1
|
Cui X, Fu Z, Wang H, Yu W, Han F. Cloning and characterization of a hyaluronate lyase EsHyl8 from Escherichia sp. A99. Protein Expr Purif 2024; 223:106551. [PMID: 38997076 DOI: 10.1016/j.pep.2024.106551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/30/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Hyaluronidase, an enzyme that degrades hyaluronic acid (HA), is utilized in clinical settings to facilitate drug diffusion, manage extravasation, and address injection-related complications linked to HA-based fillers. In this study, a novel hyaluronate lyase EsHyl8 was cloned, expressed, and characterized from Escherichia sp. A99 of human intestinal origin. This lyase belongs to polysaccharide lyase (PL) family 8, and showed specific activity towards HA. EsHyl8 exhibited optimal degradation at 40 °C and pH 6.0. EsHyl8 exhibited a high activity of 376.32 U/mg among hyaluronidases of human gut microorganisms. EsHyl8 was stable at 37 °C and remained about 70 % of activity after incubation at 37 °C for 24 h, demonstrating excellent thermostability. The activity of EsHyl8 was inhibited by Zn2+, Cu2+, Fe3+, and SDS. EsHyl8 was an endo-type enzyme whose end-product was unsaturated disaccharide. This study enhances our understanding of hyaluronidases from human gut microorganisms.
Collapse
Affiliation(s)
- Xiuli Cui
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Zheng Fu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Hainan Wang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Wengong Yu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Feng Han
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China.
| |
Collapse
|
2
|
Rabapane KJ, Matambo TS. Profiling the dynamic adaptations of CAZyme-Producing microorganisms in the gastrointestinal tract of South African goats. Heliyon 2024; 10:e37508. [PMID: 39290285 PMCID: PMC11407064 DOI: 10.1016/j.heliyon.2024.e37508] [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: 10/09/2023] [Revised: 08/25/2024] [Accepted: 09/04/2024] [Indexed: 09/19/2024] Open
Abstract
The gastrointestinal tract of goats serves as a habitat for anaerobic microbial populations that work together to break down complex plant material, including lignocellulose. This study explored the microbial diversity and metabolic profiles across different gastrointestinal tract compartments. Significant diversity differences among the compartments were observed (ANOSIM p < 0.006), with the abomasum showing a distinct species composition and a decreased alpha diversity (Mann-Whitney/Kruskal-Wallis test p = 0.00096), possibly due to its acidic environment. Dominant microbial phyla included Proteobacteria, Bacteroidetes, and Firmicutes, with Proteobacteria being the most prevalent in the abomasum (50.06 %). Genera like Proteus and Bacteroides were particularly prominent in the rumen and reticulum, highlighting their significant role in feed degradation and fermentation processes. Over 65 % of genes at Kyoto Encyclopedia of Genes and Genomes level 1 were involved in metabolism with significant xenobiotic biodegradation in the abomasum. The dbCAN2 search identified Glycoside Hydrolases as the most prevalent CAZyme class (79 %), followed by Glycosyltransferases, Polysaccharide Lyases, and Carbohydrate Esterases, with Carbohydrate-Binding Modules and Auxiliary Activities accounting for 1 % of the hits. Higher CAZyme abundance was observed in the reticulum and omasum compartments, possibly due to MAGs diversity. In conclusion, the gastrointestinal tract of South African goats harbors diverse CAZyme classes, with Glycoside Hydrolases predominating. Interestingly, higher CAZyme abundance in specific compartments suggested compartmentalized microbial activity, reflecting adaptation to dietary substrates.
Collapse
Affiliation(s)
- Kgodiso J Rabapane
- Centre of Competence in Environmental Biotechnology, Department of Environmental Science, University of South Africa's College of Agriculture and Environmental Science, Cnr Pioneer and Christian De Wet Roads, Private Bag X6, Florida, 1710, South Africa
- Institute for Catalysis and Energy Solutions, University of South Africa's College of Science, Engineering, and Technology, Cnr Pioneer and Christian De Wet Roads, Private Bag X6, Florida, 1710, South Africa
| | - Tonderayi S Matambo
- Centre of Competence in Environmental Biotechnology, Department of Environmental Science, University of South Africa's College of Agriculture and Environmental Science, Cnr Pioneer and Christian De Wet Roads, Private Bag X6, Florida, 1710, South Africa
| |
Collapse
|
3
|
Fu Y, Fu Z, Yu J, Wang H, Zhang Y, Liu M, Wang X, Yu W, Han F. Biochemical Characterization of Hyaluronate Lyase CpHly8 from an Intestinal Microorganism Clostridium perfringens G1121. Appl Biochem Biotechnol 2024:10.1007/s12010-024-05025-y. [PMID: 39235659 DOI: 10.1007/s12010-024-05025-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 09/06/2024]
Abstract
Hyaluronic acid (HA) is an important component of extracellular matrices (ECM) and a linear polysaccharide involved in various physiological and pathological processes within the biological system. Several pathogens exploit HA degradation within the extracellular matrix to facilitate infection. While many intestinal microorganisms play significant roles in HA utilization in the human body, there remains a scarcity of related studies. This paper addressed this gap by screening intestinal microorganisms capable of degrading HA, resulting in the isolation of Clostridium perfringens G1121, which had been demonstrated the ability to degrade HA. Subsequent genome sequencing and analysis of C. perfringens G1121 revealed its utilization of the polysaccharide utilization loci of HA (PULHA), which was obtained by horizontal gene transfer. The PULHA contains a sequence encoding a hyaluronic acid-specific degradation enzyme designated CpHly8, belonging to polysaccharide lyase family 8. The specific activity of CpHly8 towards HA was 142.98 U/mg, with the optimum reaction temperature and pH observed at 50℃ and 6.0, respectively. The final product of HA degradation by CpHly8 was unsaturated hyaluronic acid disaccharide. Moreover, subcutaneous diffusion experiments with trypan blue in mice revealed that CpHly8 effectively promoted subcutaneous diffusion and sustained its effects long-term, suggesting its potential application as an adjunct in drug delivery. Overall, our study enriches our understanding of intestinal microbial degradation of HA, provides new evidence for horizontal gene transfer among intestinal microorganisms, and confirms that CpHly8 is a promising candidate for intestinal microbial hyaluronidase.
Collapse
Affiliation(s)
- Yongqing Fu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Zheng Fu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Jing Yu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Hainan Wang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Yuzhu Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Mei Liu
- School of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266071, China
| | - Xiaolei Wang
- School of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266071, China
| | - Wengong Yu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Feng Han
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China.
| |
Collapse
|
4
|
Wardman JF, Withers SG. Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening. RSC Chem Biol 2024; 5:595-616. [PMID: 38966674 PMCID: PMC11221537 DOI: 10.1039/d4cb00024b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) constitute a diverse set of enzymes that catalyze the assembly, degradation, and modification of carbohydrates. These enzymes have been fashioned into potent, selective catalysts by millennia of evolution, and yet are also highly adaptable and readily evolved in the laboratory. To identify and engineer CAZymes for different purposes, (ultra)high-throughput screening campaigns have been frequently utilized with great success. This review provides an overview of the different approaches taken in screening for CAZymes and how mechanistic understandings of CAZymes can enable new approaches to screening. Within, we also cover how cutting-edge techniques such as microfluidics, advances in computational approaches and synthetic biology, as well as novel assay designs are leading the field towards more informative and effective screening approaches.
Collapse
Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
| |
Collapse
|
5
|
Pandey S, Berger BW, Acharya R. Structural Analyses of Substrate-pH Activity Pairing Observed across Diverse Polysaccharide Lyases. Biochemistry 2023; 62:2775-2790. [PMID: 37620757 DOI: 10.1021/acs.biochem.3c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Anionic polysaccharides found in nature are functionally and structurally diverse, and so are the polysaccharide lyases (PLs) that catalyze their degradation. Atomic superposition of various PL folds according to their cleavable substrate structure confirms the occurrence of structural convergence at PL active sites. This suggests that various PL folds have emerged to cleave a particular class of anionic polysaccharide during the course of evolution. Whereas the structural and mechanistic similarity of PL active site has been highlighted in earlier studies, a detailed understanding regarding functional properties of this catalytic convergence remains an open question, especially the role of extrinsic factors such as pH in the context of substrate binding and catalysis. Our earlier structural and functional work on pH directed multisubstrate specificity of Smlt1473 inspired us to regroup PLs according to substrate type to analyze the pH dependence of their catalytic activity. Interestingly, we find that particular groups of substrates are cleaved in a particular pH range (acidic/neutral/basic) irrespective of PL fold, boosting the idea of functional convergence as well. On the basis of this observation, we set out to define structurally and computationally the key constituents of an active site among PL families. This study delineates the structural determinants of conserved "substrate-pH activity pairing" within and between PL families.
Collapse
Affiliation(s)
- Shubhant Pandey
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050 Odisha, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094 Maharashtra, India
| | - Bryan W Berger
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Rudresh Acharya
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050 Odisha, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094 Maharashtra, India
| |
Collapse
|
6
|
Zhou L, Meng Q, Zhang R, Jiang B, Liu X, Chen J, Zhang T. Characterization of a Novel Polysaccharide Lyase Family 5 Alginate Lyase with PolyM Substrate Specificity. Foods 2022; 11:3527. [PMID: 36360141 PMCID: PMC9655155 DOI: 10.3390/foods11213527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 09/19/2023] Open
Abstract
Alginate lyases (ALyases) have been widely applied in enzymatically degrading alginate for the preparation of alginate oligosaccharides (AOS), which possess a range of excellent physiological benefits including immunoregulatory, antivirus, and antidiabetic properties. Among the characterized ALyases, the number of ALyases with strict substrate specificity which possess potential in directed preparation of AOS is quite small. ALyases of polysaccharides lyase (PL) 5 family have been reported to perform poly-β-D-mannuronic acid (Poly-M) substrate specificity. However, there have been fewer studies with a comprehensive characterization and comparison of PL 5 family ALyases. In this study, a putative PL 5 family ALyase PMD was cloned from Pseudomonas mendocina and expressed in Escherichia coli. The novel ALyase presented maximum activity at 30 °C and pH 7.0. PMD displayed pH stability properties under the range of pH 5 to pH 9, which retained more than 80% relative activity, even when incubated for 48 h. Product analysis indicated that PMD might be an endolytic ALyase with strict Poly M substrate specificity and yield disaccharide and trisaccharide as main products. In addition, residues K58, R66, Y248, and R344 were proposed to be the potential key residues for catalysis via site-directed mutation. Detailed characterization of PMD and comprehensive comparisons could supply some different information about properties of PL 5 ALyases which might be helpful for its application in the directed production of AOS.
Collapse
Affiliation(s)
- Licheng Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Qing Meng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Ran Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiaoyong Liu
- Shandong Haizhibao Ocean Technology Co., Ltd., Weihai 264333, China
| | - Jingjing Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
7
|
Fluit AC, Bayjanov JR, Aguilar MD, Cantón R, Elborn S, Tunney MM, Scharringa J, Benaissa-Trouw BJ, Ekkelenkamp MB. Taxonomic position, antibiotic resistance and virulence factor production by Stenotrophomonas isolates from patients with cystic fibrosis and other chronic respiratory infections. BMC Microbiol 2022; 22:129. [PMID: 35549675 PMCID: PMC9097388 DOI: 10.1186/s12866-022-02466-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 02/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The potential pathogenic role of Stenotrophomonas maltophilia in lung disease and in particular in cystic fibrosis is unclear. To develop further understanding of the biology of this taxa, the taxonomic position, antibiotic resistance and virulence factors of S. maltophilia isolates from patients with chronic lung disease were studied. RESULTS A total of 111 isolates recovered between 2003 and 2016 from respiratory samples from patients in five different countries were included. Based on a cut-off of 95%, analysis of average nucleotide identity by BLAST (ANIb) showed that the 111 isolates identified as S. maltophilia by Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) belonged to S. maltophilia (n = 65), S. pavanii (n = 6) and 13 putative novel species (n = 40), which each included 1-5 isolates; these groupings coincided with the results of the 16S rDNA analysis, and the L1 and L2 ß-lactamase Neighbor-Joining phylogeny. Chromosomally encoded aminoglycoside resistance was identified in all S. maltophilia and S. pavani isolates, while acquired antibiotic resistance genes were present in only a few isolates. Nevertheless, phenotypic resistance levels against commonly used antibiotics, determined by standard broth microbroth dilution, were high. Although putative virulence genes were present in all isolates, the percentage of positive isolates varied. The Xps II secretion system responsible for the secretion of the StmPr1-3 proteases was mainly limited to isolates identified as S. maltophilia based on ANIb, but no correlation with phenotypic expression of protease activity was found. The RPF two-component quorum sensing system involved in virulence and antibiotic resistance expression has two main variants with one variant lacking 190 amino acids in the sensing region. CONCLUSIONS The putative novel Stenotrophomonas species recovered from patient samples and identified by MALDI-TOF/MS as S. maltophilia, differed from S. maltophilia in resistance and virulence genes, and therefore possibly in pathogenicity. Revision of the Stenotrophomonas taxonomy is needed in order to reliably identify strains within the genus and elucidate the role of the different species in disease.
Collapse
Affiliation(s)
- Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands.
| | - Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - María Díez Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.,Present Address: Servicio de Microbiología, Hospital Universitario La Princesa, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Stuart Elborn
- Queen's University Belfast, School of Pharmacy, Belfast, UK
| | | | - Jelle Scharringa
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - Barry J Benaissa-Trouw
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| |
Collapse
|
8
|
Performance of halotolerant bacteria associated with Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L. ameliorate tomato plant growth and tolerance to saline stress: from selective isolation to genomic analysis of potential determinants. World J Microbiol Biotechnol 2021; 38:16. [PMID: 34897563 DOI: 10.1007/s11274-021-03203-2] [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: 04/14/2021] [Accepted: 12/05/2021] [Indexed: 11/25/2022]
Abstract
The use of halotolerant beneficial plant-growth-promoting (PGP) bacteria is considered as a promising eco-friendly approach to improve the salt tolerance of cash crops. One strategy to enhance the possibility of obtaining stress-alleviating bacteria is to screen salt impacted soils. In this study, amongst the 40 endophytic bacteria isolated from the roots of Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L., 8 showed interesting NaCl tolerance in vitro. Their evaluation, through different tomato plant trials, permitted the isolate IS26 to be distinguished as the most effective seed inoculum for both plant growth promotion and mitigation of salt stress. On the basis of 16S rRNA gene sequence, the isolate was closely related to Stenotrophomonas rhizophila. It was then screened in vitro for multiple PGP traits and the strain-complete genome was sequenced and analysed to further decipher the genomic basis of the putative mechanisms underlying its osmoprotective and plant growth abilities. A remarkable number of genes putatively involved in mechanisms responsible for rhizosphere colonization, plant association, strong competition for nutrients, and the production of important plant growth regulator compounds, such as AIA and spermidine, were highlighted, as were substances protecting against stress, including different osmolytes like trehalose, glucosylglycerol, proline, and glycine betaine. By having genes related to complementary mechanisms of osmosensing, osmoregulation and osmoprotection, the strain confirmed its great capacity to adapt to highly saline environments. Moreover, the presence of various genes potentially related to multiple enzymatic antioxidant processes, able to reduce salt-induced overproduction of ROS, was also detected.
Collapse
|
9
|
Sindelar M, Jilkova J, Kubala L, Velebny V, Turkova K. Hyaluronidases and hyaluronate lyases: From humans to bacteriophages. Colloids Surf B Biointerfaces 2021; 208:112095. [PMID: 34507069 DOI: 10.1016/j.colsurfb.2021.112095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 08/05/2021] [Accepted: 09/01/2021] [Indexed: 12/26/2022]
Abstract
Hyaluronan is a non-sulfated negatively-charged linear polymer distributed in most parts of the human body, where it is located around cells in the extracellular matrix of connective tissues and plays an essential role in the organization of tissue architecture. Moreover, hyaluronan is involved in many biological processes and used in many clinical, cosmetic, pharmaceutic, and biotechnological applications worldwide. As interest in hyaluronan applications increases, so does interest in hyaluronidases and hyaluronate lyases, as these enzymes play a major part in hyaluronan degradation. Many hyaluronidases and hyaluronate lyases produced by eukaryotic cells, bacteria, and bacteriophages have so far been described and annotated, and their ability to cleave hyaluronan has been experimentally proven. These enzymes belong to several carbohydrate-active enzyme families, share very low sequence identity, and differ in their cleaving mechanisms and in their structural and functional properties. This review presents a summary of annotated and characterized hyaluronidases and hyaluronate lyases isolated from different sources belonging to distinct protein families, with a main focus on the binding and catalytic residues of the discussed enzymes in the context of their biochemical properties. In addition, the application potential of individual groups of hyaluronidases and hyaluronate lyases is evaluated.
Collapse
Affiliation(s)
- Martin Sindelar
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic; Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Jana Jilkova
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic; Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Lukas Kubala
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic; Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 65691, Brno, Czech Republic
| | - Vladimir Velebny
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic
| | - Kristyna Turkova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 65691, Brno, Czech Republic.
| |
Collapse
|
10
|
Pandey S, Mahanta P, Berger BW, Acharya R. Structural insights into the mechanism of pH-selective substrate specificity of the polysaccharide lyase Smlt1473. J Biol Chem 2021; 297:101014. [PMID: 34358563 PMCID: PMC8511899 DOI: 10.1016/j.jbc.2021.101014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/01/2022] Open
Abstract
Polysaccharide lyases (PLs) are a broad class of microbial enzymes that degrade anionic polysaccharides. Equally broad diversity in their polysaccharide substrates has attracted interest in biotechnological applications such as biomass conversion to value-added chemicals and microbial biofilm removal. Unlike other PLs, Smlt1473 present in the clinically relevant Stenotrophomonas maltophilia strain K279a demonstrates a wide range of pH-dependent substrate specificities toward multiple, diverse polysaccharides: hyaluronic acid (pH 5.0), poly-β-D-glucuronic (celluronic) acid (pH 7.0), poly-β-D-mannuronic acid, and poly-α-L-guluronate (pH 9.0). To decode the pH-driven multiple substrate specificities and selectivity in this single enzyme, we present the X-ray structures of Smlt1473 determined at multiple pH values in apo and mannuronate-bound states as well as the tetra-hyaluronate-docked structure. Our results indicate that structural flexibility in the binding site and N-terminal loop coupled with specific substrate stereochemistry facilitates distinct modes of entry for substrates having diverse charge densities and chemical structures. Our structural analyses of wild-type apo structures solved at different pH values (5.0–9.0) and pH-trapped (5.0 and 7.0) catalytically relevant wild-type mannuronate complexes (1) indicate that pH modulates the catalytic microenvironment for guiding structurally and chemically diverse polysaccharide substrates, (2) further establish that molecular-level fluctuation in the enzyme catalytic tunnel is preconfigured, and (3) suggest that pH modulates fluctuations resulting in optimal substrate binding and cleavage. Furthermore, our results provide key insight into how strategies to reengineer both flexible loop and regions distal to the active site could be developed to target new and diverse substrates in a wide range of applications.
Collapse
Affiliation(s)
- Shubhant Pandey
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050, Odisha, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Pranjal Mahanta
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050, Odisha, India
| | - Bryan W Berger
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States.
| | - Rudresh Acharya
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050, Odisha, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India.
| |
Collapse
|
11
|
Qiu Y, Ma Y, Huang Y, Li S, Xu H, Su E. Current advances in the biosynthesis of hyaluronic acid with variable molecular weights. Carbohydr Polym 2021; 269:118320. [PMID: 34294332 DOI: 10.1016/j.carbpol.2021.118320] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/05/2021] [Accepted: 06/06/2021] [Indexed: 12/26/2022]
Abstract
Hyaluronic acid (HA) is a naturally formed acidic mucopolysaccharide, with excellent moisturising properties and used widely in the medicine, cosmetics, and food industries. The industrial production of specific molecular weight HA has become imperative. Different biological activities and physiological functions of HA mainly depend on the degree of polymerisation. This article reviews the research status and development prospects of the green biosynthesis and molecular weight regulation of HA. There is an application-based prerequisite of specific molecular weight of HA that could be regulated either during the fermentation process or via a controlled HA degradation process. This work provides an important theoretical basis for the downstream efficient production of diversified HA, which will further accelerate the research applications of HA and provide a good scientific basis and method reference for the study of the molecular weight regulation of similar biopolymers.
Collapse
Affiliation(s)
- Yibin Qiu
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, PR China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, PR China; Yangzhou Rixing Bio-Tech Co., Ltd., Yangzhou 225601, PR China.
| | - Yanqin Ma
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Yanyan Huang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Sha Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Erzheng Su
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, PR China.
| |
Collapse
|
12
|
Abstract
Stenotrophomonas maltophilia is an opportunistic pathogen of significant concern to susceptible patient populations. This pathogen can cause nosocomial and community-acquired respiratory and bloodstream infections and various other infections in humans. Sources include water, plant rhizospheres, animals, and foods. Studies of the genetic heterogeneity of S. maltophilia strains have identified several new genogroups and suggested adaptation of this pathogen to its habitats. The mechanisms used by S. maltophilia during pathogenesis continue to be uncovered and explored. S. maltophilia virulence factors include use of motility, biofilm formation, iron acquisition mechanisms, outer membrane components, protein secretion systems, extracellular enzymes, and antimicrobial resistance mechanisms. S. maltophilia is intrinsically drug resistant to an array of different antibiotics and uses a broad arsenal to protect itself against antimicrobials. Surveillance studies have recorded increases in drug resistance for S. maltophilia, prompting new strategies to be developed against this opportunist. The interactions of this environmental bacterium with other microorganisms are being elucidated. S. maltophilia and its products have applications in biotechnology, including agriculture, biocontrol, and bioremediation.
Collapse
|
13
|
Draft genome of the glucose tolerant β-glucosidase producing rare Aspergillus unguis reveals complete cellulolytic machinery with multiple beta-glucosidase genes. Fungal Genet Biol 2021; 151:103551. [PMID: 33737204 DOI: 10.1016/j.fgb.2021.103551] [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: 10/29/2020] [Revised: 02/24/2021] [Accepted: 03/07/2021] [Indexed: 11/20/2022]
Abstract
Draft genome sequence of the glucose tolerant beta glucosidase (GT-BGL) producing rare fungus Aspergillus unguis NII 08,123 was generated through Next Generation Sequencing (NGS). The genome size of the fungus was estimated to be 37.1 Mb. A total of 3116 contigs were assembled using SPades, and 15,161 proteins were predicted using AUGUSTUS 3.1. Among them, 13,850 proteins were annotated using UniProt. Distribution of CAZyme genes specifically those encoding lignocellulose degrading enzymes were analyzed and compared with those from the industrial cellulase producer Trichoderma reesei in view of the huge differences in detectable enzyme activities between the fungi, despite the ability of A. unguis to grow on lignocellulose as sole carbon source. Full length gene sequence of the inducible GT-BGL could be identified through tracing back from peptide mass fingerprint. A total of 403 CAZymes were predicted from the genome, which includes 232 glycoside hydrolases (GHs), 12 carbohydrate esterases (CEs), 109 glycosyl transferases (GTs), 15 polysaccharide lyases (PLs), and 35 genes with auxiliary activities (AAs). The high level of zinc finger motif containing transcription factors could possibly hint a tight regulation of the cellulolytic machinery, which may also explain the low cellulase activities even when a complete repertoire of cellulase degrading enzyme genes are present in the fungus.
Collapse
|
14
|
Inoue A, Kudo M, Werner E, Ojima T. Identification and characterization of cellouronate (β-1,4-linked polyglucuronic acid) lyase from the scallop Mizuhopecten yessoensis. Carbohydr Polym 2021; 254:117306. [PMID: 33357872 DOI: 10.1016/j.carbpol.2020.117306] [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: 07/28/2020] [Revised: 10/11/2020] [Accepted: 10/20/2020] [Indexed: 10/23/2022]
Abstract
The semisynthetic polysaccharide cellouronate is a β-1,4-linked polyglucuronic acid prepared from regenerated cellulose by chemical oxidation. Here, we isolated a novel enzyme, MyAly, as a cellouronate lyase from a scallop Mizuhopecten yessoensis. Its optimum temperature, pH, and NaCl concentration for cellouronate degradation were determined to be 30 °C, 6.9, and 200-500 mM, respectively. MyAly endolytically degraded cellouronate into unsaturated di-, tri-, and tetrasaccharides with kcat of 31.1 s-1. MyAly also showed an alginate-degradation activity with a kcat value of 0.58 s-1. However, there was no significant difference in Km values between cellouronate and alginate. MyAly consisted of 280 amino acids and shared 36.5-44.1 % identity with known marine gastropod alginate lyases belonging to the polysaccharide lyase family 14. This is the first study to identify and characterize a cellouronate-degrading lyase from a marine organism, providing a better understanding of the biodegradability of the industrially important polysaccharide, cellouronate, in marine environments.
Collapse
Affiliation(s)
- Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Division of Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, Hokkaido, 041-8611, Japan.
| | - Masataka Kudo
- Laboratory of Marine Biotechnology and Microbiology, Division of Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, Hokkaido, 041-8611, Japan
| | - Elisa Werner
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, D-85748, Garching, Germany
| | - Takao Ojima
- Laboratory of Marine Biotechnology and Microbiology, Division of Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, Hokkaido, 041-8611, Japan
| |
Collapse
|
15
|
Dharani SR, Srinivasan R, Sarath R, Ramya M. Recent progress on engineering microbial alginate lyases towards their versatile role in biotechnological applications. Folia Microbiol (Praha) 2020; 65:937-954. [DOI: 10.1007/s12223-020-00802-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/16/2020] [Indexed: 11/30/2022]
|
16
|
Wong S, Eckersley EL, Berger B, Klauda JB. Probing the pH Effects on Sugar Binding to a Polysaccharide Lyase. J Phys Chem B 2019; 123:7123-7136. [DOI: 10.1021/acs.jpcb.9b04672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Evan L. Eckersley
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Bryan Berger
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | | |
Collapse
|
17
|
Badur AH, Plutz MJ, Yalamanchili G, Jagtap SS, Schweder T, Unfried F, Markert S, Polz MF, Hehemann JH, Rao CV. Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions. J Biol Chem 2017; 292:13056-13067. [PMID: 28592491 DOI: 10.1074/jbc.m117.787192] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 06/01/2017] [Indexed: 01/18/2023] Open
Abstract
Polysaccharide degradation by marine microbes represents one of the largest and most rapid heterotrophic transformations of organic matter in the environment. Microbes employ systems of complementary carbohydrate-specific enzymes to deconstruct algal or plant polysaccharides (glycans) into monosaccharides. Because of the high diversity of glycan substrates, the functions of these enzymes are often difficult to establish. One solution to this problem may lie within naturally occurring microdiversity; varying numbers of enzymes, due to gene loss, duplication, or transfer, among closely related environmental microbes create metabolic differences akin to those generated by knock-out strains engineered in the laboratory used to establish the functions of unknown genes. Inspired by this natural fine-scale microbial diversity, we show here that it can be used to develop hypotheses guiding biochemical experiments for establishing the role of these enzymes in nature. In this work, we investigated alginate degradation among closely related strains of the marine bacterium Vibrio splendidus One strain, V. splendidus 13B01, exhibited high extracellular alginate lyase activity compared with other V. splendidus strains. To identify the enzymes responsible for this high extracellular activity, we compared V. splendidus 13B01 with the previously characterized V. splendidus 12B01, which has low extracellular activity and lacks two alginate lyase genes present in V. splendidus 13B01. Using a combination of genomics, proteomics, biochemical, and functional screening, we identified a polysaccharide lyase family 7 enzyme that is unique to V. splendidus 13B01, secreted, and responsible for the rapid digestion of extracellular alginate. These results demonstrate the value of querying the enzymatic repertoires of closely related microbes to rapidly pinpoint key proteins with beneficial functions.
Collapse
Affiliation(s)
- Ahmet H Badur
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Matthew J Plutz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Geethika Yalamanchili
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Sujit Sadashiv Jagtap
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst Moritz Arndt University of Greifswald, D-17489 Greifswald, Germany
| | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst Moritz Arndt University of Greifswald, D-17489 Greifswald, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst Moritz Arndt University of Greifswald, D-17489 Greifswald, Germany
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jan-Hendrik Hehemann
- Center for Marine Environmental Sciences University of Bremen (MARUM), Bremen 28359, Germany; Max Planck-Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany.
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
| |
Collapse
|
18
|
Cho H, Huang X, Lan Piao Y, Eun Kim D, Yeon Lee S, Jeong Yoon E, Hee Park S, Lee K, Ho Jang C, Zhan CG. Molecular modeling and redesign of alginate lyase from Pseudomonas aeruginosa for accelerating CRPA biofilm degradation. Proteins 2016; 84:1875-1887. [PMID: 27676452 DOI: 10.1002/prot.25171] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/31/2016] [Accepted: 09/16/2016] [Indexed: 11/12/2022]
Abstract
Administration of an efficient alginate lyase (AlgL) or AlgL mutant may be a promising therapeutic strategy for treatment of cystic fibrosis patients with Pseudomonas aeruginosa infections. Nevertheless, the catalytic activity of wild-type AlgL is not sufficiently high. It is highly desired to design and discover an AlgL mutant with significantly improved catalytic efficiency against alginate substrates. For the purpose of identifying an AlgL mutant with significantly improved catalytic activity, in this study, we first constructed and validated a structural model of AlgL interacting with substrate, providing a better understanding of the interactions between AlgL and its substrate. Based on the modeling insights, further enzyme redesign and experimental testing led to discovery of AlgL mutants, including the K197D/K321A mutant, with significantly improved catalytic activities against alginate and acetylated alginate in ciprofloxacin-resistant P. aeruginosa (CRPA) biofilms. Further anti-biofilm activity assays have confirmed that the K197D/K321A mutant with piperacillin/tazobactam is indeed effective in degrading the CRPA biofilms. Co-administration of the potent mutant AlgL and an antibiotic (such as a nebulizer) could be effective for therapeutic treatment of CRPA-infected patients with cystic fibrosis. Proteins 2016; 84:1875-1887. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Hoon Cho
- Department of Polymer Science & Engineering, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Xiaoqin Huang
- Molecular Modeling and Biopharmaceutical Center, Center of Pharmaceutical Research and Innovation, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky
| | - Yu Lan Piao
- Department of Polymer Science & Engineering, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Da Eun Kim
- Department of Polymer Science & Engineering, Chosun University, Gwangju, 501-759, Republic of Korea
| | - So Yeon Lee
- Department of Polymer Science & Engineering, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Eun Jeong Yoon
- Department of Polymer Science & Engineering, Chosun University, Gwangju, 501-759, Republic of Korea
| | - So Hee Park
- Department of Polymer Science & Engineering, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Kyoung Lee
- Department of Microbiology, Changwon National University, Changwon, Kyongnam, 641-773, Republic of Korea
| | - Chul Ho Jang
- Department of Otolaryngology, Chonnam National University Medical School, Gwangju, 501-757, Republic of Korea
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center, Center of Pharmaceutical Research and Innovation, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky
| |
Collapse
|
19
|
Marine Microbiological Enzymes: Studies with Multiple Strategies and Prospects. Mar Drugs 2016; 14:md14100171. [PMID: 27669268 PMCID: PMC5082319 DOI: 10.3390/md14100171] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/04/2016] [Accepted: 09/14/2016] [Indexed: 11/16/2022] Open
Abstract
Marine microorganisms produce a series of promising enzymes that have been widely used or are potentially valuable for our daily life. Both classic and newly developed biochemistry technologies have been broadly used to study marine and terrestrial microbiological enzymes. In this brief review, we provide a research update and prospects regarding regulatory mechanisms and related strategies of acyl-homoserine lactones (AHL) lactonase, which is an important but largely unexplored enzyme. We also detail the status and catalytic mechanism of the main types of polysaccharide-degrading enzymes that broadly exist among marine microorganisms but have been poorly explored. In order to facilitate understanding, the regulatory and synthetic biology strategies of terrestrial microorganisms are also mentioned in comparison. We anticipate that this review will provide an outline of multiple strategies for promising marine microbial enzymes and open new avenues for the exploration, engineering and application of various enzymes.
Collapse
|
20
|
MacDonald LC, O’Keefe S, Parnes MF, MacDonald H, Stretz L, Templer SJ, Wong EL, Berger BW. A Secreted Ankyrin-Repeat Protein from Clinical Stenotrophomonas maltophilia Isolates Disrupts Actin Cytoskeletal Structure. ACS Infect Dis 2016; 2:62-70. [PMID: 27622948 DOI: 10.1021/acsinfecdis.5b00103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Stenotrophomonas maltophilia is an emerging, multidrug-resistant pathogen of increasing importance for the immunocompromised, including cystic fibrosis patients. Despite its significance as an emerging pathogen, relatively little is known regarding the specific factors and mechanisms that contribute to its pathogenicity. We identify and characterize a putative ankyrin-repeat protein (Smlt3054) unique to clinical S. maltophilia isolates that binds F-actin in vitro and co-localizes with actin in transfected HEK293a cells. Smlt3054 is endogenously expressed and secreted from clinical S. maltophilia isolates, but not an environmental isolate (R551-3). The in vitro binding of Smlt3054 to F-actin resulted in a thickening of the filaments as observed by TEM. Ectopic expression of Smlt3054-GFP exhibits strong co-localization with F-actin, with distinct, retrograde F-actin waves specifically associated with Smlt3054 in individual cells as well as formation of dense, internal inclusions at the expense of retrograde F-actin waves. Collectively, our results point to an interaction between Smlt3054 and F-actin. Furthermore, as a potentially secreted protein unique to clinical S. maltophilia isolates, Smlt3054 may serve as a starting point for understanding the mechanisms by which S. maltophilia has become an emergent pathogen.
Collapse
Affiliation(s)
- Logan C. MacDonald
- Program in Bioengineering and Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Sean O’Keefe
- Program in Bioengineering and Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Mei-Fan Parnes
- Program in Bioengineering and Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Hanlon MacDonald
- Program in Bioengineering and Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Lindsey Stretz
- Program in Bioengineering and Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Suzanne J. Templer
- Division of Infectious Disease, Lehigh Valley Health Network, 1250 South Cedar Crest Boulevard, Suite 200, Allentown, Pennsylvania 18103, United States
| | - Emily L. Wong
- Division of Infectious Disease, Lehigh Valley Health Network, 1250 South Cedar Crest Boulevard, Suite 200, Allentown, Pennsylvania 18103, United States
| | - Bryan W. Berger
- Program in Bioengineering and Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|
21
|
MacDonald LC, Weiler EB, Berger BW. Engineering broad-spectrum digestion of polyuronides from an exolytic polysaccharide lyase. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:43. [PMID: 26913076 PMCID: PMC4765187 DOI: 10.1186/s13068-016-0455-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/09/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Macroalgae represents a promising source of fermentable carbohydrates for use in the production of energy efficient biofuel. The primary carbohydrate in brown algae is the uronic acid-containing alginate, whereas green algae contains a significant amount of glucuronan. A necessary step in the conversion of these polyuronides to bioethanol is saccharification, which can be achieved by enzymatic or chemical degradation. RESULTS Polysaccharide lyases are a class of enzymes which cleave uronic acid-containing glycans via a β-elimination mechanism, acting both endo- and exolytically on their substrates. In the present work, we characterize a putative alginate lyase from Stenotrophomonas maltophilia K279a (Smlt2602) and describe a H208F mutant that, in addition to cleaving alginate-based substrates, displays significant, exolytic glucuronan activity. CONCLUSIONS To our knowledge this is the first polysaccharide lyase to act exolytically on glucuronan and is an attractive candidate for the broad-spectrum digestion of polyuronides into fermentable monomers.
Collapse
Affiliation(s)
- Logan C. MacDonald
- />Program in Bioengineering, Lehigh University, B320 Iacocca Hall, 111 Research Drive, Bethlehem, PA 18015 USA
| | - Elizabeth B. Weiler
- />Program in Bioengineering, Lehigh University, B320 Iacocca Hall, 111 Research Drive, Bethlehem, PA 18015 USA
| | - Bryan W. Berger
- />Program in Bioengineering, Lehigh University, B320 Iacocca Hall, 111 Research Drive, Bethlehem, PA 18015 USA
- />Department of Chemical and Biomolecular Engineering, Lehigh University, B320 Iacocca Hall, 111 Research Drive, Bethlehem, PA 18015 USA
| |
Collapse
|
22
|
Brummett AE, Schnicker NJ, Crider A, Todd JD, Dey M. Biochemical, Kinetic, and Spectroscopic Characterization of Ruegeria pomeroyi DddW--A Mononuclear Iron-Dependent DMSP Lyase. PLoS One 2015; 10:e0127288. [PMID: 25993446 PMCID: PMC4437653 DOI: 10.1371/journal.pone.0127288] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/13/2015] [Indexed: 11/19/2022] Open
Abstract
The osmolyte dimethylsulfoniopropionate (DMSP) is a key nutrient in marine environments and its catabolism by bacteria through enzymes known as DMSP lyases generates dimethylsulfide (DMS), a gas of importance in climate regulation, the sulfur cycle, and signaling to higher organisms. Despite the environmental significance of DMSP lyases, little is known about how they function at the mechanistic level. In this study we biochemically characterize DddW, a DMSP lyase from the model roseobacter Ruegeria pomeroyi DSS-3. DddW is a 16.9 kDa enzyme that contains a C-terminal cupin domain and liberates acrylate, a proton, and DMS from the DMSP substrate. Our studies show that as-purified DddW is a metalloenzyme, like the DddQ and DddP DMSP lyases, but contains an iron cofactor. The metal cofactor is essential for DddW DMSP lyase activity since addition of the metal chelator EDTA abolishes its enzymatic activity, as do substitution mutations of key metal-binding residues in the cupin motif (His81, His83, Glu87, and His121). Measurements of metal binding affinity and catalytic activity indicate that Fe(II) is most likely the preferred catalytic metal ion with a nanomolar binding affinity. Stoichiometry studies suggest DddW requires one Fe(II) per monomer. Electronic absorption and electron paramagnetic resonance (EPR) studies show an interaction between NO and Fe(II)-DddW, with NO binding to the EPR silent Fe(II) site giving rise to an EPR active species (g = 4.29, 3.95, 2.00). The change in the rhombicity of the EPR signal is observed in the presence of DMSP, indicating that substrate binds to the iron site without displacing bound NO. This work provides insight into the mechanism of DMSP cleavage catalyzed by DddW.
Collapse
Affiliation(s)
- Adam E. Brummett
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Nicholas J. Schnicker
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Alexander Crider
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Mishtu Dey
- Department of Chemistry, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
| |
Collapse
|
23
|
Garron ML, Cygler M. Uronic polysaccharide degrading enzymes. Curr Opin Struct Biol 2014; 28:87-95. [PMID: 25156747 DOI: 10.1016/j.sbi.2014.07.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/24/2014] [Accepted: 07/30/2014] [Indexed: 12/13/2022]
Abstract
In the past several years progress has been made in the field of structure and function of polysaccharide lyases (PLs). The number of classified polysaccharide lyase families has increased to 23 and more detailed analysis has allowed the identification of more closely related subfamilies, leading to stronger correlation between each subfamily and a unique substrate. The number of as yet unclassified polysaccharide lyases has also increased and we expect that sequencing projects will allow many of these unclassified sequences to emerge as new families. The progress in structural analysis of PLs has led to having at least one representative structure for each of the families and for two unclassified enzymes. The newly determined structures have folds observed previously in other PL families and their catalytic mechanisms follow either metal-assisted or Tyr/His mechanisms characteristic for other PL enzymes. Comparison of PLs with glycoside hydrolases (GHs) shows several folds common to both classes but only for the β-helix fold is there strong indication of divergent evolution from a common ancestor. Analysis of bacterial genomes identified gene clusters containing multiple polysaccharide cleaving enzymes, the Polysaccharides Utilization Loci (PULs), and their gene complement suggests that they are organized to process completely a specific polysaccharide.
Collapse
Affiliation(s)
- Marie-Line Garron
- Aix-Marseille University, AFMB UMR7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR7257, 163 Avenue de Luminy, 13288 Marseille, France
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.
| |
Collapse
|
24
|
MacDonald LC, Berger BW. Insight into the role of substrate-binding residues in conferring substrate specificity for the multifunctional polysaccharide lyase Smlt1473. J Biol Chem 2014; 289:18022-32. [PMID: 24808176 DOI: 10.1074/jbc.m114.571299] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Anionic polysaccharides are of growing interest in the biotechnology industry due to their potential pharmaceutical applications in drug delivery and wound treatment. Chemical composition and polymer length strongly influence the physical and biological properties of the polysaccharide and thus its potential industrial and medical applications. One promising approach to determining monomer composition and controlling the degree of polymerization involves the use of polysaccharide lyases, which catalyze the depolymerization of anionic polysaccharides via a β-elimination mechanism. Utilization of these enzymes for the production of custom-made oligosaccharides requires a high degree of control over substrate specificity. Previously, we characterized a polysaccharide lyase (Smlt1473) from Stenotrophomonas maltophilia k279a, which exhibited significant activity against hyaluronan (HA), poly-β-d-glucuronic acid (poly-GlcUA), and poly-β-d-mannuronic acid (poly-ManA) in a pH-regulated manner. Here, we utilize a sequence structure guided approach based on a homology model of Smlt1473 to identify nine putative substrate-binding residues and examine their effect on substrate specificity via site-directed mutagenesis. Interestingly, single point mutations H221F and R312L resulted in increased activity and specificity toward poly-ManA and poly-GlcUA, respectively. Furthermore, a W171A mutant nearly eliminated HA activity, while increasing poly-ManA and poly-GlcUA activity by at least 35%. The effect of these mutations was analyzed by comparison with the high resolution structure of Sphingomonas sp. A1-III alginate lyase in complex with poly-ManA tetrasaccharide and by taking into account the structural differences between HA, poly-GlcUA, and poly-ManA. Overall, our results demonstrate that even minor changes in active site architecture have a significant effect on the substrate specificity of Smlt1473, whose structural plasticity could be applied to the design of highly active and specific polysaccharide lyases.
Collapse
Affiliation(s)
| | - Bryan W Berger
- From the Program in Bioengineering and Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015
| |
Collapse
|