1
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Song P, Zhang X, Wang S, Xu W, Wang F, Fu R, Wei F. Microbial proteases and their applications. Front Microbiol 2023; 14:1236368. [PMID: 37779686 PMCID: PMC10537240 DOI: 10.3389/fmicb.2023.1236368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Proteases (proteinases or peptidases) are a class of hydrolases that cleave peptide chains in proteins. Endopeptidases are a type of protease that hydrolyze the internal peptide bonds of proteins, forming shorter peptides; exopeptidases hydrolyze the terminal peptide bonds from the C-terminal or N-terminal, forming free amino acids. Microbial proteases are a popular instrument in many industrial applications. In this review, the classification, detection, identification, and sources of microbial proteases are systematically introduced, as well as their applications in food, detergents, waste treatment, and biotechnology processes in the industry fields. In addition, recent studies on techniques used to express heterologous microbial proteases are summarized to describe the process of studying proteases. Finally, future developmental trends for microbial proteases are discussed.
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Affiliation(s)
- Peng Song
- College of Life Sciences, Liaocheng University, Liaocheng, China
- Shandong Aobo Biotech Co. Ltd., Liaocheng, China
- Jiangxi Zymerck Biotech Co. Ltd., Nanchang, China
| | - Xue Zhang
- College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Shuhua Wang
- Shandong Aobo Biotech Co. Ltd., Liaocheng, China
| | - Wei Xu
- College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Fei Wang
- College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Rongzhao Fu
- Jiangxi Zymerck Biotech Co. Ltd., Nanchang, China
| | - Feng Wei
- College of Life Sciences, Liaocheng University, Liaocheng, China
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2
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Saticioglu IB, Ay H, Altun S, Karakaya E, Gunduz ES, Aydogdu D, Yarim D, Erkek N, Duman M. Genomic insight into Myroides oncorhynchi sp. nov., a new member of the Myroides genus, isolated from the internal organ of rainbow trout (Oncorhynchus mykiss). Antonie Van Leeuwenhoek 2023; 116:291-302. [PMID: 36586048 DOI: 10.1007/s10482-022-01804-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/24/2022] [Indexed: 01/01/2023]
Abstract
The strain M-43T was isolated from the Oncorhynchus mykiss from a fish farm in Mugla, Turkey. Pairwise 16S rRNA gene sequence analysis was used to identify strain M-43T. The strain was a member of the genus Myroides sharing the highest 16S rRNA gene sequence identity levels of 98.7%, 98.3%, and 98.3% with the type strains of M. profundi D25T, M. odoratimimus subsp. odoratimimus CCUG 39352T and M. odoratimimus subsp. xuanwuensis DSM27251T, respectively. A polyphasic taxonomic approach including whole genome-based analyses was employed to confirm the taxonomic provenance of strain M-43T within the genus Myroides. The overall genome relatedness indices (OGRI) for strain M-43T compared with its most closely related type strains M. odoratimimus subsp. xuanwuensis DSM 27251T, M. profundi D25T, and M. odoratimimus subsp. odoratimimus ATCC BAA-634T, were calculated as 25.3%, 25.1%, and 25% for digital DNA-DNA hybridization (dDDH), 83.3%, 83.6%, and 83.4% for average nucleotide identity (ANI) analyses, respectively. The OGRI values between strain M-43T and its close neighbors confirmed that the strain represents a novel species in the genus Myroides. The DNA G + C content of the strain is 33.7%. The major fatty acids are iso-C15:0 and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0). The predominant polar lipids are phosphatidylethanolamine, an amino-lipid and five unidentified lipids. The major respiratory quinone is MK-6. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Myroides oncorhynchi sp. nov. is proposed, with M-43T as the type strain (JCM 34205T = KCTC 82265T).
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey.
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
| | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Enes Said Gunduz
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Duygu Aydogdu
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Dogancan Yarim
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Neslihan Erkek
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
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Ghattavi S, Homaei A. Marine enzymes: Classification and application in various industries. Int J Biol Macromol 2023; 230:123136. [PMID: 36621739 DOI: 10.1016/j.ijbiomac.2023.123136] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/23/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.
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Affiliation(s)
- Saba Ghattavi
- Fisheries Department, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
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Cui H, Zhou G, Ruan H, Zhao J, Hasi A, Zong N. Genome-Wide Identification and Analysis of the Maize Serine Peptidase S8 Family Genes in Response to Drought at Seedling Stage. PLANTS (BASEL, SWITZERLAND) 2023; 12:369. [PMID: 36679082 PMCID: PMC9865268 DOI: 10.3390/plants12020369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Subtilisin-like proteases (subtilases) are found in almost all plant species and are involved in regulating various biotic and abiotic stresses. Although the literature on subtilases in different plant species is vast, the gene function of the serine peptidase S8 family and its maize subfamily is still unknown. Here, a bioinformatics analysis of this gene family was conducted by describing gene structure, conserved motifs, phylogenetic relationships, chromosomal distributions, gene duplications, and promoter cis-elements. In total, we identified 18 ZmSPS8 genes in maize, distributed on 7 chromosomes, and half of them were hydrophilic. Most of these proteins were located at the cell wall and had similar secondary and tertiary structures. Prediction of cis-regulatory elements in promoters illustrated that they were mainly associated with hormones and abiotic stress. Maize inbred lines B73, Zheng58, and Qi319 were used to analyze the spatial-temporal expression patterns of ZmSPS8 genes under drought treatment. Seedling drought results showed that Qi319 had the highest percent survival after 14 d of withholding irrigation, while B73 was the lowest. Leaf relative water content (LRWC) declined more rapidly in B73 and to lower values, and the nitrotetrazolium blue chloride (NBT) contents of leaves were higher in Qi319 than in the other inbreds. The qPCR results indicated that 6 serine peptidase S8 family genes were positively or negatively correlated with plant tolerance to drought stress. Our study provides a detailed analysis of the ZmSPS8s in the maize genome and finds a link between drought tolerance and the family gene expression, which was established by using different maize inbred lines.
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Affiliation(s)
- Hongwei Cui
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010020, China
| | - Guyi Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongqiang Ruan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Agula Hasi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010020, China
| | - Na Zong
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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5
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Cheng JH, Zhao WX, Cao HY, Wang Z, Wang Y, Sheng Q, Chen Y, Wang P, Chen XL, Zhang YZ. Mechanistic Insight Into the Production of Collagen Oligopeptides by the S8 Family Protease A4095. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:603-614. [PMID: 36577515 DOI: 10.1021/acs.jafc.2c05402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Collagen oligopeptides have wide applications in foods, pharmaceuticals, cosmetics, and others due to their high bioactivities and bioavailability. The S8 family is the second-largest family of serine proteases. Several collagenolytic proteases from this family have been reported to have good potential in the preparation of collagen oligopeptides, however, the underlying mechanism remains unknown. A4095 was the most abundant S8 protease secreted by the protease-producing bacterium Anoxybacillus caldiproteolyticus 1A02591. Here, we characterized A4095 as an S8 collagenolytic protease and illustrated its structural basis to produce collagen oligopeptides. Protease A4095 preferentially hydrolyzed the Y-Gly peptide bonds in denatured bovine bone collagen, leading to high production (62.48% <1000 Da) of collagen oligopeptides. Structural and mutational analyses indicated that A4095 has a unique S1' substrate-binding pocket to preferentially bind Gly, which is the structural determinant for the high production of collagen oligopeptides. This study provides mechanistic insight into the advantage of the S8 collagenolytic proteases in preparing collagen oligopeptides.
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Affiliation(s)
- Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Wen-Xiao Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Hai-Yan Cao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Zhen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Yan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Qi Sheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Yin Chen
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Peng Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao266237, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao266237, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao266237, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
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6
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Sec-Dependent Secretion of Subtilase SptE in Haloarchaea Facilitates Its Proper Folding and Heterocatalytic Processing by Halolysin SptA Extracellularly. Appl Environ Microbiol 2022; 88:e0024622. [PMID: 35348390 DOI: 10.1128/aem.00246-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In response to high-salt conditions, haloarchaea export most secretory proteins through the Tat pathway in folded states; however, it is unclear why some haloarchaeal proteins are still routed to the Sec pathway. SptE is an extracellular subtilase of Natrinema sp. strain J7-2. Here, we found that SptE precursor comprises a Sec signal peptide, an N-terminal propeptide, a catalytic domain, and a long C-terminal extension (CTE) containing seven domains (C1 to C7). SptE is produced extracellularly as a mature form (M180) in strain J7-2 and a proform (ΔS) in the ΔsptA mutant strain, indicating that halolysin SptA mediates the conversion of the secreted proform into M180. The proper folding of ΔS is more efficient in the presence of NaCl than KCl. ΔS requires SptA for cleavage of the N-terminal propeptide and C-terminal C6 and C7 domains to generate M180, accompanied by the appearance of autoprocessing product M120 lacking C5. At lower salinities or elevated temperatures, M180 and M120 could be autoprocessed into M90, which comprises the catalytic and C1 domains and has a higher activity than M180. When produced in Haloferax volcanii, SptE could be secreted as a properly folded proform, but its variant (TSptE) with a Tat signal peptide does not fold properly and suffers from severe proteolysis extracellularly; meanwhile, TSptE is more inclined to aggregate intracellularly than SptE. Systematic domain deletion analysis reveals that the long CTE is an important determinant for secretion of SptE via the Sec rather than Tat pathway to prevent enzyme aggregation before secretion. IMPORTANCE While Tat-dependent haloarchaeal subtilases (halolysins) have been extensively studied, the information about Sec-dependent subtilases of haloarchaea is limited. Our results demonstrate that proper maturation of Sec-dependent subtilase SptE of Natrinema sp. strain J7-2 depends on the action of halolysin SptA from the same strain, yielding multiple hetero- and autocatalytic mature forms. Moreover, we found that the different extra- and intracellular salt types (NaCl versus KCl) of haloarchaea and the long CTE are extrinsic and intrinsic factors crucial for routing SptE to the Sec rather than Tat pathway. This study provides new clues about the secretion and adaptation mechanisms of Sec substrates in haloarchaea.
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7
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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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Fan S, Wang M, Ding W, Li YX, Zhang YZ, Zhang W. Scientific and technological progress in the microbial exploration of the hadal zone. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:127-137. [PMID: 37073349 PMCID: PMC10077178 DOI: 10.1007/s42995-021-00110-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/11/2021] [Indexed: 05/03/2023]
Abstract
The hadal zone is the deepest point in the ocean with a depth that exceeds 6000 m. Exploration of the biological communities in hadal zone began in the 1950s (the first wave of hadal exploration) and substantial advances have been made since the turn of the twenty-first century (the second wave of hadal exploration), resulting in a focus on the hadal sphere as a research hotspot because of its unique physical and chemical conditions. A variety of prokaryotes are found in the hadal zone. The mechanisms used by these prokaryotes to manage the high hydrostatic pressures and acquire energy from the environment are of substantial interest. Moreover, the symbioses between microbes and hadal animals have barely been studied. In addition, equipment has been developed that can now mimic hadal environments in the laboratory and allow cultivation of microbes under simulated in situ pressure. This review provides a brief summary of recent progress in the mechanisms by which microbes adapt to high hydrostatic pressures, manage limited energy resources and coexist with animals in the hadal zone, as well as technical developments in the exploration of hadal microbial life.
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Affiliation(s)
- Shen Fan
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Meng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Wei Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
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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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10
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A Novel Gelatinase from Marine Flocculibacter collagenilyticus SM1988: Characterization and Potential Application in Collagen Oligopeptide-Rich Hydrolysate Preparation. Mar Drugs 2022; 20:md20010048. [PMID: 35049903 PMCID: PMC8780967 DOI: 10.3390/md20010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
Although the S8 family in the MEROPS database contains many peptidases, only a few S8 peptidases have been applied in the preparation of bioactive oligopeptides. Bovine bone collagen is a good source for preparing collagen oligopeptides, but has been so far rarely applied in collagen peptide preparation. Here, we characterized a novel S8 gelatinase, Aa2_1884, from marine bacterium Flocculibacter collagenilyticus SM1988T, and evaluated its potential application in the preparation of collagen oligopeptides from bovine bone collagen. Aa2_1884 is a multimodular S8 peptidase with a distinct domain architecture from other reported peptidases. The recombinant Aa2_1884 over-expressed in Escherichia coli showed high activity toward gelatin and denatured collagens, but no activity toward natural collagens, indicating that Aa2_1884 is a gelatinase. To evaluate the potential of Aa2_1884 in the preparation of collagen oligopeptides from bovine bone collagen, three enzymatic hydrolysis parameters, hydrolysis temperature, hydrolysis time and enzyme-substrate ratio (E/S), were optimized by single factor experiments, and the optimal hydrolysis conditions were determined to be reaction at 60 ℃ for 3 h with an E/S of 400 U/g. Under these conditions, the hydrolysis efficiency of bovine bone collagen by Aa2_1884 reached 95.3%. The resultant hydrolysate contained 97.8% peptides, in which peptides with a molecular weight lower than 1000 Da and 500 Da accounted for 55.1% and 39.5%, respectively, indicating that the hydrolysate was rich in oligopeptides. These results indicate that Aa2_1884 likely has a promising potential application in the preparation of collagen oligopeptide-rich hydrolysate from bovine bone collagen, which may provide a feasible way for the high-value utilization of bovine bone collagen.
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11
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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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12
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Nishimura K, Higashiya K, Ueshima N, Kojima K, Takita T, Abe T, Takahashi T, Yasukawa K. Insight into the collagen-degrading activity of a serine protease in the latex of Ficus carica cultivar Masui Dauphine. Biosci Biotechnol Biochem 2021; 85:1147-1156. [PMID: 33580958 DOI: 10.1093/bbb/zbab025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/05/2021] [Indexed: 02/02/2023]
Abstract
Ficus carica produces, in addition to the cysteine protease ficin, a serine protease. Earlier study on a serine protease from F. carica cultivar Brown Turkey showed that it specifically degraded collagen. In this study, we characterized the collagenolytic activity of a serine protease in the latex of F. carica cultivar Masui Dauphine. The serine protease degraded denatured, but not undenatured, acid-solubilized type I collagen. It also degraded bovine serum albumin, while the collagenase from Clostridium histolyticum did not. These results indicated that the serine protease in Masui Dauphine is not collagen-specific. The protease was purified to homogeneity by two-dimensional gel electrophoresis, and its partial amino acid sequence was determined by liquid chromatography-tandem mass spectrometry. BLAST searches against the Viridiplantae (green plants) genome database revealed that the serine protease was a subtilisin-like protease. Our results contrast with the results of the earlier study stating that the serine protease from F. carica is collagen-specific.
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Affiliation(s)
- Kosaku Nishimura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.,Toyo Institute of Food Technology, Kawanishi, Hyogo, Japan
| | - Keisuke Higashiya
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Naoki Ueshima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Tatsuya Abe
- Toyo Institute of Food Technology, Kawanishi, Hyogo, Japan
| | - Toru Takahashi
- Toyo Institute of Food Technology, Kawanishi, Hyogo, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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13
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Li J, Cheng JH, Teng ZJ, Sun ZZ, He XY, Wang P, Shi M, Song XY, Chen XL, Zhang YZ, Tian X, Zhang XY. Taxonomic and Enzymatic Characterization of Flocculibacter collagenilyticus gen. nov., sp. nov., a Novel Gammaproteobacterium With High Collagenase Production. Front Microbiol 2021; 12:621161. [PMID: 33786038 PMCID: PMC8005334 DOI: 10.3389/fmicb.2021.621161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
Collagens from marine animals are an important component of marine organic nitrogen. Collagenase-producing bacteria and their collagenases play important roles in collagen degradation and organic nitrogen recycling in the ocean. However, only a few collagenase-producing marine bacteria have been so far discovered. Here, we reported the isolation and characterization of a collagenase-secreting bacterium, designated strain SM1988T, isolated from a green alga Codium fragile sample. Strain SM1988T is a Gram-negative, aerobic, oxidase-, and catalase-positive, unipolar flagellated, and rod-shaped bacterium capable of hydrolyzing casein, gelatin and collagens. Phylogenetic analysis revealed that strain SM1988T formed a distinct phylogenetic lineage along with known genera within the family Pseudoalteromonadaceae, with 16S rRNA gene sequence similarity being less than 93.3% to all known species in the family. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data, strain SM1988T was considered to represent a novel species in a novel genus in the family Pseudoalteromonadaceae, for which the name Flocculibacter collagenilyticus gen. nov., sp. nov. is proposed, with the type strain being SM1988T (= MCCC 1K04279T = KCTC 72761T). Strain SM1988T showed a high production of extracellular collagenases, which had high activity against both bovine collagen and codfish collagen. Biochemical tests combined with genome and secretome analyses indicated that the collagenases secreted by strain SM1988T are serine proteases from the MEROPS S8 family. These data suggest that strain SM1988T acts as an important player in marine collagen degradation and recycling and may have a promising potential in collagen resource utilization.
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Affiliation(s)
- Jian Li
- College of Life Science and Technology, Xinjiang University, Urumqi, China.,State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Zhong-Zhi Sun
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Yan He
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Peng Wang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xinmin Tian
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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14
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Cheng JH, Wang Y, Zhang XY, Sun ML, Zhang X, Song XY, Zhang YZ, Zhang Y, Chen XL. Characterization and Diversity Analysis of the Extracellular Proteases of Thermophilic Anoxybacillus caldiproteolyticus 1A02591 From Deep-Sea Hydrothermal Vent Sediment. Front Microbiol 2021; 12:643508. [PMID: 33796092 PMCID: PMC8007923 DOI: 10.3389/fmicb.2021.643508] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/24/2021] [Indexed: 11/13/2022] Open
Abstract
Protease-producing bacteria play key roles in the degradation of marine organic nitrogen. Although some deep-sea bacteria are found to produce proteases, there has been no report on protease-secreting Anoxybacillus from marine hydrothermal vent regions. Here, we analyzed the diversity and functions of the proteases, especially the extracellular proteases, of Anoxybacillus caldiproteolyticus 1A02591, a protease-secreting strain isolated from a deep-sea hydrothermal vent sediment of the East Pacific Ocean. Strain 1A02591 is a thermophilic bacterium with a strong protease-secreting ability, which displayed the maximum growth rate (0.139 h–1) and extracellular protease production (307.99 U/mL) at 55°C. Strain 1A02591 contains 75 putative proteases, including 65 intracellular proteases and 10 extracellular proteases according to signal peptide prediction. When strain 1A02591 was cultured with casein, 12 proteases were identified in the secretome, in which metalloproteases (6/12) and serine proteases (4/12) accounted for the majority, and a thermolysin-like protease of the M4 family was the most abundant, suggesting that strain 1A02591 mainly secreted a thermophilic metalloprotease. Correspondingly, the secreted proteases of strain 1A02591 showed the highest activity at the temperature as high as 70°C, and was inhibited 70% by metalloprotease inhibitor o-phenanthroline and 50% by serine protease inhibitor phenylmethylsulfonyl fluoride. The secreted proteases could degrade different proteins, suggesting the role of strain 1A02591 in organic nitrogen degradation in deep-sea hydrothermal ecosystem. These results provide the first insight into the proteases of an Anoxybacillus strain from deep-sea hydrothermal ecosystem, which is helpful in understanding the function of Anoxybacillus in the marine biogeochemical cycle.
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Affiliation(s)
- Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yan Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Yu Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Mei-Ling Sun
- College of Marine Life Sciences, and 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
| | - Xiao-Yan Song
- 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
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,College of Marine Life Sciences, and 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
| | - Yi Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, 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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15
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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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16
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Huan R, Huang J, Liu D, Wang M, Liu C, Zhang Y, Yi C, Xiao D, He H. Genome Sequencing of Mesonia algae K4-1 Reveals Its Adaptation to the Arctic Ocean. Front Microbiol 2019; 10:2812. [PMID: 31866978 PMCID: PMC6905171 DOI: 10.3389/fmicb.2019.02812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022] Open
Abstract
The special ecological environment of the Arctic has brought about a large number of salt-tolerant and psychrotolerant microorganisms. We isolated two culturable bacterial strains of the genus Mesonia; one from the Arctic ocean, Mesonia algae K4-1, and one from the tropical sea, Mesonia sp. HuA40. Our genome analysis and phenotypic experiments indicated that Mesonia algae K4-1 is a moderately halophilic and psychrophilic bacterium. Mesonia algae K4-1 can tolerate 3–14% NaCl and grow at a wide range of temperatures from 4 to 50°C. Mesonia sp. HuA40 is a mesophilic bacterium that can only grow with 3–9% NaCl. In addition, the salt adaptation strategy of Mesonia algae K4-1 accumulates organic osmolytes in the cell. RNA helicases, glutathione and organic compatible solutes may play important roles in maintaining the metabolism and physiological function of Mesonia algae K4-1 under cold stress. Moreover, the ability of Mesonia algae K4-1 to adapt to an oligotrophic marine environment is likely due to the synthesis of a large number of extracellular polysaccharides and the secretion of various families of extracellular proteases. This study systematically analyzed the relationship between genomic differentiation and environmental factors of the Mesonia genus and revealed the possible adaptation mechanism of Mesonia algae K4-1 in the extreme Arctic marine environment at the genomic level.
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Affiliation(s)
- Ran Huan
- School of Life Sciences, Central South University, Changsha, China
| | - JiaFeng Huang
- School of Life Sciences, Central South University, Changsha, China
| | - Dan Liu
- School of Life Sciences, Central South University, Changsha, China
| | - Meng Wang
- School of Life Sciences, Central South University, Changsha, China
| | - CongLing Liu
- School of Life Sciences, Central South University, Changsha, China
| | - YunQian Zhang
- School of Life Sciences, Central South University, Changsha, China
| | - CuiPing Yi
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, China
| | - Dong Xiao
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Xuzhou, China
| | - HaiLun He
- School of Life Sciences, Central South University, Changsha, China
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17
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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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18
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Chen XL, Yang JY, Zheng XY, Sheng Q, Wang L, Zhang YZ, Qin QL, Zhang XY. Tripeptides From Casein Are Signal Molecules to Induce the Expression of the Extracellular Protease MCP-01 Gene in Marine Bacterium Pseudoalteromonas sp. SM9913. Front Microbiol 2019; 10:1354. [PMID: 31293532 PMCID: PMC6606773 DOI: 10.3389/fmicb.2019.01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 01/29/2023] Open
Abstract
Microbial extracellular proteases play crucial roles in marine protein degradation and nitrogen recycling. Although a large number of marine bacteria are found to produce extracellular proteases, it is still unknown how marine bacteria respond to environmental proteins to activate the expression of genes encoding extracellular proteases. The inducing signal molecule for marine bacterial extracellular proteases has never been identified. In this study, we identified tripeptides as the inducing signal molecules for the extracellular protease MCP-01 of the deep-sea bacterium Pseudoalteromonas sp. SM9913. We found that casein, but not casamino acids, can induce the gene expression and synthesis of MCP-01, suggesting that peptides rather than amino acids derived from casein induce the gene expression and synthesis of MCP-01 in SM9913. Then, casein was hydrolyzed by SM9913 extracellular proteases, and the peptides with inducing effect were isolated and characterized. Finally, four tripeptides, SPP, RYP, RQF and FRQ, were shown to have significant inducing effect on the expression of MCP-01 gene, indicating that they are likely the inducing signal molecules for the expression of protease MCP-01 gene in SM9913. This study sheds light on the induction mechanism for the gene expression and biosynthesis of marine microbial extracellular proteases, which is helpful in better understanding the adaptation of bacteria to deep-sea sedimental environment.
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Affiliation(s)
- Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jin-Yu Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Xiao-Yu Zheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi Sheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Lei Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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19
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Abstract
The streamlining hypothesis is usually used to explain the genomic reduction events in free-living bacteria like SAR11. However, we find that the genomic reduction phenomenon in the bacterial genus Idiomarina is different from that in SAR11. Therefore, we propose a new hypothesis to explain genomic reduction in this genus based on trophic specialization that could result in genomic reduction, which would be not uncommon in nature. Not only can the trophic specialization hypothesis explain the genomic reduction in the genus Idiomarina, but it also sheds new light on our understanding of the genomic reduction processes in other free-living bacterial lineages. The streamlining hypothesis is generally used to explain the genomic reduction events related to the small genome size of free-living bacteria like marine bacteria SAR11. However, our current understanding of the correlation between bacterial genome size and environmental adaptation relies on too few species. It is still unclear whether there are other paths leading to genomic reduction in free-living bacteria. The genome size of marine free-living bacteria of the genus Idiomarina belonging to the order Alteromonadales (Gammaproteobacteria) is much smaller than the size of related genomes from bacteria in the same order. Comparative genomic and physiological analyses showed that the genomic reduction pattern in this genus is different from that of the classical SAR11 lineage. Genomic reduction reconstruction and substrate utilization profile showed that Idiomarina spp. lost a large number of genes related to carbohydrate utilization, and instead they specialized on using proteinaceous resources. Here we propose a new hypothesis to explain genomic reduction in this genus; we propose that trophic specialization increasing the metabolic efficiency for using one kind of substrate but reducing the substrate utilization spectrum could result in bacterial genomic reduction, which would be not uncommon in nature. This hypothesis was further tested in another free-living genus, Kangiella, which also shows dramatic genomic reduction. These findings highlight that trophic specialization is potentially an important path leading to genomic reduction in some marine free-living bacteria, which is distinct from the classical lineages like SAR11.
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20
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Nguyen TH, Nguyen VD. Characterization and Applications of Marine Microbial Enzymes in Biotechnology and Probiotics for Animal Health. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 80:37-74. [PMID: 28215328 DOI: 10.1016/bs.afnr.2016.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Marine microorganisms have been recognized as potential sources of novel enzymes because they are relatively more stable than the corresponding enzymes derived from plants and animals. Enzymes from marine microorganisms also differ from homologous enzymes in terrestrial microorganisms based on salinity, pressure, temperature, and lighting conditions. Marine microbial enzymes can be used in diverse industrial applications. This chapter will focus on the biotechnological applications of marine enzymes and also their use as a tool of marine probiotics to improve host digestion (food digestion, food absorption, and mucus utilization) and cleave molecular signals involved in quorum sensing in pathogens to control disease in aquaculture.
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Affiliation(s)
- T H Nguyen
- Faculty of Food Technology, Nha Trang University, Nha Trang, Vietnam.
| | - V D Nguyen
- Institute of Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam.
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21
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Li HJ, Tang BL, Shao X, Liu BX, Zheng XY, Han XX, Li PY, Zhang XY, Song XY, Chen XL. Characterization of a New S8 serine Protease from Marine Sedimentary Photobacterium sp. A5-7 and the Function of Its Protease-Associated Domain. Front Microbiol 2016; 7:2016. [PMID: 28066343 PMCID: PMC5177683 DOI: 10.3389/fmicb.2016.02016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/01/2016] [Indexed: 11/13/2022] Open
Abstract
Bacterial extracellular proteases are important for bacterial nutrition and marine sedimentary organic nitrogen degradation. However, only a few proteases from marine sedimentary bacteria have been characterized. Some subtilases have a protease-associated (PA) domain inserted in the catalytic domain. Although structural analysis and deletion mutation suggests that the PA domain in subtilases is involved in substrate binding, direct evidence to support this function is still absent. Here, a protease, P57, secreted by Photobacterium sp. A5-7 isolated from marine sediment was characterized. P57 could hydrolyze casein, gelatin and collagen. It showed the highest activity at 40°C and pH 8.0. P57 is a new subtilase, with 63% sequence identity to the closest characterized protease. Mature P57 contains a catalytic domain and an inserted PA domain. The recombinant PA domain from P57 was shown to have collagen-binding ability, and Phe349 and Tyr432 were revealed to be key residues for collagen binding in the PA domain. This study first shows direct evidence that the PA domain of a subtilase can bind substrate, which provides a better understanding of the function of the PA domain of subtilases and bacterial extracellular proteases from marine sediment.
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Affiliation(s)
- Hui-Juan Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
- College of Chemical and Environmental Engineering, Shandong University of Science and TechnologyQingdao, China
| | - Bai-Lu Tang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xuan Shao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Bai-Xue Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiao-Yu Zheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiao-Xu Han
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
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22
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Yang J, Yu Y, Tang BL, Zhong S, Shi M, Xie BB, Zhang XY, Zhou BC, Zhang YZ, Chen XL. Pilot-Scale Production and Thermostability Improvement of the M23 Protease Pseudoalterin from the Deep Sea Bacterium Pseudoalteromonas sp. CF6-2. Molecules 2016; 21:molecules21111567. [PMID: 27869696 PMCID: PMC6273387 DOI: 10.3390/molecules21111567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/09/2016] [Accepted: 11/14/2016] [Indexed: 01/05/2023] Open
Abstract
Pseudoalterin is the most abundant protease secreted by the marine sedimental bacterium Pseudoalteromonas sp. CF6-2 and is a novel cold-adapted metalloprotease of the M23 family. Proteases of the M23 family have high activity towards peptidoglycan and elastin, suggesting their promising biomedical and biotechnological potentials. To lower the fermentive cost and improve the pseudoalterin production of CF6-2, we optimized the fermentation medium by using single factor experiments, added 0.5% sucrose as a carbon source, and lowered the usage of artery powder from 1.2% to 0.6%. In the optimized medium, pseudoalterin production reached 161.15 ± 3.08 U/mL, 61% greater than that before optimization. We further conducted a small-scale fermentation experiment in a 5-L fermenter and a pilot-scale fermentation experiment in a 50-L fermenter. Pseudoalterin production during pilot-scale fermentation reached 103.48 ± 8.64 U/mL, 77% greater than that before the medium was optimized. In addition, through single factor experiments and orthogonal tests, we developed a compound stabilizer for pseudoalterin, using medically safe sugars and polyols. This stabilizer showed a significant protective effect for pseudoalterin against enzymatic thermal denaturation. These results lay a solid foundation for the industrial production of pseudoalterin and the development of its biomedical and biotechnological potentials.
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Affiliation(s)
- Jie Yang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Yang Yu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Bai-Lu Tang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Shuai Zhong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China.
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.
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23
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Nascent Genomic Evolution and Allopatric Speciation of Myroides profundi D25 in Its Transition from Land to Ocean. mBio 2016; 7:e01946-15. [PMID: 26758181 PMCID: PMC4725012 DOI: 10.1128/mbio.01946-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A large amount of bacterial biomass is transferred from land to ocean annually. Most transferred bacteria should not survive, but undoubtedly some do. It is unclear what mechanisms these bacteria use in order to survive and even thrive in a new marine environment. Myroides profundi D25T, a member of the Bacteroidetes phylum, was isolated from deep-sea sediment of the southern Okinawa Trough near the China mainland and had high genomic sequence identity to and synteny with the human opportunistic pathogen Myroides odoratimimus. Phylogenetic and physiological analyses suggested that M. profundi recently transitioned from land to the ocean. This provided an opportunity to explore how a bacterial genome evolved to survive in a novel environment. Changes in the transcriptome were evaluated when both species were cultured under low-salinity conditions and then transferred to high-salinity conditions. Comparative genomic and transcriptomic analyses showed that M. profundi altered transcription regulation in the early stages of survival. In these stages, vertically inherited genes played a key role in the survival of M. profundi. The contribution of M. profundi unique genes, some possibly acquired by horizontal gene transfer (HGT), appeared relatively small, and expression levels of unique genes were diminished under the high-salinity conditions. We postulate that HGT genes might play an important role in longer-term adaptation. These results suggested that some human pathogens might have the ability to survive in and adapt to the marine environment, which may have important implications for public health control in coastal regions. Horizontal gene transfer (HGT) is considered to be important for bacteria to adapt to a different microhabitat. However, our results showed that vertically inherited genes might play more important roles than HGT genes in the nascent adaptation to the marine environment in the bacterium Myroides profundi, which has recently been transferred from land to ocean. M. profundi unique genes had low expression levels and were less regulated under high-salinity conditions, indicating that the contribution of HGT genes to survival of this bacterium under marine high-salinity conditions was limited. In the early adaptation stages, M. profundi apparently survived and adapted mainly by regulating the expression of inherited core genes. These results may explain in part why human pathogens can easily be detected in marine environments.
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24
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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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25
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Stokke R, Dahle H, Roalkvam I, Wissuwa J, Daae FL, Tooming-Klunderud A, Thorseth IH, Pedersen RB, Steen IH. Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm. Environ Microbiol 2015; 17:4063-77. [PMID: 26147346 DOI: 10.1111/1462-2920.12970] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/25/2015] [Accepted: 06/25/2015] [Indexed: 11/30/2022]
Abstract
Little is known about how lithoautotrophic primary production is connected to microbial organotrophic consumption in hydrothermal systems. Using a multifaceted approach, we analysed the structure and metabolic capabilities within a biofilm growing on the surface of a black smoker chimney in the Loki's Castle vent field. Imaging revealed the presence of rod-shaped Bacteroidetes growing as ectobionts on long, sheathed microbial filaments (> 100 μm) affiliated with the Sulfurovum genus within Epsilonproteobacteria. The filaments were composed of a thick (> 200 nm) stable polysaccharide, representing a substantial fraction of organic carbon produced by primary production. An integrated -omics approach enabled us to assess the metabolic potential and in situ metabolism of individual taxonomic and morphological groups identified by imaging. Specifically, we provide evidence that organotrophic Bacteroidetes attach to and glide along the surface of Sulfurovum filaments utilizing organic polymers produced by the lithoautotrophic Sulfurovum. Furthermore, in situ expression of acetyl-CoA synthetase by Sulfurovum suggested the ability to assimilate acetate, indicating recycling of organic matter in the biofilm. This study expands our understanding of the lifestyles of Epsilonproteobacteria in hydrothermal vents, their metabolic properties and co-operative interactions in deep-sea hydrothermal vent food webs.
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Affiliation(s)
- Runar Stokke
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Irene Roalkvam
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Juliane Wissuwa
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Frida Lise Daae
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Ingunn H Thorseth
- Centre for Geobiology.,Department of Earth Science, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Rolf B Pedersen
- Centre for Geobiology.,Department of Earth Science, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Ida Helene Steen
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
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26
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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: 74] [Impact Index Per Article: 8.2] [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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27
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Park BR, Zielke RA, Wierzbicki IH, Mitchell KC, Withey JH, Sikora AE. A metalloprotease secreted by the type II secretion system links Vibrio cholerae with collagen. J Bacteriol 2015; 197:1051-64. [PMID: 25561716 PMCID: PMC4336349 DOI: 10.1128/jb.02329-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/31/2014] [Indexed: 01/13/2023] Open
Abstract
Vibrio cholerae is autochthonous to various aquatic niches and is the etiological agent of the life-threatening diarrheal disease cholera. The persistence of V. cholerae in natural habitats is a crucial factor in the epidemiology of cholera. In contrast to the well-studied V. cholerae-chitin connection, scarce information is available about the factors employed by the bacteria for the interaction with collagens. Collagens might serve as biologically relevant substrates, because they are the most abundant protein constituents of metazoan tissues and V. cholerae has been identified in association with invertebrate and vertebrate marine animals, as well as in a benthic zone of the ocean where organic matter, including collagens, accumulates. Here, we describe the characterization of the V. cholerae putative collagenase, VchC, encoded by open reading frame VC1650 and belonging to the subfamily M9A peptidases. Our studies demonstrate that VchC is an extracellular collagenase degrading native type I collagen of fish and mammalian origin. Alteration of the predicted catalytic residues coordinating zinc ions completely abolished the protein enzymatic activity but did not affect the translocation of the protease by the type II secretion pathway into the extracellular milieu. We also show that the protease undergoes a maturation process with the aid of a secreted factor(s). Finally, we propose that V. cholerae is a collagenovorous bacterium, as it is able to utilize collagen as a sole nutrient source. This study initiates new lines of investigations aiming to uncover the structural and functional components of the V. cholerae collagen utilization program.
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Affiliation(s)
- Bo R Park
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Igor H Wierzbicki
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Kristie C Mitchell
- Department of Immunology and Microbiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jeffrey H Withey
- Department of Immunology and Microbiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
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28
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Su HN, Ran LY, Chen ZH, Qin QL, Shi M, Song XY, Chen XL, Zhang YZ, Xie BB. The ultrastructure of type I collagen at nanoscale: large or small D-spacing distribution? NANOSCALE 2014; 6:8134-8139. [PMID: 24922185 DOI: 10.1039/c4nr01268b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
D-Spacing is the most significant topographic feature of type I collagen fibril, and it is important for our understanding of the structure and function in collagens. Traditionally, the D-spacing of type I collagen fibril was shown to have a singular value of 67 nm, but recent works indicated that the D-spacing values have a large distribution of up to 10 nm when measured by atomic force microscopy. We found that this large distribution of D-spacing values mainly resulted from image drift during measurement. Note that the D-spacing was homogeneous in a single type I collagen fibril. Our statistical analysis indicated that the D-spacing values of type I collagen fibrils exhibited only a narrow distribution of 2.5 nm around the value of 67 nm. In addition, the D-spacing values of the collagen fibrils were nearly identical not only within a single fibril bundle, but also in different fibril bundles. The measurement of the D-spacing values of collagen may provide important structural information in many research areas such as collagen related diseases, construction of molecular model of collagen, and collagen fibrogenesis.
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Affiliation(s)
- Hai-Nan Su
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
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