, one with laminaritetraose and the other with a trisaccharide of 1,3-1,4-β-d-glucan, have been determined at 1.5, 1.35, and 1.13 Å resolution, respectively. The structural comparison of substrate recognition pattern between these complexes allows the proposition that ZgLamAGH16 likely diverged from an ancestral broad specificity GH16 β-glucanase and evolved toward a bent active site topology adapted to efficient degradation of algal laminarin.
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Affiliation(s)
- Aurore Labourel
- From Sorbonne Universités, UPMC Université Paris 06, UMR 7139, Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France and
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25
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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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26
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Eckhard U, Huesgen PF, Brandstetter H, Overall CM. Proteomic protease specificity profiling of clostridial collagenases reveals their intrinsic nature as dedicated degraders of collagen. J Proteomics 2013; 100:102-14. [PMID: 24125730 PMCID: PMC3985423 DOI: 10.1016/j.jprot.2013.10.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 09/27/2013] [Accepted: 10/03/2013] [Indexed: 12/15/2022]
Abstract
Clostridial collagenases are among the most efficient degraders of collagen. Most clostridia are saprophytes and secrete proteases to utilize proteins in their environment as carbon sources; during anaerobic infections, collagenases play a crucial role in host colonization. Several medical and biotechnological applications have emerged utilizing their high collagenolytic efficiency. However, the contribution of the functionally most important peptidase domain to substrate specificity remains unresolved. We investigated the active site sequence specificity of the peptidase domains of collagenase G and H from Clostridium histolyticum and collagenase T from Clostridium tetani. Both prime and non-prime cleavage site specificity were simultaneously profiled using Proteomic Identification of protease Cleavage Sites (PICS), a mass spectrometry-based method utilizing database searchable proteome-derived peptide libraries. For each enzyme we identified > 100 unique-cleaved peptides, resulting in robust cleavage logos revealing collagen-like specificity patterns: a strong preference for glycine in P3 and P1′, proline at P2 and P2′, and a slightly looser specificity at P1, which in collagen is typically occupied by hydroxyproline. This specificity for the classic collagen motifs Gly-Pro-X and Gly-X-Hyp represents a remarkable adaptation considering the complex requirements for substrate unfolding and presentation that need to be fulfilled before a single collagen strand becomes accessible for cleavage. Biological significance We demonstrate the striking sequence specificity of a family of clostridial collagenases using proteome derived peptide libraries and PICS, Proteomic Identification of protease Cleavage Sites. In combination with the previously published crystal structures of these proteases, our results represent an important piece of the puzzle in understanding the complex mechanism underlying collagen hydrolysis, and pave the way for the rational design of specific test substrates and selective inhibitors. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes? Active site specificity profiling of 3 clostridial collagenases—ColG and H from C. histolyticum, and ColT from C. tetani. Their high sequence specificity to collagen-like sequence points towards a co-evolution with the mammalian substrate. Significant differences to MMPs and a more promiscuous cleavage mechanism facilitating rapid collagenolysis were revealed. Human proteome-derived peptide libraries & PICS are suitable for active site specificity profiling of pathogenic proteases. Results pave the way for rational design of test substrates and selective inhibitors.
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Affiliation(s)
- Ulrich Eckhard
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Billrothstr, 11, 5020 Salzburg, Austria
| | - Pitter F Huesgen
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hans Brandstetter
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Billrothstr, 11, 5020 Salzburg, Austria
| | - Christopher M Overall
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.
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Edwin A, Rompikuntal P, Björn E, Stier G, Wai SN, Sauer-Eriksson AE. Calcium binding by the PKD1 domain regulates interdomain flexibility in Vibrio cholerae metalloprotease PrtV. FEBS Open Bio 2013; 3:263-70. [PMID: 23905008 PMCID: PMC3722578 DOI: 10.1016/j.fob.2013.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 01/06/2023] Open
Abstract
Vibrio cholerae, the causative agent of cholera, releases several virulence factors including secreted proteases when it infects its host. These factors attack host cell proteins and break down tissue barriers and cellular matrix components such as collagen, laminin, fibronectin, keratin, elastin, and they induce necrotic tissue damage. The secreted protease PrtV constitutes one virulence factors of V. cholerae. It is a metalloprotease belonging to the M6 peptidase family. The protein is expressed as an inactive, multidomain, 102 kDa pre-pro-protein that undergoes several N- and C-terminal modifications after which it is secreted as an intermediate variant of 81 kDa. After secretion from the bacteria, additional proteolytic steps occur to produce the 55 kDa active M6 metalloprotease. The domain arrangement of PrtV is likely to play an important role in these maturation steps, which are known to be regulated by calcium. However, the molecular mechanism by which calcium controls proteolysis is unknown. In this study, we report the atomic resolution crystal structure of the PKD1 domain from V. cholera PrtV (residues 755–838) determined at 1.1 Å. The structure reveals a previously uncharacterized Ca2+-binding site located near linker regions between domains. Conformational changes in the Ca2+-free and Ca2+-bound forms suggest that Ca2+-binding at the PKD1 domain controls domain linker flexibility, and plays an important structural role, providing stability to the PrtV protein. The PKD1 domain was expressed in E. coli and purified to homogeneity. Purified PKD1 domains are not toxic for human HTC8 cells. The atomic 1.1 Å crystal structure of the PKD1 domain revealed a Ca2+-binding site. Ca2+ binding causes large conformational changes in the N-terminal half of the PKD1 domain. Ca2+ stabilizes the 81 kDa pro-protein outside the bacterial cell, preventing its degradation.
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Affiliation(s)
- Aaron Edwin
- Department of Chemistry, Umeå University, Umeå SE-901 87, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-901 87, Sweden
| | - Pramod Rompikuntal
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-901 87, Sweden
- Department of Molecular Biology, Umeå University, Umeå SE-901 87, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå SE-901 87, Sweden
| | - Erik Björn
- Department of Chemistry, Umeå University, Umeå SE-901 87, Sweden
| | - Gunter Stier
- Department of Chemistry, Umeå University, Umeå SE-901 87, Sweden
| | - Sun N. Wai
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-901 87, Sweden
- Department of Molecular Biology, Umeå University, Umeå SE-901 87, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå SE-901 87, Sweden
| | - A. Elisabeth Sauer-Eriksson
- Department of Chemistry, Umeå University, Umeå SE-901 87, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-901 87, Sweden
- Corresponding author at: Department of Chemistry, Umeå University, Umeå SE-901 87, Sweden. Tel.: +46 90 7865923; fax: +46 90 7865944.
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28
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Jeon E, Yun YR, Kim HW, Jang JH. Engineering and application of collagen-binding fibroblast growth factor 2 for sustained release. J Biomed Mater Res A 2013; 102:1-7. [DOI: 10.1002/jbm.a.34689] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 02/20/2013] [Accepted: 02/26/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Eunyi Jeon
- Department of Biochemistry; Inha University School of Medicine; Incheon 400-712 Korea
| | - Ye-Rang Yun
- Institute of Tissue Regeneration Engineering (ITREN); Dankook University; Cheonan South Korea
- Department of Nanobiomedical Science and WCU Research Center; Dankook University Graduate School; Cheonan 330-714 Korea
| | - Hae-Won Kim
- Institute of Tissue Regeneration Engineering (ITREN); Dankook University; Cheonan South Korea
- Department of Nanobiomedical Science and WCU Research Center; Dankook University Graduate School; Cheonan 330-714 Korea
- Department of Biomaterials Science; School of Dentistry; Dankook University; Cheonan 330-714 Korea
| | - Jun-Hyeog Jang
- Department of Biochemistry; Inha University School of Medicine; Incheon 400-712 Korea
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29
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Abstract
Interstitial collagen mechanical and biological properties are altered by proteases that catalyze the hydrolysis of the collagen triple-helical structure. Collagenolysis is critical in development and homeostasis but also contributes to numerous pathologies. Mammalian collagenolytic enzymes include matrix metalloproteinases, cathepsin K, and neutrophil elastase, and a variety of invertebrates and pathogens possess collagenolytic enzymes. Components of the mechanism of action for the collagenolytic enzyme MMP-1 have been defined experimentally, and insights into other collagenolytic mechanisms have been provided. Ancillary biomolecules may modulate the action of collagenolytic enzymes.
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Affiliation(s)
- Gregg B Fields
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL 34987, USA.
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30
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Bauer R, Wilson JJ, Philominathan STL, Davis D, Matsushita O, Sakon J. Structural comparison of ColH and ColG collagen-binding domains from Clostridium histolyticum. J Bacteriol 2013; 195:318-27. [PMID: 23144249 PMCID: PMC3553835 DOI: 10.1128/jb.00010-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 11/02/2012] [Indexed: 12/29/2022] Open
Abstract
Clostridium histolyticum secretes collagenases, ColG and ColH, that cause extensive tissue destruction in myonecrosis. The C-terminal collagen-binding domain (CBD) of collagenase is required for insoluble collagen fibril binding and subsequent collagenolysis. The high-resolution crystal structures of ColG-CBD (s3b) and ColH-CBD (s3) are reported in this paper. The new X-ray structure of s3 was solved at 2.0-Å resolution (R = 17.4%; R(free) = 23.3%), while the resolution of the previously determined s3b was extended to 1.4 Å (R = 17.9%; R(free) = 21.0%). Despite sharing only 30% sequence identity, the molecules resemble one another closely (root mean square deviation [RMSD] C(α) = 1.5 Å). All but one residue, whose side chain chelates with Ca(2+), are conserved. The dual Ca(2+) binding site in s3 is completed by an unconserved aspartate. Differential scanning calorimetric measurements showed that s3 gains thermal stability, comparable to s3b, by binding to Ca(2+) (holo T(m) = 94.1°C; apo T(m) = 70.2°C). holo s3 is also stabilized against chemical denaturants urea and guanidine HCl. The three most critical residues for collagen interaction in s3b are conserved in s3. The general shape of the binding pocket is retained by altered loop structures and side chain positions. Small-angle X-ray scattering data revealed that s3 also binds asymmetrically to minicollagen. Besides the calcium-binding sites and the collagen-binding pocket, architecturally important hydrophobic residues and the hydrogen-bonding network around the cis-peptide bond are well conserved within the metallopeptidase subfamily M9B. CBDs were previously shown to bind to the extracellular matrix of various tissues. Compactness and extreme stability in physiological Ca(2+) concentration possibly make both CBDs suitable for targeted growth factor delivery.
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Affiliation(s)
- Ryan Bauer
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Jeffrey J. Wilson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | | | - Dan Davis
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Osamu Matsushita
- Department of Bacteriology, Okayama University Medical School, Okayama, Japan
| | - Joshua Sakon
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
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Genome sequence of the protease-producing bacterium Rheinheimera nanhaiensis E407-8T, isolated from deep-sea sediment of the South China Sea. J Bacteriol 2012; 194:7001-2. [PMID: 23209246 DOI: 10.1128/jb.01922-12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The protease-producing bacterium E407-8(T) was isolated from deep-sea sediment of the South China Sea and has been identified recently as representing a new species, Rheinheimera nanhaiensis. The draft genome of R. nanhaiensis E407-8(T) consists of 3,987,205 bp and contains 3,730 predicated protein-coding genes, including 82 extracellular peptidase genes.
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32
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Structure of collagenase G reveals a chew-and-digest mechanism of bacterial collagenolysis. Nat Struct Mol Biol 2011; 18:1109-14. [PMID: 21947205 PMCID: PMC3191118 DOI: 10.1038/nsmb.2127] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 07/21/2011] [Indexed: 11/10/2022]
Abstract
Collagen constitutes one third of the body protein in humans, reflecting its extraordinary role in health and disease. Of similar importance, therefore, are the idiosyncratic proteases that nature evolved for collagen remodeling. Intriguingly, the most efficient collagenases are those that enable clostridial bacteria to colonize their host tissues, but despite intense studies, the structural and mechanistic basis of these enzymes has remained elusive. Here we present the crystal structure of collagenase G from Clostridium histolyticum at 2.55 Å resolution. By combining the structural data with enzymatic and mutagenesis studies, we derive a conformational two-state model of bacterial collagenolysis, in which the recognition and unraveling of collagen microfibrils into triple helices as well as the unwinding of the latter go hand in hand with collagenase opening and closing.
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33
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Eckhard U, Brandstetter H. Polycystic kidney disease-like domains of clostridial collagenases and their role in collagen recruitment. Biol Chem 2011; 392:1039-45. [PMID: 21871007 DOI: 10.1515/bc.2011.099] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Bacterial collagenases exhibit a multimodular domain organization. While the N-terminal collagenase unit harbors the catalytic zinc and suffices to degrade peptidic substrates, collagen substrates come in different types, explaining the requirement for accessory domains such as polycystic kidney disease (PKD)-like domains for efficient catalysis. How the recognition and unfolding of (micro-)fibrillar or triple-helical collagen is accomplished are only poorly understood. Here, we present the crystal structure of the PKD-like domain of collagenase G from Clostridium histolyticum. The β-barrel structure reveals a two-tier architecture, connected by kinked hinge segments. Together with sheet extension as a generic oligomerization mechanism, this explains the cooperativity among accessory domains as well as their adaptivity to varying substrates.
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Affiliation(s)
- Ulrich Eckhard
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Billrothstraße 11, A-5020 Salzburg, Austria
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34
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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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Cloning of a novel collagenase gene from the gram-negative bacterium Grimontia (Vibrio) hollisae 1706B and its efficient expression in Brevibacillus choshinensis. J Bacteriol 2011; 193:3049-56. [PMID: 21515782 DOI: 10.1128/jb.01528-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The collagenase gene was cloned from Grimontia (Vibrio) hollisae 1706B, and its complete nucleotide sequence was determined. Nucleotide sequencing showed that the open reading frame was 2,301 bp in length and encoded an 84-kDa protein of 767 amino acid residues. The deduced amino acid sequence contains a putative signal sequence and a zinc metalloprotease consensus sequence, the HEXXH motif. G. hollisae collagenase showed 60 and 59% amino acid sequence identities to Vibrio parahaemolyticus and Vibrio alginolyticus collagenase, respectively. In contrast, this enzyme showed < 20% sequence identity with Clostridium histolyticum collagenase. When the recombinant mature collagenase, which consisted of 680 amino acids with a calculated molecular mass of 74 kDa, was produced by the Brevibacillus expression system, a major gelatinolytic protein band of ~ 60 kDa was determined by zymographic analysis. This result suggested that cloned collagenase might undergo processing after secretion. Moreover, the purified recombinant enzyme was shown to possess a specific activity of 5,314 U/mg, an ~ 4-fold greater activity than that of C. histolyticum collagenase.
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Drummond IA. Polycystins, focal adhesions and extracellular matrix interactions. Biochim Biophys Acta Mol Basis Dis 2011; 1812:1322-6. [PMID: 21396443 DOI: 10.1016/j.bbadis.2011.03.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Accepted: 03/02/2011] [Indexed: 11/29/2022]
Abstract
Polycystic kidney disease is the most common heritable disease in humans. In addition to epithelial cysts in the kidney, liver and pancreas, patients with autosomal dominant polycystic kidney disease (ADPKD) also suffer from abdominal hernia, intracranial aneurysm, gastrointestinal cysts, and cardiac valvular defects, conditions often associated with altered extracellular matrix production or integrity. Despite more than a decade of work on the principal ADPKD genes, PKD1 and PKD2, questions remain about the basis of cystic disease and the role of extracellular matrix in ADPKD pathology. This review explores the links between polycystins, focal adhesions, and extracellular matrix gene expression. These relationships suggest roles for polycystins in cell-matrix mechanosensory signaling that control matrix production and morphogenesis. This article is part of a Special Issue entitled: Polycystic Kidney Disease.
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