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Arakawa K, Yanai J, Watanabe K. Study of the Ca2+-dependent gene expression of EuPrt, an extracellular metalloprotease produced by the psychro-tolerant bacterium Exiguobacterium undae Su-1. Biosci Biotechnol Biochem 2022; 86:1308-1317. [PMID: 35776951 DOI: 10.1093/bbb/zbac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/31/2022] [Indexed: 11/14/2022]
Abstract
The effect of a Ca2+ ion on the gene expression of an on-demand type of metalloprotease from psychrotrophic Exiguobacterium undae Su-1 (EuPrt) was studied. We first established a modified mM9 medium for strain Su-1 to examine its effect in more detail. Then, when the strain was cultured in mM9 medium and 1.0 mM CaCl2 was added, we detected the mature EuPrt and its precursor proteins via Western blotting analysis and found the relative protease activity and its transcription increased by 50-fold and 7-fold, respectively, at the peak. Furthermore, the intracellular concentration of Ca2+ ions was analyzed using inductively coupled plasma atomic emission spectroscopy (ICP-AES) with other metal ions along the growth of strain Su-1. The intracellular concentration of Ca2+ ion was found to increase as much as 3-fold in response to the addition of an extracellular Ca2+ ions, indicating that euPrt gene expression is regulated by sensing its intracellular concentration.
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Affiliation(s)
- Kiyoaki Arakawa
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto, Japan
| | - Junta Yanai
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto, Japan
| | - Kunihiko Watanabe
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto, Japan
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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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3
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Yamamoto F, Morisaka H, Ueda M, Watanabe K. Molecular characterization of a prolyl endopeptidase from a feather-degrading thermophile Meiothermus ruber H328. J Biochem 2020; 168:499-508. [PMID: 32597969 DOI: 10.1093/jb/mvaa069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/07/2020] [Indexed: 12/23/2022] Open
Abstract
Prolyl endopeptidase from an aerobic and Gram-negative thermophile Meiothermus ruber H328 (MrPEP) was purified in native and recombinant forms, but both preparations had comparable characteristics. Production of the native MrPEP was increased 10-fold by adding intact chicken feathers. The gene for MrPEP (mrH_2860) was cloned from the genome of strain H328 and found to have no signal sequence at the N-terminus. MrPEP is composed of two major domains: the β-propeller domain and the peptidase domain with a typical active site motif and catalytic triad. Based on extensive investigations with different types of peptide substrates and FRETS-25Xaa libraries, MrPEP showed strict preferences for Pro residue at the P1 position but broader preferences at the P2 and P3 positions in substrate specificity with stronger affinity for residues at the P3 position of substrate peptides that are longer than four residues in length. In conclusion, the molecular characterization of MrPEP resembles its animal counterparts more closely than bacterial counterparts in function and structure.
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Affiliation(s)
- Fumi Yamamoto
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Hironobu Morisaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo, Kyoto 606-8502, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo, Kyoto 606-8502, Japan
| | - Kunihiko Watanabe
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
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4
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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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5
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Abstract
The genus Geobacillus comprises a group of Gram-positive thermophilic bacteria, including obligate aerobes, denitrifiers, and facultative anaerobes that can grow over a range of 45-75°C. Originally classified as group five Bacillus spp., strains of Bacillus stearothermophilus came to prominence as contaminants of canned food and soon became the organism of choice for comparative studies of metabolism and enzymology between mesophiles and thermophiles. More recently, their catabolic versatility, particularly in the degradation of hemicellulose and starch, and rapid growth rates have raised their profile as organisms with potential for second-generation (lignocellulosic) biorefineries for biofuel or chemical production. The continued development of genetic tools to facilitate both fundamental investigation and metabolic engineering is now helping to realize this potential, for both metabolite production and optimized catabolism. In addition, this catabolic versatility provides a range of useful thermostable enzymes for industrial application. A number of genome-sequencing projects have been completed or are underway allowing comparative studies. These reveal a significant amount of genome rearrangement within the genus, the presence of large genomic islands encompassing all the hemicellulose utilization genes and a genomic island incorporating a set of long chain alkane monooxygenase genes. With G+C contents of 45-55%, thermostability appears to derive in part from the ability to synthesize protamine and spermine, which can condense DNA and raise its Tm.
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6
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Abstract
Bacterial collagenases are metalloproteinases involved in the degradation of the extracellular matrices of animal cells, due to their ability to digest native collagen. These enzymes are important virulence factors in a variety of pathogenic bacteria. Nonetheless, there is a lack of scientific consensus for a proper and well-defined classification of these enzymes and a vast controversy regarding the correct identification of collagenases. Clostridial collagenases were the first ones to be identified and characterized and are the reference enzymes for comparison of newly discovered collagenolytic enzymes. In this review we present the most recent data regarding bacterial collagenases and overview the functional and structural diversity of bacterial collagenases. An overall picture of the molecular diversity and distribution of these proteins in nature will also be given. Particular aspects of the different proteolytic activities will be contextualized within relevant areas of application, mainly biotechnological processes and therapeutic uses. At last, we will present a new classification guide for bacterial collagenases that will allow the correct and straightforward classification of these enzymes.
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Affiliation(s)
- Ana Sofia Duarte
- a Department of Biology and Cesam , University of Aveiro, Campus Universitario de Santiago , Aveiro , Portugal
| | - Antonio Correia
- a Department of Biology and Cesam , University of Aveiro, Campus Universitario de Santiago , Aveiro , Portugal
| | - Ana Cristina Esteves
- a Department of Biology and Cesam , University of Aveiro, Campus Universitario de Santiago , Aveiro , Portugal
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7
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Sakamoto T, Otokawa T, Kono R, Shigeri Y, Watanabe K. A C69-family cysteine dipeptidase from Lactobacillus farciminis JCM1097 possesses strong Gly-Pro hydrolytic activity. J Biochem 2013; 154:419-27. [PMID: 23986487 DOI: 10.1093/jb/mvt069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dipeptide Gly-Pro, a hard-to-degrade and collagenous peptide, is thought to be hydrolysed by prolidases that can work on various X-Pro dipeptides. Here, we found an entirely different type of dipeptidase from Lactobacillus farciminis JCM1097 that cleaves Gly-Pro far more efficiently and with higher specificity than prolidases, and then investigated its properties by use of a recombinant enzyme. Although L. farciminis dipeptidase was expressed in the form of an inclusion body in Escherichia coli at 37 °C, it was smoothly over-expressed in a soluble form at a lower temperature. The maximal Gly-Pro hydrolytic activity was attained in E. coli at 30 °C. In contrast to prolidases that are metallopeptidases showing the modest or marginal activity toward Gly-Pro, this L. farciminis dipeptidase belongs to the cysteine peptidase family C69. Lactobacillus farciminis dipeptidase occurs in cytoplasm and utilizes the side chain of an amino-terminal cysteine residue to perform the nucleophilic attack on the target amide bond between Gly-Pro after processing eight amino acid residues at the N-terminus. Furthermore, L. farciminis dipeptidase is potent enough to synthesize Gly-Pro from Gly and Pro by a reverse reaction. These novel properties could be revealed by virtue of the success in preparing recombinant enzymes in higher yield and in a stable form.
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Affiliation(s)
- Takuma Sakamoto
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University; and Health Research Institute, National Institute of Advanced Industrial Science and Technology
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8
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Nakano H, Hosokawa A, Tagawa R, Inaka K, Ohta K, Nakatsu T, Kato H, Watanabe K. Crystallization and preliminary X-ray crystallographic analysis of Pz peptidase B from Geobacillus collagenovorans MO-1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:757-759. [PMID: 22750857 PMCID: PMC3388914 DOI: 10.1107/s1744309112018969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 04/27/2012] [Indexed: 06/01/2023]
Abstract
Pz peptidase B is an intracellular M3 metallopeptidase that is found together with Pz peptidase A in the thermophile Geobacillus collagenovorans MO-1 and recognizes collagen-specific tripeptide units (-Gly-Pro-X-). These peptidases have low homology in their primary structures; however, their cleavage patterns towards peptide substrates are similar. In this work, Pz peptidase B was crystallized using the counter-diffusion method. Data were collected to a resolution of 1.6 Å at 100 K from a crystal obtained in the Japanese Experiment Module (JEM; also known as `Kibo') at the International Space Station (ISS). The crystal belonged to the trigonal space group P3(1)21, with unit-cell parameters a = b = 87.64, c = 210.5 Å. A complete data set was also obtained from crystals of selenomethionine-substituted protein.
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Affiliation(s)
- Hiroaki Nakano
- Department of Pharmacy, Hyogo University of Health Sciences, 1-3-6 Minatojima, Chuo, Kobe 650-8530, Japan
| | - Allin Hosokawa
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Ryuji Tagawa
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences Inc., 170-1 Tsutsui-cho, Yamatokoriyama, Nara 639-1123, Japan
| | - Kazunori Ohta
- Space Environment Utilization Center, Japan Aerospace Exploration Agency (JAXA), 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Toru Nakatsu
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan
| | - Hiroaki Kato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan
| | - Kunihiko Watanabe
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
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9
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Kawasaki A, Nakano H, Hosokawa A, Nakatsu T, Kato H, Watanabe K. The exquisite structure and reaction mechanism of bacterial Pz-peptidase A toward collagenous peptides: X-ray crystallographic structure analysis of PZ-peptidase a reveals differences from mammalian thimet oligopeptidase. J Biol Chem 2010; 285:34972-80. [PMID: 20817732 PMCID: PMC2966111 DOI: 10.1074/jbc.m110.141838] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 06/30/2010] [Indexed: 11/06/2022] Open
Abstract
Pz-peptidase A, from the thermophilic bacterium Geobacillus collagenovorans MO-1, hydrolyzes a synthetic peptide substrate, 4-phenylazobenzyloxycarbonyl-Pro-Leu-Gly-Pro-D-Arg (Pz-PLGPR), which contains a collagen-specific tripeptide sequence, -Gly-Pro-X-, but does not act on collagen proteins themselves. The mammalian enzyme, thimet oligopeptidase (TOP), which has comparable functions with bacterial Pz-peptidases but limited identity at the primary sequence level, has recently been subjected to x-ray crystallographic analysis; however, no crystal structure has yet been reported for complexes of TOP with substrate analogues. Here, we report crystallization of recombinant Pz-peptidase A in complex with two phosphinic peptide inhibitors (PPIs) that also function as inhibitors of TOP and determination of the crystal structure of these complexes at 1.80-2.00 Å resolution. The most striking difference between Pz-peptidase A and TOP is that there is no channel running the length of bacterial protein. Whereas the structure of TOP resembles an open bivalve, that of Pz-peptidase A is closed and globular. This suggests that collagenous peptide substrates enter the tunnel at the top gateway of the closed Pz-peptidase A molecule, and reactant peptides are released from the bottom gateway after cleavage at the active site located in the center of the tunnel. One of the two PPIs, PPI-2, which contains the collagen-specific sequence, helped to clarify the exquisite structure and reaction mechanism of Pz-peptidase A toward collagenous peptides. This study describes the mode of substrate binding and its implication for the mammalian enzymes.
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Affiliation(s)
- Akio Kawasaki
- From the Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Hiroaki Nakano
- the Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan, and
- the Department of Pharmacy, Hyogo University of Health Sciences, 1-3-6 Minatojima, Chuo, Kobe 650-8530, Japan
| | - Allin Hosokawa
- From the Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Toru Nakatsu
- the Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan, and
| | - Hiroaki Kato
- the Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan, and
| | - Kunihiko Watanabe
- From the Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
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10
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Enzymatic degradation of fibroin fiber by a fibroinolytic enzyme of Brevibacillus thermoruber YAS-1. J Biosci Bioeng 2009; 108:211-5. [DOI: 10.1016/j.jbiosc.2009.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 04/03/2009] [Accepted: 04/04/2009] [Indexed: 11/21/2022]
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11
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Matsui T, Yamada Y, Mitsuya H, Shigeri Y, Yoshida Y, Saito Y, Matsui H, Watanabe K. Sustainable and practical degradation of intact chicken feathers by cultivating a newly isolated thermophilic Meiothermus ruber H328. Appl Microbiol Biotechnol 2009; 82:941-50. [PMID: 19194700 DOI: 10.1007/s00253-009-1880-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 01/16/2009] [Accepted: 01/17/2009] [Indexed: 02/05/2023]
Affiliation(s)
- Tatsunobu Matsui
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto, 606-8522, Japan
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12
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Zhao GY, Chen XL, Zhao HL, Xie BB, Zhou BC, Zhang YZ. Hydrolysis of insoluble collagen by deseasin MCP-01 from deep-sea Pseudoalteromonas sp. SM9913: collagenolytic characters, collagen-binding ability of C-terminal polycystic kidney disease domain, and implication for its novel role in deep-sea sedimentary particulate organic nitrogen degradation. J Biol Chem 2008; 283:36100-7. [PMID: 18977758 DOI: 10.1074/jbc.m804438200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Collagens are the most abundant proteins in marine animals and their degradation is important for the recycling of marine nitrogen. However, it is rather unclear how marine collagens are degraded because few marine collagenolytic proteases are studied in detail. Deseasins are a new type of multidomain subtilases. Here, the collagenolytic activity of deseasin MCP-01, the type example of deseasins, was studied. MCP-01 had broad substrate specificity to various type collagens from terrestrial and marine animals. It completely decomposed insoluble collagen into soluble peptides and amino acids, and was more prone to degrade marine collagen than terrestrial collagen. Thirty-seven cleavage sites of MCP-01 on bovine collagen chains were elucidated, showing the cleavage is various but specific. As the main extracellular cold-adapted protease from deep-sea bacterium Pseudoalteromonas sp. SM9913, MCP-01 displayed high activity at low temperature and alkaline range. Our data also showed that the C-terminal polycystic kidney disease (PKD) domain of MCP-01 was able to bind insoluble collagen and facilitate the insoluble collagen digestion by MCP-01. Site-directed mutagenesis demonstrated that Trp-36 of the PKD domain played a key role in its binding to insoluble collagen. It is the first time that the structure and function of a marine collagenolytic protease, deseasin MCP-01, has been studied in detail. Moreover, the PKD domain was experimentally proven to bind to insoluble protein for the first time. These results imply that MCP-01 would play an important role in the degradation of deep-sea sedimentary particulate organic nitrogen.
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Affiliation(s)
- Guo-Yan Zhao
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
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13
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Miyake R, Kawamoto J, Wei YL, Kitagawa M, Kato I, Kurihara T, Esaki N. Construction of a low-temperature protein expression system using a cold-adapted bacterium, Shewanella sp. strain Ac10, as the host. Appl Environ Microbiol 2007; 73:4849-56. [PMID: 17526788 PMCID: PMC1951021 DOI: 10.1128/aem.00824-07] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A recombinant protein expression system working at low temperatures is expected to be useful for the production of thermolabile proteins. We constructed a low-temperature expression system using an Antarctic cold-adapted bacterium, Shewanella sp. strain Ac10, as the host. We evaluated the promoters for proteins abundantly produced at 4 degrees C in this bacterium to express foreign proteins. We used 27 promoters and a broad-host-range vector, pJRD215, to produce beta-lactamase in Shewanella sp. strain Ac10. The maximum yield was obtained when the promoter for putative alkyl hydroperoxide reductase (AhpC) was used and the recombinant cells were grown to late stationary phase. The yield was 91 mg/liter of culture at 4 degrees C and 139 mg/liter of culture at 18 degrees C. We used this system to produce putative peptidases, PepF, LAP, and PepQ, and a putative glucosidase, BglA, from a psychrophilic bacterium, Desulfotalea psychrophila DSM12343. We obtained 48, 7.1, 28, and 5.4 mg/liter of culture of these proteins, respectively, in a soluble fraction. The amounts of PepF and PepQ produced by this system were greater than those produced by the Escherichia coli T7 promoter system.
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Affiliation(s)
- Ryoma Miyake
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
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14
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Kawasaki A, Nakano H, Tsujimoto Y, Matsui H, Shimizu T, Nakatsu T, Kato H, Watanabe K. Crystallization and preliminary X-ray crystallographic studies of Pz peptidase A from Geobacillus collagenovorans MO-1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:142-4. [PMID: 17277461 PMCID: PMC2330125 DOI: 10.1107/s174430910700334x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Accepted: 01/22/2007] [Indexed: 11/10/2022]
Abstract
Pz peptidase A is an intracellular M3 metallopeptidase found in the thermophile Geobacillus collagenovorans MO-1 that recognizes collagen-specific tripeptide units (Gly-Pro-Xaa). Pz peptidase A shares common reactions with mammalian thimet oligopeptidase (TOP) and neurolysin, but has extremely low primary sequence identity to these enzymes. In this work, Pz peptidase A was cocrystallized with a phosphine peptide inhibitor (PPI) that selectively inhibits TOP and neurolysin. The crystals belong to space group P2(1), with unit-cell parameters a = 56.38, b = 194.15, c = 59.93 A, beta = 106.22 degrees . This is the first crystallographic study of an M3 family peptidase-PPI complex.
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Affiliation(s)
- Akio Kawasaki
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Hiroaki Nakano
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan
| | - Yoshiyuki Tsujimoto
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Hiroshi Matsui
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Tetsuya Shimizu
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan
| | - Toru Nakatsu
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan
| | - Hiroaki Kato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan
| | - Kunihiko Watanabe
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
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15
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Itoi Y, Horinaka M, Tsujimoto Y, Matsui H, Watanabe K. Characteristic features in the structure and collagen-binding ability of a thermophilic collagenolytic protease from the thermophile Geobacillus collagenovorans MO-1. J Bacteriol 2006; 188:6572-9. [PMID: 16952949 PMCID: PMC1595469 DOI: 10.1128/jb.00767-06] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A collagen-degrading thermophile, Geobacillus collagenovorans MO-1, extracellularly produces a collagenolytic protease with a large molecular mass. Complete nucleotide sequencing of this gene after gene cloning revealed that the collagenolytic protease is a member of the subtilisin family of serine proteases and consists of a signal sequence for secretion, a prosequence for maturation, a catalytic region, 14 direct repeats of 20 amino acids at the C terminus, and a region with unknown function intervening between the catalytic region and the numerous repeats. Since the unusual repeats are most likely to be cleaved in the secreted form of the enzyme, the intervening region was investigated to determine whether it participates in collagen binding to facilitate collagen degradation. It was found that the mature collagenolytic protease containing the intervening region at the C terminus bound collagen but not the other insoluble proteins, elastin and keratin. Furthermore, the intervening region fused with glutathione S-transferase showed a collagen-binding ability comparable to that of the mature collagenolytic protease. The collagen-binding ability was finally attributed to two-thirds of the intervening region which is rich in beta-strands and is approximately 35 kDa in molecular mass. In the collagenolytic protease from strain MO-1, hydrogen bonds most likely predominate over the hydrophobic interaction for collagen binding, since a higher concentration of NaCl released collagen from the enzyme surface but a nonionic detergent could not. To the best of our knowledge, this is the first report of a thermophilic collagenolytic protease containing the collagen-binding segment.
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Affiliation(s)
- Yuichi Itoi
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
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16
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Suzuki Y, Tsujimoto Y, Matsui H, Watanabe K. Decomposition of extremely hard-to-degrade animal proteins by thermophilic bacteria. J Biosci Bioeng 2006; 102:73-81. [PMID: 17027867 DOI: 10.1263/jbb.102.73] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 05/15/2006] [Indexed: 11/17/2022]
Abstract
Hard-to-degrade animal proteins are ubiquitously present throughout animal bodies. Enormous numbers of these proteins generated in the meat industry are converted to industrial wastes, the disposal of which is tremendously difficult. Most hard-to-degrade animal proteins are currently disposed of by incineration; however, this method has ecological disadvantages in terms of an apparent energy loss and the production of a large amount of carbon dioxide. As a result, an innovative solution to these problems has been sought. In this review, we focus on the degradation of three hard-to-degrade animal proteins (extracellular matrix proteins, collagen in particular, keratin, and prion proteins) and discuss the decomposing capability of thermophilic bacteria. These proteins are strongly resistant to proteinases because of their structural features; therefore, new approaches employing bacterial proteases with strong activity and broad specificity are required for practical application.
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Affiliation(s)
- Yasunori Suzuki
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
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