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Unuofin JO, Odeniyi OA, Majengbasan OS, Igwaran A, Moloantoa KM, Khetsha ZP, Iwarere SA, Daramola MO. Chitinases: expanding the boundaries of knowledge beyond routinized chitin degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-33728-6. [PMID: 38789707 DOI: 10.1007/s11356-024-33728-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/15/2024] [Indexed: 05/26/2024]
Abstract
Chitinases, enzymes that degrade chitin, have long been studied for their role in various biological processes. They play crucial roles in the moulting process of invertebrates, the digestion of chitinous food, and defense against chitin-bearing pathogens. Additionally, chitinases are involved in physiological functions in crustaceans, such as chitinous food digestion, moulting, and stress response. Moreover, chitinases are universally distributed in organisms from viruses to mammals and have diverse functions including tissue degradation and remodeling, nutrition uptake, pathogen invasion, and immune response regulation. The discovery of these diverse functions expands our understanding of the biological significance and potential applications of chitinases. However, recent research has shown that chitinases possess several other functions beyond just chitin degradation. Their potential as biopesticides, therapeutic agents, and tools for bioremediation underscores their significance in addressing global challenges. More importantly, we noted that they may be applied as bioweapons if ethical regulations regarding production, engineering and application are overlooked.
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Affiliation(s)
- John Onolame Unuofin
- Sustainable Energy and Environment Research Group (SEERG), Department of Chemical Engineering, Faculty of Engineering, Built Environment and Information Technology, University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa.
| | | | | | - Aboi Igwaran
- The Life Science Center Biology, School of Sciences and Technology, Örebro University, 701 82, Örebro, Sweden
| | - Karabelo MacMillan Moloantoa
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwazulu Natal, Private Bag X540001, Durban, 4000, South Africa
| | - Zenzile Peter Khetsha
- Department of Agriculture, Central University of Technology, Free State, Private Bag X20539, Bloemfontein, 9300, South Africa
| | - Samuel Ayodele Iwarere
- Sustainable Energy and Environment Research Group (SEERG), Department of Chemical Engineering, Faculty of Engineering, Built Environment and Information Technology, University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa
| | - Michael Olawale Daramola
- Sustainable Energy and Environment Research Group (SEERG), Department of Chemical Engineering, Faculty of Engineering, Built Environment and Information Technology, University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa
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2
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Kaur M, Nagpal M, Dhingra GA, Rathee A. Exploring chitin: novel pathways and structures as promising targets for biopesticides. Z NATURFORSCH C 2024; 0:znc-2024-0027. [PMID: 38760917 DOI: 10.1515/znc-2024-0027] [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: 02/01/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024]
Abstract
Chitin, the most prevalent polymer in nature, a significant structural polysaccharide that comes in second only to cellulose. Chitin is a crucial component of fungal cell walls and also present in many other creatures, such as viruses, plants, animals, insect exoskeletons, and crustacean shells. Chitin presents itself as a promising target for the development of biopesticides. It focuses on unraveling the unique structures and biochemical pathways associated with chitin, aiming to identify vulnerabilities that can be strategically leveraged for effective and environmentally sustainable pest control. It involves a comprehensive analysis of chitinase enzymes, chitin biosynthesis, and chitin-related processes across diverse organisms. By elucidating the molecular intricacies involved in chitin metabolism, this review seeks to unveil potential points of intervention that can disrupt essential biological processes in target pests without harming non-target species. This holistic approach to understanding chitin-related pathways aims to inform the design and optimization of biopesticides with enhanced specificity and reduced ecological impact. The outcomes of this study hold great promise for advancing innovative and eco-friendly pest management strategies. By targeting chitin structures and pathways, biopesticides developed based on these findings may offer a sustainable and selective alternative to conventional chemical pesticides, contributing to the ongoing efforts towards more environmentally conscious and effective pest control solutions.
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Affiliation(s)
- Malkiet Kaur
- 418665 University Institute of Pharma Sciences, Chandigarh University , Mohali, Punjab, India
| | - Manju Nagpal
- Chitkara College of Pharmacy, 154025 Chitkara University , Rajpura, Punjab, India
| | | | - Ankit Rathee
- 418665 University Institute of Pharma Sciences, Chandigarh University , Mohali, Punjab, India
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3
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Giraldo JD, García Y, Vera M, Garrido-Miranda KA, Andrade-Acuña D, Marrugo KP, Rivas BL, Schoebitz M. Alternative processes to produce chitin, chitosan, and their oligomers. Carbohydr Polym 2024; 332:121924. [PMID: 38431399 DOI: 10.1016/j.carbpol.2024.121924] [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: 11/30/2023] [Revised: 01/20/2024] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Abstract
Sustainable recovery of chitin and its derivatives from shellfish waste will be achieved when the industrial production of these polymers is achieved with a high control of their molecular structure, low costs, and acceptable levels of pollution. Therefore, the conventional chemical method for obtaining these biopolymers needs to be replaced or optimized. The goal of the present review is to ascertain what alternative methods are viable for the industrial-scale production of chitin, chitosan, and their oligomers. Therefore, a detailed review of recent literature was undertaken, focusing on the advantages and disadvantages of each method. The analysis of the existing data allows suggesting that combining conventional, biological, and alternative methods is the most efficient strategy to achieve sustainable production, preventing negative impacts and allowing for the recovery of high added-value compounds from shellfish waste. In conclusion, a new process for obtaining chitinous materials is suggested, with the potential of reducing the consumption of reagents, energy, and water by at least 1/10, 1/4, and 1/3 part with respect to the conventional process, respectively.
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Affiliation(s)
- Juan D Giraldo
- Escuela de Ingeniería Ambiental, Instituto de Acuicultura, Universidad Austral de Chile, Sede Puerto Montt, Balneario Pelluco, Los Pinos s/n, Chile.
| | - Yadiris García
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile
| | - Myleidi Vera
- Departamento de Polímeros, Facultad de Ciencias Químicas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Karla A Garrido-Miranda
- Center of Waste Management and Bioenergy, Scientific and Technological Bioresource Nucleus, BIOREN-UFRO, Universidad de la Frontera, Temuco 4811230, Chile; Agriaquaculture Nutritional Genomic Center (CGNA), Temuco 4780000, Chile
| | - Daniela Andrade-Acuña
- Centro de Docencia Superior en Ciencias Básicas, Universidad Austral de Chile, Sede Puerto Montt, Los Pinos s/n. Balneario Pelluco, Puerto Montt, Chile
| | - Kelly P Marrugo
- Departamento de Química Orgánica, Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; Centro de Investigaciones en Nanotecnología y Materiales Avanzados, CIEN-UC, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Bernabé L Rivas
- Universidad San Sebastián, Sede Concepción 4080871, Concepción, Chile
| | - Mauricio Schoebitz
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Campus Concepción, Casilla 160-C, Universidad de Concepción, Chile; Laboratory of Biofilms and Environmental Microbiology, Center of Biotechnology, Universidad de Concepción, Barrio Universitario s/n, Concepción, Chile
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Kumari R, Kumar M, Dadheech PK, Vivekanand V, Pareek N. Response surface optimization, purification, characterization and short-chain chitooligosaccharides production from an acidic, thermostable chitinase from Thermomyces dupontii. Int J Biol Macromol 2024; 267:131362. [PMID: 38583843 DOI: 10.1016/j.ijbiomac.2024.131362] [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: 07/21/2023] [Revised: 02/10/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Chitin, recovered in huge amounts from coastal waste, may biocatalytically valorized for utilization in food and biotech sectors. Conventional chemical-based conversion makes use of significant volumes of hazardous acid and alkali. Alternatively, enzymes offer better process control and generation of homogeneous products. Process variables were derived to achieve augmented levels of chitinase (3.8809 Ul-1 h-1) productivity from a novel thermophilic fungal strain Thermomyces dupontii, ITCC 9104 following incubation (96 h, 45 °C). An acidic thermostable chitinase TdChiT having molecular mass of 60 kDa has been purified. Optimal TdChiT activity has been demonstrated at 70 °C and pH 5. Notably decreased activity over a broad range of temperature and pH was observed following deglycosylation. Half-life, activation energy, Gibbs free energy, enthalpy and entropy for denaturation of TdChiT at its optimum temperature were 197.40 min, 105.48 kJ mol-1, 100.59 kJ mol-1, 102.64 kJ mol-1 and 5.95 J mol-1 K-1. TdChiT has specificity towards colloidal chitin and (GlcNAc)2-4. Metal ions viz. Mn2+, Ca2+ and Co2+ and nonionic surfactants notably enhanced chitinase activity. Thin layer chromatography analysis has revealed effective hydrolysis of colloidal chitin and (GlcNAc)2-4. TdChiT may potentially be employed for design of better, eco-friendly and less resource-intensive industrial procedures for upcycling of crustacean waste into value-added organonitrogens.
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Affiliation(s)
- Rajni Kumari
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan Bandarsindri, Kishangarh, Ajmer 305801, Rajasthan, India
| | - Manish Kumar
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan Bandarsindri, Kishangarh, Ajmer 305801, Rajasthan, India
| | - Pawan K Dadheech
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan Bandarsindri, Kishangarh, Ajmer 305801, Rajasthan, India
| | - V Vivekanand
- Centre for Energy and Environment, Malaviya National Institute of Technology, Jaipur 302017, Rajasthan, India
| | - Nidhi Pareek
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan Bandarsindri, Kishangarh, Ajmer 305801, Rajasthan, India.
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Bhairamkar S, Kadam P, Anjulal H, Joshi A, Chaudhari R, Bagul D, Javdekar V, Zinjarde S. Comprehensive updates on the biological features and metabolic potential of the versatile extremophilic actinomycete Nocardiopsis dassonvillei. Res Microbiol 2024; 175:104171. [PMID: 37995890 DOI: 10.1016/j.resmic.2023.104171] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
Nocardiopsis dassonvillei prevails under harsh environmental conditions and the purpose of this review is to highlight its biological features and recent biotechnological applications. The organism prevails in salt-rich soils/marine systems and some strains endure extreme temperatures and pH. A few isolates are associated with marine organisms and others cause human diseases. Comparative genomic analysis indicates its versatility in producing biotechnologically relevant metabolites. Antimicrobial, cytotoxic, anticancer and growth promoting biomolecules are obtained from this organism. It also synthesizes biotechnologically important enzymes. Bioactive compounds and enzymes obtained from this actinomycete provide evidence regarding its metabolic competence and its potential economic value.
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Affiliation(s)
- Shivani Bhairamkar
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Pratik Kadam
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - H Anjulal
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Avani Joshi
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Riddhi Chaudhari
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Dimpal Bagul
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Vaishali Javdekar
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Smita Zinjarde
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India.
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6
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Qi Z, Lei B, Xiong M, Li W, Liao Y, Cai D, Ma X, Zhang R, Chen S. High-level production of chitinase by multi-strategy combination optimization in Bacillus licheniformis. World J Microbiol Biotechnol 2024; 40:181. [PMID: 38668833 DOI: 10.1007/s11274-024-03995-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
In view of the extensive potential applications of chitinase (ChiA) in various fields such as agriculture, environmental protection, medicine, and biotechnology, the development of a high-yielding strain capable of producing chitinase with enhanced activity holds significant importance. The objective of this study was to utilize the extracellular chitinase from Bacillus thuringiensis as the target, and Bacillus licheniformis as the expression host to achieve heterologous expression of ChiA with enhanced activity. Initially, through structural analysis and molecular dynamics simulation, we identified key amino acids to improve the enzymatic performance of chitinase, and the specific activity of chitinase mutant D116N/E118N was 48% higher than that of the natural enzyme, with concomitant enhancements in thermostability and pH stability. Subsequently, the expression elements of ChiA(D116N/E118N) were screened and modified in Bacillus licheniformis, resulting in extracellular ChiA activity reached 89.31 U/mL. Further efforts involved the successful knockout of extracellular protease genes aprE, bprA and epr, along with the gene clusters involved in the synthesis of by-products such as bacitracin and lichenin from Bacillus licheniformis. This led to the development of a recombinant strain, DW2△abelA, which exhibited a remarkable improvement in chitinase activity, reaching 145.56 U/mL. To further improve chitinase activity, a chitinase expression frame was integrated into the genome of DW2△abelA, resulting in a significant increas to 180.26 U/mL. Optimization of fermentation conditions and medium components further boosted shake flask enzyme activity shake flask enzyme activity, achieving 200.28 U/mL, while scale-up fermentation experiments yielded an impressive enzyme activity of 338.79 U/mL. Through host genetic modification, expression optimization and fermentation optimization, a high-yielding ChiA strain was successfully constructed, which will provide a solid foundation for the extracellular production of ChiA.
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Affiliation(s)
- Zhimin Qi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Bo Lei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Min Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Weijia Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Yongqing Liao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Ruibin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China.
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7
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Chaulagain D, Shamabadi NS, Leslie SA, Karig DK. From Natural Microbe Screening to Sustained Chitinase Activity in Exogenous Hosts. ACS Synth Biol 2024; 13:1165-1176. [PMID: 38587290 DOI: 10.1021/acssynbio.3c00637] [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] [Indexed: 04/09/2024]
Abstract
Genetic parts and hosts can be sourced from nature to realize new functions for synthetic biology or to improve performance in a particular application environment. Here, we proceed from the discovery and characterization of new parts to stable expression in new hosts with a particular focus on achieving sustained chitinase activity. Chitinase is a key enzyme for various industrial applications that require the breakdown of chitin, the second most abundant biopolymer on the earth. Diverse microbes exhibit chitinase activity, but for applications, the environmental conditions for optimal enzyme activity and microbe fitness must align with the application context. Achieving sustained chitinase activity under broad conditions in heterologous hosts has also proven difficult due to toxic side effects. Toward addressing these challenges, we first screen ocean water samples to identify microbes with chitinase activity. Next, we perform whole genome sequencing and analysis and select a chitinase gene for heterologous expression. Then, we optimize transformation methods for target hosts and introduce chitinase. Finally, to achieve robust function, we optimize ribosome binding sites and discover a beneficial promoter that upregulates chitinase expression in the presence of colloidal chitin in a sense-and-respond fashion. We demonstrate chitinase activity for >21 days in standard (Escherichia coli) and nonstandard (Roseobacter denitrificans) hosts. Besides enhancing chitinase applications, our pipeline is extendable to other functions, identifies natural microbes that can be used directly in non-GMO contexts, generates new parts for synthetic biology, and achieves weeks of stable activity in heterologous hosts.
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Affiliation(s)
- Diptee Chaulagain
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Narges S Shamabadi
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Skylar A Leslie
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - David K Karig
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
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Wang L, Xue M, Yan R, Xue J, Lu Z, Wen C. Insights into Chitin-Degradation Potential of Shewanella khirikhana JW44 with Emphasis on Characterization and Function of a Chitinase Gene SkChi65. Microorganisms 2024; 12:774. [PMID: 38674717 PMCID: PMC11052142 DOI: 10.3390/microorganisms12040774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/05/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
Chitin, a polymer of β-1,4-linked N-acetylglucosamine (GlcNAc), can be degraded into valuable oligosaccharides by various chitinases. In this study, the genome of Shewanella khirikhana JW44, displaying remarkable chitinolytic activity, was investigated to understand its chitin-degradation potential. A chitinase gene SkChi65 from this strain was then cloned, expressed, and purified to characterize its enzymatic properties and substrate hydrolysis. Genome analysis showed that, of the 14 genes related to chitin utilization in JW44, six belonged to glycoside hydrolase (GH) families because of their functional domains for chitin binding and catalysis. The recombinant chitinase SkChi65, consisting of 1129 amino acids, was identified as a member of the GH18 family and possessed two chitin-binding domains with a typical motif of [A/N]KWWT[N/S/Q] and one catalytic domain with motifs of DxxDxDxE, SxGG, YxR, and [E/D]xx[V/I]. SkChi65 was heterologously expressed as an active protein of 139.95 kDa best at 37 °C with 1.0 mM isopropyl-β-d-thiogalactopyranoside induction for 6 h. Purified SkChi65 displayed high stability over the ranges of 30-50 °C and pH 5.5-8.0 with optima at 40 °C and pH 7.0. The kinetic parameters Km, Vmax, and kcat of SkChi65 towards colloidal chitin were 27.2 μM, 299.2 μMs-1, and 10,203 s-1, respectively. In addition to colloidal chitin, SkChi65 showed high activity towards glycol chitosan and crystalline chitin. After analysis by thin-layer chromatography, the main products were N,N'-diacetylchitobiose, and GlcNAc with (GlcNAc)2-6 used as substrates. Collectively, SkChi65 could exhibit both exo- and endochitinase activities towards diverse substrates, and strain JW44 has a high potential for industrial application with an excellent capacity for chitin bioconversion.
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Affiliation(s)
- Ling Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ming Xue
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Rui Yan
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jiawei Xue
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhipeng Lu
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Chongqing Wen
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
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Zhou Z, Li Y, Shen Y, Zang X, Wang Q, Liu X, Wang Z. Integration of transcriptome and whole-genome re-sequencing analyses reveal growth-related candidate genes in Procambarus clarkii. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101198. [PMID: 38306949 DOI: 10.1016/j.cbd.2024.101198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/15/2024] [Accepted: 01/27/2024] [Indexed: 02/04/2024]
Abstract
Growth is a crucial economic trait of all aquaculture species. It is important to explore the molecular regulation on growth, which could help improve the growth rate of species. Mining the growth-related genes is the foundation for revealing its molecular regulation on growth. Presently, the molecular regulation of growth in Procambarus clarkii is not clear, and the study on exploring growth-related genes is limited. In this study, RNA-Seq was used to compare gene expression profiles of the individuals with different growth rates involved in four groups including Big Male (BM), Big Female (BF), Small male (SM), and Small Female (SF) from one P. clarkii family, and the analyses were performed in combination with sex. Meanwhile, whole-genome resequencing data was used to get growth-specific SNP (Single Nucleotide Polymorphism)/InDel (Insertion/Deletion) sites information. Totally, we identified 16,127 genes, of which 9065 were successfully annotated in the GO database. Among these, 1328 DEGs were identified in BM vs. SM, with 357 up-regulated and 971 down-regulated. Additionally, 3507 DEGs were identified in BF vs. SF, with 241 up-regulated and 3266 down-regulated. 96 DEGs were up-regulated and 820 DEGs were down-regulated in Growth-related Group. The expression levels of nine DEGs were validated by RT-qPCR to verify the analysis results of sequencing. 684,040 growth-related SNPs and 182,050 growth-related InDels were obtained after screened. These findings provide candidate growth-related genes and growth-specific SNP/InDel sites for regulation of growth traits in P. clarkii, and new insight into the molecular regulation of P. clarkii growth.
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Affiliation(s)
- Zihao Zhou
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanhe Li
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yudong Shen
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolei Zang
- Animal Husbandry and Fisheries Research Center, Guangdong Haid Group Co., Ltd., Guangzhou 511400, China.
| | - Qishuai Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaolong Liu
- Animal Husbandry and Fisheries Research Center, Guangdong Haid Group Co., Ltd., Guangzhou 511400, China.
| | - Zhengkai Wang
- Animal Husbandry and Fisheries Research Center, Guangdong Haid Group Co., Ltd., Guangzhou 511400, China.
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10
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Correa KCS, Facchinatto WM, Habitzreuter FB, Ribeiro GH, Rodrigues LG, Micocci KC, Campana-Filho SP, Colnago LA, Souza DHF. Activity of a Recombinant Chitinase of the Atta sexdens Ant on Different Forms of Chitin and Its Fungicidal Effect against Lasiodiplodia theobromae. Polymers (Basel) 2024; 16:529. [PMID: 38399907 PMCID: PMC10892911 DOI: 10.3390/polym16040529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
This study evaluates the activity of a recombinant chitinase from the leaf-cutting ant Atta sexdens (AsChtII-C4B1) against colloidal and solid α- and β-chitin substrates. 1H NMR analyses of the reaction media showed the formation of N-acetylglucosamine (GlcNAc) as the hydrolysis product. Viscometry analyses revealed a reduction in the viscosity of chitin solutions, indicating that the enzyme decreases their molecular masses. Both solid state 13C NMR and XRD analyses showed minor differences in chitin crystallinity pre- and post-reaction, indicative of partial hydrolysis under the studied conditions, resulting in the formation of GlcNAc and a reduction in molecular mass. However, the enzyme was unable to completely degrade the chitin samples, as they retained most of their solid-state structure. It was also observed that the enzyme acts progressively and with a greater activity on α-chitin than on β-chitin. AsChtII-C4B1 significantly changed the hyphae of the phytopathogenic fungus Lasiodiplodia theobromae, hindering its growth in both solid and liquid media and reducing its dry biomass by approximately 61%. The results demonstrate that AsChtII-C4B1 could be applied as an agent for the bioproduction of chitin derivatives and as a potential antifungal agent.
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Affiliation(s)
- Katia Celina Santos Correa
- Department of Chemistry, Federal University of Sao Carlos, 13565-905 Sao Carlos, Brazil; (K.C.S.C.); (L.G.R.); (K.C.M.)
| | - William Marcondes Facchinatto
- Aveiro Institute of Materials, CICECO, Department of Chemistry, University of Aveiro, St. Santiago, 3810-193 Aveiro, Portugal;
| | - Filipe Biagioni Habitzreuter
- Sao Carlos Institute of Chemistry, University of Sao Paulo, Ave. Trabalhador Sao-carlense 400, 13560-590 Sao Carlos, Brazil; (F.B.H.); (S.P.C.-F.)
| | - Gabriel Henrique Ribeiro
- Brazilian Corporation for Agricultural Research, Embrapa Instrumentation, St. XV de Novembro 1452, 13560-970 Sao Carlos, Brazil; (G.H.R.); (L.A.C.)
| | - Lucas Gomes Rodrigues
- Department of Chemistry, Federal University of Sao Carlos, 13565-905 Sao Carlos, Brazil; (K.C.S.C.); (L.G.R.); (K.C.M.)
| | - Kelli Cristina Micocci
- Department of Chemistry, Federal University of Sao Carlos, 13565-905 Sao Carlos, Brazil; (K.C.S.C.); (L.G.R.); (K.C.M.)
| | - Sérgio Paulo Campana-Filho
- Sao Carlos Institute of Chemistry, University of Sao Paulo, Ave. Trabalhador Sao-carlense 400, 13560-590 Sao Carlos, Brazil; (F.B.H.); (S.P.C.-F.)
| | - Luiz Alberto Colnago
- Brazilian Corporation for Agricultural Research, Embrapa Instrumentation, St. XV de Novembro 1452, 13560-970 Sao Carlos, Brazil; (G.H.R.); (L.A.C.)
| | - Dulce Helena Ferreira Souza
- Department of Chemistry, Federal University of Sao Carlos, 13565-905 Sao Carlos, Brazil; (K.C.S.C.); (L.G.R.); (K.C.M.)
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11
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Blazevic N, Rogic D, Pelajic S, Miler M, Glavcic G, Ratkajec V, Vrkljan N, Bakula D, Hrabar D, Pavic T. YKL-40 as a biomarker in various inflammatory diseases: A review. Biochem Med (Zagreb) 2024; 34:010502. [PMID: 38125621 PMCID: PMC10731731 DOI: 10.11613/bm.2024.010502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/04/2023] [Indexed: 12/23/2023] Open
Abstract
YKL-40 or Chitinase-3-Like Protein 1 (CHI3L1) is a highly conserved glycoprotein that binds heparin and chitin in a non-enzymatic manner. It is a member of the chitinase protein family 18, subfamily A, and unlike true chitinases, YKL-40 is a chitinase-like protein without enzymatic activity for chitin. Although its accurate function is yet unknown, the pattern of its expression in the normal and disease states suggests its possible engagement in apoptosis, inflammation and remodeling or degradation of the extracellular matrix. During an inflammatory response, YKL-40 is involved in a complicated interaction between host and bacteria, both promoting and attenuating immune response and potentially being served as an autoantigen in a vicious circle of autoimmunity. Based on its pathophysiology and mechanism of action, the aim of this review was to summarize research on the growing role of YKL-40 as a persuasive biomarker for inflammatory diseases' early diagnosis, prediction and follow-up (e.g., cardiovascular, gastrointestinal, endocrinological, immunological, musculoskeletal, neurological, respiratory, urinary, infectious) with detailed structural and functional background of YKL-40.
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Affiliation(s)
- Nina Blazevic
- Department of Gastroenterology and Hepatology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Dunja Rogic
- Department of Laboratory Diagnostics, University Hospital Center Zagreb, Zagreb, Croatia
| | - Stipe Pelajic
- Department of Gastroenterology and Hepatology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Marijana Miler
- Department of Clinical Chemistry, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Goran Glavcic
- Department of Surgery, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Valentina Ratkajec
- Department of Gastroenterology, General Hospital Virovitica, Virovitica, Croatia
| | - Nikolina Vrkljan
- Department of Internal Medicine, Intensive Care Unit, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Dejan Bakula
- Department of Gastroenterology and Hepatology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Davor Hrabar
- Department of Gastroenterology and Hepatology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Tajana Pavic
- Department of Gastroenterology and Hepatology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
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12
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Shobade SO, Zabotina OA, Nilsen-Hamilton M. Plant root associated chitinases: structures and functions. FRONTIERS IN PLANT SCIENCE 2024; 15:1344142. [PMID: 38362446 PMCID: PMC10867124 DOI: 10.3389/fpls.2024.1344142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024]
Abstract
Chitinases degrade chitin, a linear homopolymer of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc) residues found in the cell walls of fungi and the exoskeletons of arthropods. They are secreted by the roots into the rhizosphere, a complex and dynamic environment where intense nutrient exchange occurs between plants and microbes. Here we modeled, expressed, purified, and characterized Zea mays and Oryza sativa root chitinases, and the chitinase of a symbiotic bacterium, Chitinophaga oryzae 1303 for their activities with chitin, di-, tri-, and tetra-saccharides and Aspergillus niger, with the goal of determining their role(s) in the rhizosphere and better understanding the molecular mechanisms underlying plant-microbe interactions. We show that Zea mays basic endochitinase (ZmChi19A) and Oryza sativa chitinase (OsChi19A) are from the GH19 chitinase family. The Chitinophaga oryzae 1303 chitinase (CspCh18A) belongs to the GH18 family. The three enzymes have similar apparent K M values of (20-40 µM) for the substrate 4-MU-GlcNAc3. They vary in their pH and temperature optima with OsChi19A activity optimal between pH 5-7 and 30-40°C while ZmChi19A and CspCh18A activities were optimal at pH 7-9 and 50-60°C. Modeling and site-directed mutation of ZmChi19A identified the catalytic cleft and the active residues E147 and E169 strategically positioned at ~8.6Å from each other in the folded protein. Cleavage of 4-MU-GlcNAc3 was unaffected by the absence of the CBD but diminished in the absence of the flexible C-terminal domain. However, unlike for the soluble substrate, the CBD and the newly identified flexible C-terminal domain were vital for inhibiting Aspergillus niger growth. The results are consistent with the involvement of the plant chitinases in defense against pathogens like fungi that have chitin exoskeletons. In summary, we have characterized the functional features and structural domains necessary for the activity of two plant root chitinases that are believed to be involved in plant defense and a bacterial chitinase that, along with the plant chitinases, may participate in nutrient recycling in the rhizosphere.
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Affiliation(s)
- Samuel O. Shobade
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Olga A. Zabotina
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Marit Nilsen-Hamilton
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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13
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Minguet-Lobato M, Cervantes FV, Míguez N, Plou FJ, Fernández-Lobato M. Chitinous material bioconversion by three new chitinases from the yeast Mestchnikowia pulcherrima. Microb Cell Fact 2024; 23:31. [PMID: 38245740 PMCID: PMC10799394 DOI: 10.1186/s12934-024-02300-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Chitinases are widely distributed enzymes that perform the biotransformation of chitin, one of the most abundant polysaccharides on the biosphere, into useful value-added chitooligosaccharides (COS) with a wide variety of biotechnological applications in food, health, and agricultural fields. One of the most important group of enzymes involved in the degradation of chitin comprises the glycoside hydrolase family 18 (GH18), which harbours endo- and exo-enzymes that act synergistically to depolymerize chitin. The secretion of a chitinase activity from the ubiquitous yeast Mestchnikowia pulcherrima and their involvement in the post-harvest biological control of fungal pathogens was previously reported. RESULTS Three new chitinases from M. pulcherrima, MpChit35, MpChit38 and MpChit41, were molecularly characterized and extracellularly expressed in Pichia pastoris to about 91, 90 and 71 mU ml- 1, respectively. The three enzymes hydrolysed colloidal chitin with optimal activity at 45 ºC and pH 4.0-4.5, increased 2-times their activities using 1 mM of Mn2+ and hydrolysed different types of commercial chitosan. The partial separation and characterization of the complex COS mixtures produced from the hydrolysis of chitin and chitosan were achieved by a new anionic chromatography HPAEC-PAD method and mass spectrometry assays. An overview of the predicted structures of these proteins and their catalytic modes of action were also presented. Depicted their high sequence and structural homology, MpChit35 acted as an exo-chitinase producing di-acetyl-chitobiose from chitin while MpChit38 and MpChit41 both acted as endo-chitinases producing tri-acetyl-chitotriose as main final product. CONCLUSIONS Three new chitinases from the yeast M. pulcherrima were molecularly characterized and their enzymatic and structural characteristics analysed. These enzymes transformed chitinous materials to fully and partially acetylated COS through different modes of splitting, which make them interesting biocatalysts for deeper structural-function studies on the challenging enzymatic conversion of chitin.
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Affiliation(s)
- Marina Minguet-Lobato
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), University Autonomous from Madrid, C/ Nicolás Cabrera, 1. Cantoblanco, Madrid, 28049, Spain
- Institute of Catalysis and Petrochemistry, CSIC. C/ Marie Curie, 2. Cantoblanco, Madrid, 28049, Spain
| | - Fadia V Cervantes
- Institute of Catalysis and Petrochemistry, CSIC. C/ Marie Curie, 2. Cantoblanco, Madrid, 28049, Spain
| | - Noa Míguez
- Institute of Catalysis and Petrochemistry, CSIC. C/ Marie Curie, 2. Cantoblanco, Madrid, 28049, Spain
| | - Francisco J Plou
- Institute of Catalysis and Petrochemistry, CSIC. C/ Marie Curie, 2. Cantoblanco, Madrid, 28049, Spain.
| | - María Fernández-Lobato
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), University Autonomous from Madrid, C/ Nicolás Cabrera, 1. Cantoblanco, Madrid, 28049, Spain.
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14
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Son DJ, Kim GG, Choo HY, Chung NJ, Choo YM. Functional Comparison of Three Chitinases from Symbiotic Bacteria of Entomopathogenic Nematodes. Toxins (Basel) 2024; 16:26. [PMID: 38251242 PMCID: PMC10821219 DOI: 10.3390/toxins16010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Xenorhabdus and Photorhabdus, bacterial symbionts of entomopathogenic nematodes Steinernema and Heterorhabditis, respectively, have several biological activities including insecticidal and antimicrobial activities. Thus, XnChi, XhChi, and PtChi, chitinases of X. nematophila, X. hominickii, and P. temperata isolated from Korean indigenous EPNs S. carpocapsae GJ1-2, S. monticolum GJ11-1, and H. megidis GJ1-2 were cloned and expressed in Escherichia coli BL21 to compare their biological activities. Chitinase proteins of these bacterial symbionts purified using the Ni-NTA system showed different chitobiosidase and endochitinase activities, but N-acetylglucosamidinase activities were not shown in the measuring of chitinolytic activity through N-acetyl-D-glucosarmine oligomers. In addition, the proteins showed different insecticidal and antifungal activities. XnChi showed the highest insecticidal activity against Galleria mellonella, followed by PtChi and XhChi. In antifungal activity, XhChi showed the highest half-maximal inhibitory concentration (IC50) against Fusarium oxysporum with 0.031 mg/mL, followed by PtChi with 0.046 mg/mL, and XnChi with 0.072 mg/mL. XhChi also showed the highest IC50 against F. graminearum with 0.040 mg/mL, but XnChi was more toxic than PtChi with 0.055 mg/mL and 0.133 mg/mL, respectively. This study provides an innovative approach to the biological control of insect pests and fungal diseases of plants with the biological activity of symbiotic bacterial chitinases of entomopathogenic nematodes.
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Affiliation(s)
- Da-Jeong Son
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea;
- Division of Research and Development, Jinju Bioindustry Foundation, Jinju 52839, Republic of Korea
| | - Geun-Gon Kim
- Division of Research and Development, Nambo Co., Ltd., Jinju 52840, Republic of Korea; (G.-G.K.); (H.-Y.C.)
| | - Ho-Yul Choo
- Division of Research and Development, Nambo Co., Ltd., Jinju 52840, Republic of Korea; (G.-G.K.); (H.-Y.C.)
| | - Nam-Jun Chung
- Division of Research and Development, Nambo Co., Ltd., Jinju 52840, Republic of Korea; (G.-G.K.); (H.-Y.C.)
| | - Young-Moo Choo
- Division of Research and Development, Jinju Bioindustry Foundation, Jinju 52839, Republic of Korea
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15
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Ramírez-Carreto S, Miranda-Zaragoza B, Simões N, González-Muñoz R, Rodríguez-Almazán C. Marine Bioprospecting: Enzymes and Stress Proteins from the Sea Anemones Anthopleura dowii and Lebrunia neglecta. Mar Drugs 2023; 22:12. [PMID: 38248637 PMCID: PMC10821040 DOI: 10.3390/md22010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
The bioprospecting of sea anemone tissues and secretions has revealed that they are natural libraries of polypeptides with diverse biological activities that can be utilized to develop of biotechnological tools with potential medical and industrial applications. This study conducted a proteomic analysis of crude venom extracts from Anthopleura dowii Verrill, 1869, and Lebrunia neglecta Duchassaing & Michelotti, 1860. The obtained data allowed us to identify 201 polypeptides, of which 39% were present in both extracts. Among the obtained sequences, hydrolase-type enzymes, oxidoreductases, transferases, heat shock proteins, adhesion proteins, and protease inhibitors, among others, were identified. Interaction analysis and functional annotation indicated that these proteins are primarily involved in endoplasmic reticulum metabolic processes such as carbon metabolism and protein processing. In addition, several proteins related to oxidative stress were identified, including superoxide dismutase, peroxiredoxins, thioredoxin, and glutathione oxidase. Our results provide novel information on the polypeptide composition of the crude venom extract from sea anemones, which can be utilized to develop molecules for therapeutic tools and industrial applications.
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Affiliation(s)
- Santos Ramírez-Carreto
- Instituto Nacional de Salud Pública, Centro de Investigación Sobre Enfermedades Infecciosas, Av. Universidad #655, Santa María Ahuacatitlan, Cuernavaca C.P. 62100, Mexico;
| | - Beatriz Miranda-Zaragoza
- Departamento de Micro y Nanotecnologías, Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Cto. Exterior S/N, C.U., Coyoacán, Ciudad de México C.P. 04510, Mexico;
| | - Nuno Simões
- Unidad Multidisciplinaria de Docencia e Investigación en Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Puerto Abrigo s/n, Sisal C.P. 97356, Mexico;
- International Chair for Coastal and Marine Studies, Harte Research Institute for Gulf of Mexico Studies, Texas A and M University-Corpus Christi, Corpus Christi, TX 78412, USA
- Laboratorio Nacional de Resiliencia Costera (LANRESC), Laboratorios Nacionales, CONACYT, Sisal C.P. 97356, Mexico
| | - Ricardo González-Muñoz
- Instituto de Investigaciones Marinas y Costeras, CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Dean Funes 3350, Mar del Plata C.P. 7600, Argentina;
| | - Claudia Rodríguez-Almazán
- Departamento de Micro y Nanotecnologías, Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Cto. Exterior S/N, C.U., Coyoacán, Ciudad de México C.P. 04510, Mexico;
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16
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de Oliveira EG, Filho CADC, Rodrigues RAL. An overview of viral chitinases: General properties and biotechnological potential. Exp Biol Med (Maywood) 2023; 248:2053-2061. [PMID: 38057942 PMCID: PMC10800131 DOI: 10.1177/15353702231208408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
Chitin is a biopolymer profusely present in nature and of pivotal importance as a structural component in cells. It is degraded by chitinases, enzymes naturally produced by different organisms. Chitinases are proteins enrolled in many cellular mechanisms, including the remodeling process of the fungal cell wall, the cell growth process, the autolysis of filamentous fungi, and cell separation of yeasts, among others. These enzymes also have properties with different biotechnological applications. They are used to produce polymers, for biological control, biofilm formation, and as antitumor and anti-inflammatory target molecules. Chitinases are classified into different glycoside hydrolase (GH) families and are widespread in microorganisms, including viruses. Among them, the GH18 family is highly predominant in the viral genomes, being present and active enzymes in baculoviruses and nucleocytoplasmic large DNA viruses (NCLDV), especially chloroviruses from the Phycodnaviridae family. These viral enzymes contain one or more GH domains and seem to be involved during the viral replication cycle. Curiously, only a few DNA viruses have these enzymes, and studying their properties could be a key feature for biological and biotechnological novelties. Here, we provide an overview of viral chitinases and their probable function in viral infection, showing evidence of at least two distinct origins for these enzymes. Finally, we discuss how these enzymes can be applied as biotechnological tools and what one can expect for the coming years on these GHs.
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Affiliation(s)
- Ellen Gonçalves de Oliveira
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Clécio Alonso da Costa Filho
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
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17
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Kim Y, Li H, Choi J, Boo J, Jo H, Hyun JY, Shin I. Glycosidase-targeting small molecules for biological and therapeutic applications. Chem Soc Rev 2023; 52:7036-7070. [PMID: 37671645 DOI: 10.1039/d3cs00032j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Glycosidases are ubiquitous enzymes that catalyze the hydrolysis of glycosidic linkages in oligosaccharides and glycoconjugates. These enzymes play a vital role in a wide variety of biological events, such as digestion of nutritional carbohydrates, lysosomal catabolism of glycoconjugates, and posttranslational modifications of glycoproteins. Abnormal glycosidase activities are associated with a variety of diseases, particularly cancer and lysosomal storage disorders. Owing to the physiological and pathological significance of glycosidases, the development of small molecules that target these enzymes is an active area in glycoscience and medicinal chemistry. Research efforts carried out thus far have led to the discovery of numerous glycosidase-targeting small molecules that have been utilized to elucidate biological processes as well as to develop effective chemotherapeutic agents. In this review, we describe the results of research studies reported since 2018, giving particular emphasis to the use of fluorescent probes for detection and imaging of glycosidases, activity-based probes for covalent labelling of these enzymes, glycosidase inhibitors, and glycosidase-activatable prodrugs.
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Affiliation(s)
- Yujun Kim
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hui Li
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Joohee Choi
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Jihyeon Boo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hyemi Jo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
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18
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Rakesh V, Kalia VK, Ghosh A. Diversity of transgenes in sustainable management of insect pests. Transgenic Res 2023; 32:351-381. [PMID: 37573273 DOI: 10.1007/s11248-023-00362-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Insecticidal transgenes, when incorporated and expressed in plants, confer resistance against insects by producing several products having insecticidal properties. Protease inhibitors, lectins, amylase inhibitors, and chitinase genes are associated with the natural defenses developed by plants to counter insect attacks. Several toxin genes are also derived from spiders and scorpions for protection against insects. Bacillus thuringiensis Berliner is a microbial source of insecticidal toxins. Several methods have facilitated the large-scale production of transgenic plants. Bt-derived cry, cyt, vip, and sip genes, plant-derived genes such as lectins, protease inhibitors, and alpha-amylase inhibitors, insect cell wall-degrading enzymes like chitinase and some proteins like arcelins, plant defensins, and ribosome-inactivating proteins have been successfully utilized to impart resistance to insects. Besides, transgenic plants expressing double-stranded RNA have been developed with enhanced resistance. However, the long-term effects of transgenes on insect resistance, the environment, and human health must be thoroughly investigated before they are made available for commercial planting. In this chapter, the present status, prospects, and future scope of transgenes for insect pest management have been summarized and discussed.
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Affiliation(s)
- V Rakesh
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vinay K Kalia
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Liu Y, Qin Z, Wang C, Jiang Z. N-acetyl-d-glucosamine-based oligosaccharides from chitin: Enzymatic production, characterization and biological activities. Carbohydr Polym 2023; 315:121019. [PMID: 37230627 DOI: 10.1016/j.carbpol.2023.121019] [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: 03/10/2023] [Revised: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023]
Abstract
Chitin, the second most abundant biopolymer, possesses diverse applications in the food, agricultural, and pharmaceutical industries due to its functional properties. However, the potential applications of chitin are limited owing to its high crystallinity and low solubility. N-acetyl chitooligosaccharides and lacto-N-triose II, the two types of GlcNAc-based oligosaccharides, can be obtained from chitin by enzymatic methods. With their lower molecular weights and improved solubility, these two types of GlcNAc-based oligosaccharides display more various beneficial health effects when compared to chitin. Among their abilities, they have exhibited antioxidant, anti-inflammatory, anti-tumor, antimicrobial, and plant elicitor activities as well as immunomodulatory and prebiotic effects, which suggests they have the potential to be utilized as food additives, functional daily supplements, drug precursors, elicitors for plants, and prebiotics. This review comprehensively covers the enzymatic methods used for the two types of GlcNAc-based oligosaccharides production from chitin by chitinolytic enzymes. Moreover, current advances in the structural characterization and biological activities of these two types of GlcNAc-based oligosaccharides are summarized in the review. We also highlight current problems in the production of these oligosaccharides and trends in their development, aiming to offer some directions for producing functional oligosaccharides from chitin.
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Affiliation(s)
- Yihao Liu
- College of Food Science and Engineering, State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science & Technology, Tianjin Economy Technological Development Area, No. 29, 13th Avenue, Tianjin 300222, People's Republic of China
| | - Zhen Qin
- School of Life Sciences, Shanghai University, Baoshan District, No.99 Shangda Road, Shanghai 200444, People's Republic of China
| | - Chunling Wang
- College of Food Science and Engineering, State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science & Technology, Tianjin Economy Technological Development Area, No. 29, 13th Avenue, Tianjin 300222, People's Republic of China.
| | - Zhengqiang Jiang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, No.17 Qinghua East Road, Beijing 100083, People's Republic of China.
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20
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Chanworawit K, Wangsoonthorn P, Deevong P. Characterization of chitinolytic bacteria newly isolated from the termite Microcerotermes sp. and their biocontrol potential against plant pathogenic fungi. Biosci Biotechnol Biochem 2023; 87:1077-1091. [PMID: 37328422 DOI: 10.1093/bbb/zbad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
Chitinolytic bacteria were isolated from guts and shells of the termite Microcerotermes sp. Among the nineteen morphologically different chitinolytic isolates, three isolates with highest extracellular chitinase production ratio (≥2.26) were selected. Based on molecular identification of 16S rRNA gene sequences and biochemical characterizations using API test kits and MALDI-TOF MS, these isolates were closely related to Bacillus thuringiensis (Mc_E02) and Paenibacillus species (Mc_E07 and Mc_G06). Isolate Mc_E02 exhibited the highest chitinase-specific activity (2.45 U/mg protein) at 96 h of cultivation, and the enzyme activity was optimized at pH 7.0 and 45 °C. The isolate showed highest and broad-spectrum inhibitory effect against three phytopathogenic fungi (Curvularia lunata, Colletotrichum capsici, and Fusarium oxysporum). Its 36-kDa chitinase exhibited the biomass reduction and mycelium inhibition against all fungi, with highest effects to Curvularia lunata. This research provides novel information about termite chitinolytic bacteria and their effective chitinase, with potential use as biocontrol tool.
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Affiliation(s)
- Kittipong Chanworawit
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pachara Wangsoonthorn
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pinsurang Deevong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
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21
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Liu H, Wang S, Lang B, Li Y, Wang X, Chen J. Fused expression of Sm1-Chit42 proteins for synergistic mycoparasitic response of Trichoderma afroharzianum on Botrytis cinerea. Microb Cell Fact 2023; 22:156. [PMID: 37592265 PMCID: PMC10433591 DOI: 10.1186/s12934-023-02151-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/15/2023] [Indexed: 08/19/2023] Open
Abstract
Sm1 and Chit42 of Trichoderma have been universally confirmed as crucial biocontrol factors against pathogen infection through induced resistance and mycoparasitism, respectively. However, not enough work has been conducted to understand the novel function of fused expression of these two proteins in Trichoderma. The results of this study demonstrated that Sm1-Chit42 protein (SCf) engineered T. afroharzianum strain OE:SCf exerted synergistic inhibition to Botrytis cinerea growth at multiple stages of mycoparasitic interaction of T. afroharzianum and B. cinerea including chemotropism sensing, hyphal coiling, hydrophobicity modulation, cell wall adhesion, virulence reduction and pathogen killing by ROS. These results highlight a novel mycoparasitic system in Trichoderma strains engineered with Sm1-Chit42 chimeric protein to combat B. cinerea growth and reproduction, which would lay a strong foundation for exploring a new engineered Trichoderma biofungicide created with chimeric proteins in the future.
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Affiliation(s)
- Hongyi Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoqing Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Lang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yaqian Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinhua Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China.
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22
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Tomilova OG, Kryukov VY, Kryukova NA, Tolokonnikova KP, Tokarev YS, Rumiantseva AS, Alekseev AA, Glupov VV. Effects of passages through an insect or a plant on virulence and physiological properties of the fungus Metarhizium robertsii. PeerJ 2023; 11:e15726. [PMID: 37583910 PMCID: PMC10424674 DOI: 10.7717/peerj.15726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/18/2023] [Indexed: 08/17/2023] Open
Abstract
Species of the genus Metarhizium are characterized by a multitrophic lifestyle of being arthropod parasites, rhizosphere colonizers, endophytes, and saprophytes. The process of adaptation to various organisms and substrates may lead to specific physiological alterations that can be elucidated by passaging through different hosts. Changes in virulence and cultivation properties of entomopathogenic fungi subcultured on different media or passaged through a live insect host are well known. Nevertheless, comparative in-depth physiological studies on fungi after passaging through insect or plant organisms are scarce. Here, virulence, plant colonization, hydrolytic enzymatic activities, toxin production, and antimicrobial action were compared between stable (nondegenerative) parent strain Metarhizium robertsii MB-1 and its reisolates obtained after eight passages through Galleria mellonella larvae or Solanum lycopersicum or after subculturing on the Sabouraud medium. The passaging through the insect caused similar physiological alterations relative to the plant-based passaging: elevation of destruxin A, B, and E production, a decrease in protease and lipase activities, and lowering of virulence toward G. mellonella and Leptinotarsa decemlineata as compared to the parent strain. The reisolates passaged through the insect or plant showed a slight trend toward increased tomato colonization and enhanced antagonistic action on tomato-associated bacterium Bacillus pumilus as compared to the parental strain. Meanwhile, the subculturing of MB-1 on the Sabouraud medium showed stability of the studied parameters, with minimal alterations relative to the parental strain. We propose that the fungal virulence factors are reprioritized during adaptation of M. robertsii to insects, plants, and media.
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Affiliation(s)
- Oksana G. Tomilova
- Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia
- All-Russian Institute of Plant Protection, St. Petersburg, Russia
| | - Vadim Y. Kryukov
- Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia
| | | | | | - Yuri S. Tokarev
- All-Russian Institute of Plant Protection, St. Petersburg, Russia
| | | | - Alexander A. Alekseev
- Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Novosibirsk, Russia
| | - Viktor V. Glupov
- Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia
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23
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Arnold ND, Garbe D, Brück TB. Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species. Microbiologyopen 2023; 12:e1372. [PMID: 37642486 PMCID: PMC10404844 DOI: 10.1002/mbo3.1372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Chitin is the second most abundant polysaccharide worldwide as part of arthropods' exoskeletons and fungal cell walls. Low concentrations in soils and sediments indicate rapid decomposition through chitinolytic organisms in terrestrial and aquatic ecosystems. The enacting enzymes, so-called chitinases, and their products, chitooligosaccharides, exhibit promising characteristics with applications ranging from crop protection to cosmetics, medical, textile, and wastewater industries. Exploring novel chitinolytic organisms is crucial to expand the enzymatical toolkit for biotechnological chitin utilization and to deepen our understanding of diverse catalytic mechanisms. In this study, we present two long-read sequencing-based genomes of highly similar Jeongeupia species, which have been screened, isolated, and biochemically characterized from chitin-amended soil samples. Through metabolic characterization, whole-genome alignments, and phylogenetic analysis, we could demonstrate how the investigated strains differ from the taxonomically closest strain Jeongeupia naejangsanensis BIO-TAS4-2T (DSM 24253). In silico analysis and sequence alignment revealed a multitude of highly conserved chitinolytic enzymes in the investigated Jeongeupia genomes. Based on these results, we suggest that the two strains represent a novel species within the genus of Jeongeupia, which may be useful for environmentally friendly N-acetylglucosamine production from crustacean shell or fungal biomass waste or as a crop protection agent.
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Affiliation(s)
- Nathanael D. Arnold
- Department of ChemistryWerner‐Siemens Chair for Synthetic Biotechnology (WSSB), TUM School of Natural Sciences, Technical University of MunichGarchingGermany
| | - Daniel Garbe
- Department of ChemistryWerner‐Siemens Chair for Synthetic Biotechnology (WSSB), TUM School of Natural Sciences, Technical University of MunichGarchingGermany
| | - Thomas B. Brück
- Department of ChemistryWerner‐Siemens Chair for Synthetic Biotechnology (WSSB), TUM School of Natural Sciences, Technical University of MunichGarchingGermany
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24
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Lyagin I, Aslanli A, Domnin M, Stepanov N, Senko O, Maslova O, Efremenko E. Metal Nanomaterials and Hydrolytic Enzyme-Based Formulations for Improved Antifungal Activity. Int J Mol Sci 2023; 24:11359. [PMID: 37511117 PMCID: PMC10379199 DOI: 10.3390/ijms241411359] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Active research of metal-containing compounds and enzymes as effective antifungal agents is currently being conducted due to the growing antifungal resistance problem. Metals are attracting special attention due to the wide variety of ligands that can be used for them, including chemically synthesized and naturally obtained variants as a result of the so-called "green synthesis". The main mechanism of the antifungal action of metals is the triggering of the generation and accumulation of reactive oxygen species (ROS). Further action of ROS on various biomolecules is nonspecific. Various hydrolytic enzymes (glucanases and proteases), in turn, exhibit antifungal properties by affecting the structural elements of fungal cells (cell walls, membranes), fungal quorum sensing molecules, fungal own protective agents (mycotoxins and antibiotics), and proteins responsible for the adhesion and formation of stable, highly concentrated populations in the form of biofilms. A wide substrate range of enzymes allows the use of various mechanisms of their antifungal actions. In this review, we discuss the prospects of combining two different types of antifungal agents (metals and enzymes) against mycelial fungi and yeast cells. Special attention is paid to the possible influence of metals on the activity of the enzymes and the possible effects of proteins on the antifungal activity of metal-containing compounds.
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Affiliation(s)
- Ilya Lyagin
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Aysel Aslanli
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Maksim Domnin
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Nikolay Stepanov
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Olga Senko
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Olga Maslova
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Elena Efremenko
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
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25
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de Oliveira Viana J, Silva E Souza E, Sbaraini N, Vainstein MH, Gomes JNS, de Moura RO, Barbosa EG. Scaffold repositioning of spiro-acridine derivatives as fungi chitinase inhibitor by target fishing and in vitro studies. Sci Rep 2023; 13:7320. [PMID: 37147323 PMCID: PMC10163251 DOI: 10.1038/s41598-023-33279-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/11/2023] [Indexed: 05/07/2023] Open
Abstract
The concept of "one target, one drug, one disease" is not always true, as compounds with previously described therapeutic applications can be useful to treat other maladies. For example, acridine derivatives have several potential therapeutic applications. In this way, identifying new potential targets for available drugs is crucial for the rational management of diseases. Computational methodologies are interesting tools in this field, as they use rational and direct methods. Thus, this study focused on identifying other rational targets for acridine derivatives by employing inverse virtual screening (IVS). This analysis revealed that chitinase enzymes can be potential targets for these compounds. Subsequently, we coupled molecular docking consensus analysis to screen the best chitinase inhibitor among acridine derivatives. We observed that 3 compounds displayed potential enhanced activity as fungal chitinase inhibitors, showing that compound 5 is the most active molecule, with an IC50 of 0.6 ng/µL. In addition, this compound demonstrated a good interaction with the active site of chitinases from Aspergillus fumigatus and Trichoderma harzianum. Additionally, molecular dynamics and free energy demonstrated complex stability for compound 5. Therefore, this study recommends IVS as a powerful tool for drug development. The potential applications are highlighted as this is the first report of spiro-acridine derivatives acting as chitinase inhibitors that can be potentially used as antifungal and antibacterial candidates.
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Affiliation(s)
- Jéssika de Oliveira Viana
- Post-Graduate Program in Bioinformatics, Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Eden Silva E Souza
- School of Biomolecular and Biomedical Science & BiOrbic-Bioeconomy Research Center, University College Dublin, Dublin, Ireland
| | - Nicolau Sbaraini
- Biotechnology Center, Postgraduate Program in Cellular and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Marilene Henning Vainstein
- Biotechnology Center, Postgraduate Program in Cellular and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Euzébio Guimarães Barbosa
- Post-Graduate Program in Bioinformatics, Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil.
- Post-Graduate Program in Pharmaceutical Sciences, Faculty of Pharmacy, Federal University of Rio Grande do Norte, Natal, Brazil.
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26
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Rivera-Solís RA, Granados-Baeza MJ, Solís-Pereira SE, Lizama-Uc G, Magaña-Ortiz D, Sánchez-González MN, Rojas-Herrera RA, Rivera-Muñoz G. Establishment of the colloidal chitin enzymatic hydrolysis conditions to obtain N-acetyl glucosamine. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2023.1077429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
The wastes generated by the shrimp industry are approximately between 50 and 60% of the catch volume. These residues such as head, viscera, and shell are potential pollutants if they are not treated for proper disposal. One way to solve this problem is to use the residues as functional food ingredients. In this regard, shrimp residues are rich in chitin, the second most abundant biopolymer on the planet after cellulose. Chitin is composed of N-acetyl glucosamine, a molecule used as a sweetener in the food industry and as an aid in the treatment of coronary diseases and gonarthrosis. N-acetyl glucosamine can be obtained by the hydrolysis of colloidal chitin using chemical or enzymatic methods; however, chemical methods are associated with pollution. In this study, we determined the hydrolysis conditions of shrimp colloidal chitin for obtaining N-acetyl glucosamine, using the extracellular enzymes produced by a marine bacterium isolated in the coastal zone of Progreso, Yucatan, Mexico. The best N-acetyl glucosamine yield obtained was 2.65%, using 10 mg/mL colloidal chitin, at 60°C, and pH 8.9 with 3.5% NaCl.
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27
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Poza-Viejo L, Redondo-Nieto M, Matías J, Granado-Rodríguez S, Maestro-Gaitán I, Cruz V, Olmos E, Bolaños L, Reguera M. Shotgun proteomics of quinoa seeds reveals chitinases enrichment under rainfed conditions. Sci Rep 2023; 13:4951. [PMID: 36973333 PMCID: PMC10043034 DOI: 10.1038/s41598-023-32114-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
AbstractQuinoa is an Andean crop whose cultivation has been extended to many different parts of the world in the last decade. It shows a great capacity for adaptation to diverse climate conditions, including environmental stressors, and, moreover, the seeds are very nutritious in part due to their high protein content, which is rich in essential amino acids. They are gluten-free seeds and contain good amounts of other nutrients such as unsaturated fatty acids, vitamins, or minerals. Also, the use of quinoa hydrolysates and peptides has been linked to numerous health benefits. Altogether, these aspects have situated quinoa as a crop able to contribute to food security worldwide. Aiming to deepen our understanding of the protein quality and function of quinoa seeds and how they can vary when this crop is subjected to water-limiting conditions, a shotgun proteomics analysis was performed to obtain the proteomes of quinoa seeds harvested from two different water regimes in the field: rainfed and irrigated conditions. Differentially increased levels of proteins determined in seeds from each field condition were analysed, and the enrichment of chitinase-related proteins in seeds harvested from rainfed conditions was found. These proteins are described as pathogen-related proteins and can be accumulated under abiotic stress. Thus, our findings suggest that chitinase-like proteins in quinoa seeds can be potential biomarkers of drought. Also, this study points to the need for further research to unveil their role in conferring tolerance when coping with water-deficient conditions.
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28
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Sharma A, Arya SK, Singh J, Kapoor B, Bhatti JS, Suttee A, Singh G. Prospects of chitinase in sustainable farming and modern biotechnology: an update on recent progress and challenges. Biotechnol Genet Eng Rev 2023:1-31. [PMID: 36856523 DOI: 10.1080/02648725.2023.2183593] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023]
Abstract
Chitinases are multifunctional biocatalysts for the pest control and useful in modern biotechnology and pharmaceutical industries. Chemical-based fungicides and insecticides have caused more severe effects on environment and human health. Many pathogenic fungal species and insects became resistant to the chemical pesticides. The resistant fungi emerged as a multidrug resistant also and less susceptible insects are not possible to control adequately. Chitinases have an immense potential to be exploited as a biopesticide against fungi and insects. The direct use of chitinase in liquid formulation or whole microbial enzyme producing cells, both act as antagonistically against the pests. Chitinase can disintegrate the fungal cell wall and insect integument that holds the chitin as a vital structural component. Moreover, chitinase is applied for the synthesis of pharmaceutically important chitooligosaccharides. Chitinase producing microbes have the huge potential to utilize against the waste management of sea food remains like shells of crustaceans. Chitinase is valuable for the synthesis of protoplasts from industrially important fungi, further it act as the biocontrol agent of malaria and dengue fever causing larvae of mosquitoes. Chitinases also have been successfully used in wine and single cell protein producing industries. Present review is illustrating the updated information on the state of the art of different applications of chitinases in agriculture and biotechnology industry. It also bestows the understanding to the readers about the areas of extensively studied and the field where there is still much left to be done.
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Affiliation(s)
- Anindita Sharma
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara, India
| | | | - Jatinder Singh
- Department of Horticulture, SAGR, Lovely Professional University, Phagwara, India
| | - Bhupinder Kapoor
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, Phagwara, India
| | - Jasvinder Singh Bhatti
- Department of Human Genetics and Molecular Medicine School of Health Sciences, Central University of Punjab, India
| | - Ashish Suttee
- Department of Pharmacognosy, School of Pharmaceutical Sciences, Lovely Professional University Phagwara, India
| | - Gursharan Singh
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara, India
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29
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Roy S, Vivoli Vega M, Ames JR, Britten N, Kent A, Evans K, Isupov MN, Harmer NJ. The ROK kinase N-acetylglucosamine kinase uses a sequential random enzyme mechanism with successive conformational changes upon each substrate binding. J Biol Chem 2023; 299:103033. [PMID: 36806680 PMCID: PMC10031466 DOI: 10.1016/j.jbc.2023.103033] [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: 11/10/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
N-acetyl-d-glucosamine (GlcNAc) is a major component of bacterial cell walls. Many organisms recycle GlcNAc from the cell wall or metabolize environmental GlcNAc. The first step in GlcNAc metabolism is phosphorylation to GlcNAc-6-phosphate. In bacteria, the ROK family kinase N-acetylglucosamine kinase (NagK) performs this activity. Although ROK kinases have been studied extensively, no ternary complex showing the two substrates has yet been observed. Here, we solved the structure of NagK from the human pathogen Plesiomonas shigelloides in complex with GlcNAc and the ATP analog AMP-PNP. Surprisingly, PsNagK showed distinct conformational changes associated with the binding of each substrate. Consistent with this, the enzyme showed a sequential random enzyme mechanism. This indicates that the enzyme acts as a coordinated unit responding to each interaction. Our molecular dynamics modeling of catalytic ion binding confirmed the location of the essential catalytic metal. Additionally, site-directed mutagenesis confirmed the catalytic base and that the metal-coordinating residue is essential. Together, this study provides the most comprehensive insight into the activity of a ROK kinase.
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Affiliation(s)
| | | | | | | | - Amy Kent
- Living Systems Institute, Exeter, UK
| | - Kim Evans
- Living Systems Institute, Exeter, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Exeter, UK
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30
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Yu G, Liu G, Liu T, Fink EH, Esker AR. Activities of Family 18 Chitinases on Amorphous Regenerated Chitin Thin Films and Dissolved Chitin Oligosaccharides: Comparison with Family 19 Chitinases. Biomacromolecules 2023; 24:566-575. [PMID: 36715568 DOI: 10.1021/acs.biomac.2c00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Changes in mass and viscoelasticity of chitin layers in fungal cell walls during chitinase attack are vital for understanding bacterial invasion of and human defense against fungi. In this work, regenerated chitin (RChitin) thin films mimicked the fungal chitin layers and facilitated studies of degradation by family 18 chitinases from Trichoderma viride (T. viride) and family 19 chitinases from Streptomyces griseus (S. griseus) that possessed chitin-binding domains (CBDs) that were absent in the family 18 chitinases. Degradation was monitored via a quartz crystal microbalance with dissipation monitoring (QCM-D) in real time at various pH and temperatures. Compared to substrates of colloidal chitin or dissolved chitin derivatives and analogues, the degradation of RChitin films was deeply affected by chitinase adsorption. While the family 18 chitinases had greater solution activity on chitin oligosaccharides, the family 19 chitinases exhibited greater surface activity on RChitin films, illustrating the importance of CBDs for insoluble substrates.
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Affiliation(s)
- Guoqiang Yu
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Gehui Liu
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Tianyi Liu
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Ethan H Fink
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Alan R Esker
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia24061, United States.,Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia24061, United States
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31
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Soni T, Zhuang M, Kumar M, Balan V, Ubanwa B, Vivekanand V, Pareek N. Multifaceted production strategies and applications of glucosamine: a comprehensive review. Crit Rev Biotechnol 2023; 43:100-120. [PMID: 34923890 DOI: 10.1080/07388551.2021.2003750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Glucosamine (GlcN) and its derivatives are in high demand and used in various applications such as food, a precursor for the biochemical synthesis of fuels and chemicals, drug delivery, cosmetics, and supplements. The vast number of applications attributed to GlcN has raised its demand, and there is a growing emphasis on developing production methods that are sustainable and economical. Several: physical, chemical, enzymatic, microbial fermentation, recombinant processing methods, and their combinations have been reported to produce GlcN from chitin and chitosan available from different sources, such as animals, plants, and fungi. In addition, genetic manipulation of certain organisms has significantly improved the quality and yield of GlcN compared to conventional processing methods. This review will summarize the chitin and chitosan-degrading enzymes found in various organisms and the expression systems that are widely used to produce GlcN. Furthermore, new developments and methods, including genetic and metabolic engineering of Escherichia coli and Bacillus subtilis to produce high titers of GlcN and GlcNAc will be reviewed. Moreover, other sources of glucosamine production viz. starch and inorganic ammonia will also be discussed. Finally, the conversion of GlcN to fuels and chemicals using catalytic and biochemical conversion will be discussed.
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Affiliation(s)
- Twinkle Soni
- Microbial Catalysis and Process Engineering Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Mengchuan Zhuang
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, TX, USA
| | - Manish Kumar
- Microbial Catalysis and Process Engineering Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Venkatesh Balan
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, TX, USA
| | - Bryan Ubanwa
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, TX, USA
| | - Vivekanand Vivekanand
- Centre for Energy and Environment, Malaviya National Institute of Technology, Jaipur, India
| | - Nidhi Pareek
- Microbial Catalysis and Process Engineering Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, India
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32
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Mazumdar R, Dutta PP, Saikia J, Borah JC, Thakur D. Streptomyces sp. Strain PBR11, a Forest-Derived Soil Actinomycetia with Antimicrobial Potential. Microbiol Spectr 2023; 11:e0348922. [PMID: 36719230 PMCID: PMC10101066 DOI: 10.1128/spectrum.03489-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/21/2022] [Indexed: 02/01/2023] Open
Abstract
The Actinomycetia isolate PBR11 was isolated from the forest rhizosphere soil of Pobitora Wildlife Sanctuary (PWS), Assam, India. The isolate was identified as Streptomyces sp. with 92.91% sequence similarity to their closest type strain, Streptomyces atrovirens NRRL B-16357 DQ026672. The strain demonstrated significant antimicrobial activity against 19 test pathogens, including multidrug-resistant (MDR) clinical isolates and dermatophytes. Phenol, 2,5-bis(1,1-dimethylethyl), is the major chemical compound detected by gas chromatography-mass spectrometry in the ethyl acetate extract of PBR11 (EtAc-PBR11). The presence of the PKS type II gene (type II polyketide synthases) and chitinase gene suggested that it has been involved in the production of antimicrobial compounds. Metabolic profiling of the EtAc-PBR11 was performed by thin-layer chromatography and flash chromatography resulted in the extraction of two bioactive fractions, namely, PBR11Fr-1 and PBR11Fr-2. Liquid chromatography-tandem mass spectrometry analysis of both the fractions demonstrated the presence of significant antimicrobial compounds, including ethambutol. This is the first report on the detection of antituberculosis drug in the bioactive fractions of Streptomyces sp. PBR11. EtAc-PBR11 and PBR11Fr-1 showed the lowest MIC values (>0.097 and >0.048 μg/mL, respectively) against Candida albicans MTCC 227, whereas they showed the highest MIC values (>0.390 and >0.195 μg/mL, respectively) against Escherichia coli ATCC BAA-2469. The effects of PBR11Fr-1 were investigated on the pathogens by using a scanning electron microscope. The results indicated major morphological alterations in the cytoplasmic membrane. PBR11Fr-1 exhibited low cytotoxicity on normal hepatocyte cell line (CC-1) and the percent cell viability started to decline as the concentration increased from 50 μg/mL (87.07% ± 3.22%) to 100 μg/mL (81.26% ± 2.99%). IMPORTANCE Novel antibiotic breakthroughs are urgently required to combat antimicrobial resistance. Actinomycetia are the principal producers of antibiotics. The present study demonstrated the broad-spectrum antimicrobial potential of an Actinomycetia strain Streptomyces sp. strain PBR11 isolated from the PWS of Assam, India, which represents diverse, poorly screened habitats for novel microorganisms. The strain displayed 92.4% sequence similarity with genes of the closest type strain, indicating that the strain may represent a novel taxon within the phylum Actinomycetota. The metabolomics studies of EtAc-PBR11 revealed structurally diverse antimicrobial agents, including the detection of the antituberculosis drug ethambutol, in the bioactive fraction of Streptomyces sp. PBR11 for the first time. The PBR11 strain also yielded positive results for the antibiotic synthesis gene and the chitinase gene, both of which are responsible for broad-spectrum antimicrobial activity. This suggests that the untouched forest ecosystems have a tremendous potential to harbor potent actinomycetia for future drug discovery.
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Affiliation(s)
- Rajkumari Mazumdar
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
- Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | | | - Juri Saikia
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
- Department of Biotechnology, Gauhati University, Guwahati, India
| | - Jagat Chandra Borah
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
| | - Debajit Thakur
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
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Synergic chitin degradation by Streptomyces sp. SCUT-3 chitinases and their applications in chitinous waste recycling and pathogenic fungi biocontrol. Int J Biol Macromol 2023; 225:987-996. [PMID: 36403764 DOI: 10.1016/j.ijbiomac.2022.11.161] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/02/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022]
Abstract
The genus Streptomyces comprises the most important chitin decomposers in soil and revealing their chitinolytic machinery is beneficial for the conversion of chitinous wastes. Streptomyces sp. SCUT-3, a chitin-hydrolyzing and a robust feather-degrading bacterium, was isolated previously. The potential chitin-degrading enzymes produced by SCUT-3 were analyzed in the present study. Among these enzymes, three chitinases were successfully expressed in Pichia pastoris at comparatively high yields of 4.8 U/mL (SsExoChi18A), 11.2 U/mL (SsExoChi18B), and 17.8 U/mL (SsEndoChi19). Conserved motifs and constructive 3D structures of these three exo- and endochitinases were also analyzed. These chitinases hydrolyzed colloidal chitin to chitin oligomers. SsExoChi18A showed apparent synergic effects with SsEndoChi19 in colloidal chitin and shrimp shell hydrolysis, with an improvement of 29.3 % and 124.9 %, respectively. Compared with SsExoChi18B and SsEndoChi19, SsExoChi18A exhibited the strongest antifungal effects against four plant pathogens by inhibiting mycelial growth and spore germination. This study provided good candidates for chitinous waste-processing enzymes and antifungal biocontrol agents. These synergic chitin-degrading enzymes of SCUT-3 are good targets for its further genetical modification to construct super chitinous waste-degrading bacteria with strong abilities to hydrolyze both protein and chitin, thereby providing a direction for the future path of the chitinous waste recycling industry.
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Micocci KC, Moreira AC, Sanchez AD, Pettinatti JL, Rocha MC, Dionizio BS, Correa KCS, Malavazi I, Wouters FC, Bueno OC, Souza DHF. Identification, cloning, and characterization of a novel chitinase from leaf-cutting ant Atta sexdens: An enzyme with antifungal and insecticidal activity. Biochim Biophys Acta Gen Subj 2023; 1867:130249. [PMID: 36183893 DOI: 10.1016/j.bbagen.2022.130249] [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: 07/13/2022] [Revised: 09/16/2022] [Accepted: 09/27/2022] [Indexed: 10/14/2022]
Abstract
Chitinases are enzymes that degrade chitin, a polysaccharide found in the exoskeleton of insects, fungi, yeast, and internal structures of other vertebrates. Although chitinases isolated from bacteria, fungi and plants have been reported to have antifungal or insecticide activities, chitinases from insects with these activities have been seldomly reported. In this study, a leaf-cutting ant Atta sexdens DNA fragment containing 1623 base pairs was amplified and cloned into a vector to express the protein (AsChtII-C4B1) in Pichia pastoris. AsChtII-C4B1, which contains one catalytic domain and one carbohydrate-binding module (CBM), was secreted to the extracellular medium and purified by ammonium sulfate precipitation followed by nickel column chromatography. AsChtII-C4B1 showed maximum activity at pH 5.0 and 55 °C when tested against colloidal chitin substrate and maintained >60% of its maximal activity in different temperatures during 48 h. AsChtII-C4B1 decreased the survival of Spodoptera frugiperda larvae fed with an artificial diet that contained AsChtII-C4B1. Our results have indicated that AsChtII-C4B1 has a higher effect on larva-pupa than larva-larva molts. AsChtII-C4B1 activity targets more specifically the growth of filamentous fungus than yeast. This work describes, for the first time, the obtaining a recombinant chitinase from ants and the characterization of its insecticidal and antifungal activities.
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Affiliation(s)
- Kelli C Micocci
- Center for the Study of Social Insects, São Paulo State University "Julio de Mesquita Filho", Rio Claro, SP, Brazil
| | - Ariele C Moreira
- Department of Physics, Chemistry and Mathematics, Federal University of São Carlos, Sorocaba, SP, Brazil
| | - Amanda D Sanchez
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Jessica L Pettinatti
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Marina C Rocha
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Bruna S Dionizio
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Katia C S Correa
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Iran Malavazi
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Felipe C Wouters
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Odair C Bueno
- Center for the Study of Social Insects, São Paulo State University "Julio de Mesquita Filho", Rio Claro, SP, Brazil
| | - Dulce Helena F Souza
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil.
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Chen L, Hua Y, Ji W, Wang J, Zhao H, Wang Z. Cloning, characterization, and expression analysis of the CHITINASE gene family in Helice tientsinensis. PeerJ 2023; 11:e15045. [PMID: 36935907 PMCID: PMC10022498 DOI: 10.7717/peerj.15045] [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: 12/11/2022] [Accepted: 02/21/2023] [Indexed: 03/15/2023] Open
Abstract
Chitinase is a kind of glycoside hydrolase which is widely distributed in nature and encoded by multiple genes to catalyze the decomposition of chitin, which plays an important role in the molting and pathogen defense of crustaceans. However, the research on chitinase in crustaceans is mainly focused on a few species with economic value. In this study, full-length cDNA sequences of the HtCHT1, HtCHT3 and HtCHT4 genes were cloned from the mudflat crab Helice tientsinensis by RACE, and the sequences were analyzed. The results showed that the full-length 2,229 bp of HtCHT1 gene encoded 627 amino acids, while the full-length 2,191 bp of HtCHT3 gene produced 489 amino acids, and the full-length 3,312 bp of HtCHT4 gene encoded 664 amino acids. Bioinformatics analysis showed that all the obtained chitinase proteins had the glycosyl hydrolase family 18 (GH18) catalytic domain and chitin-binding domain (ChtBD2), furthermore, HtCHT1 and HtCHT4 proteins had signal peptide domains at N-terminal. Phylogenetic analysis showed that different types of chitinase were clustered, and HtCHTs were closely related to chitinases in the Eriocheir sinensis. Expression profile analysis showed that the HtCHT1, HtCHT3 and HtCHT4 were significantly expressed in hepatopancreas. Furthermore, the expression of three genes was significantly up-regulated in hepatopancreas after the Vibrio parahaemolyticus challenge. These results suggested that HtCHT1, HtCHT3 and HtCHT4 were belonged to the CHITINASE gene family in H. tientsinensis and were potentially involved in the antibacterial immune response. This study provides essential information for further research of chitinase in H. tientsinensis and even crustaceans.
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Affiliation(s)
- Lulu Chen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Yuyan Hua
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Wenxuan Ji
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Jiayu Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Hua Zhao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
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Di Francesco AM, Verrecchia E, Manna S, Urbani A, Manna R. The chitinases as biomarkers in immune-mediate diseases. Clin Chem Lab Med 2022:cclm-2022-0767. [DOI: 10.1515/cclm-2022-0767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]
Abstract
Abstract
The role of chitinases has been focused as potential biomarkers in a wide number of inflammatory diseases, in monitoring active disease state, and predicting prognosis and response to therapies. The main chitinases, CHIT1 and YKL-40, are derived from 18 glycosyl hydrolases macrophage activation and play important roles in defense against chitin-containing pathogens and in food processing. Moreover, chitinases may have organ- as well as cell-specific effects in the context of infectious diseases and inflammatory disorders and able to induce tissue remodelling. The CHIT1 measurement is an easy, reproducible, reliable, and cost-effective affordable assay. The clinical use of CHIT1 for the screening of lysosomal storage disorders is quite practical, when proper cut-off values are determined for each laboratory. The potential of CHIT1 and chitinases has not been fully explored yet and future studies will produce many surprising discoveries in the immunology and allergology fields of research. However, since the presence of a null CHIT1 gene in a subpopulation would be responsible of false-negative values, the assay should be completed with the other markers such ACE and, if necessary, by genetic analysis when CHIT1 is unexpected low.
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Affiliation(s)
- Angela Maria Di Francesco
- Periodic Fever and Rare Diseases Research Centre, Catholic University of Sacred Heart , Rome , Italy
| | - Elena Verrecchia
- Periodic Fever and Rare Diseases Research Centre, Catholic University of Sacred Heart , Rome , Italy
| | - Stefano Manna
- Periodic Fever and Rare Diseases Research Centre, Catholic University of Sacred Heart , Rome , Italy
| | - Andrea Urbani
- Institute of Internal Medicine, Policlinico A. Gemelli Foundation IRCCS , Rome , Italy
- Department of Chemistry, Biochemistry and Molecular Biology , Policlinico A. Gemelli Foundation IRCCS , Rome , Italy
| | - Raffaele Manna
- Periodic Fever and Rare Diseases Research Centre, Catholic University of Sacred Heart , Rome , Italy
- Institute of Internal Medicine, Policlinico A. Gemelli Foundation IRCCS , Rome , Italy
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Giant Viruses as a Source of Novel Enzymes for Biotechnological Application. Pathogens 2022; 11:pathogens11121453. [PMID: 36558786 PMCID: PMC9787589 DOI: 10.3390/pathogens11121453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application.
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Bartholomew ES, Xu S, Zhang Y, Yin S, Feng Z, Chen S, Sun L, Yang S, Wang Y, Liu P, Ren H, Liu X. A chitinase CsChi23 promoter polymorphism underlies cucumber resistance against Fusarium oxysporum f. sp. cucumerinum. THE NEW PHYTOLOGIST 2022; 236:1471-1486. [PMID: 36068958 DOI: 10.1111/nph.18463] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Fusarium wilt disease, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), leads to widespread yield loss and quality decline in cucumber. However, the molecular mechanisms underlying Foc resistance remain poorly understood. We report the mapping and functional characterisation of CsChi23, encoding a cucumber class I chitinase with antifungal properties. We assessed sequence variations at CsChi23 and the associated defence response against Foc. We functionally characterised CsChi23 using transgenic assay and expression analysis. The mechanism regulating CsChi23 expression was assessed by genetic and molecular approaches. CsChi23 was induced by Foc infection, which led to rapid upregulation in resistant cucumber lines. Overexpressing CsChi23 enhanced fusarium wilt resistance and reduced fungal biomass accumulation, whereas silencing CsChi23 causes loss of resistance. CsHB15, a homeodomain leucine zipper (HD-Zip) III transcription factor, was found to bind to the CsChi23 promoter region and activate its expression. Furthermore, silencing of CsHB15 reduces CsChi23 expression. A single-nucleotide polymorphism variation -400 bp upstream of CsChi23 abolished the HD-Zip III binding site in a susceptible cucumber line. Collectively, our study indicates that CsChi23 is sufficient to enhance fusarium wilt resistance and reveals a novel function of an HD-Zip III transcription factor in regulating chitinase expression in cucumber defence against fusarium wilt.
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Affiliation(s)
- Ezra S Bartholomew
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shuo Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yaqi Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shuai Yin
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhongxuan Feng
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shuyinq Chen
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Lei Sun
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Songlin Yang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ying Wang
- Heze Agricultural and Rural Bureau, No. 1021 Shuanghe Road, Mudan District, Heze City, Shandong, 274000, China
| | - Peng Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Huazhong Ren
- College of Horticulture, China Agricultural University, Beijing, 100193, China
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry of National Education, Beijing, 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Beijing, 100193, China
| | - Xingwang Liu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry of National Education, Beijing, 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Beijing, 100193, China
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Liu XY, Wang SS, Zhong F, Zhou M, Jiang XY, Cheng YS, Dan YH, Hu G, Li C, Tang B, Wu Y. Chitinase (CHI) of Spodoptera frugiperda affects molting development by regulating the metabolism of chitin and trehalose. Front Physiol 2022; 13:1034926. [PMID: 36262255 PMCID: PMC9574123 DOI: 10.3389/fphys.2022.1034926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Chitin is the main component of insect exoskeleton and midgut peritrophic membrane. Insect molting is the result of the balance and coordination of chitin synthesis and degradation in chitin metabolism under the action of hormones. In this study, a 678 bp dsRNA fragment was designed and synthesized according to the known CHI (Chitinase) sequence of Spodoptera frugiperda. It was injected into the larvae to observe the molting and development of S. frugiperda. At the same time, the activities of trehalase and chitinase, the contents of trehalose, chitin and other substances were detected, and the expression of related genes in the chitin synthesis pathway was determined. The results showed that CHI gene was highly expressed at the end of each instar, prepupa and pupal stage before molting; At 12 and 24 h after dsRNA injection of CHI gene of S. frugiperda, the expression of CHI gene decreased significantly, and the chitinase activity decreased significantly from 12 to 48 h. The expression of chitin synthase (CHSB) gene decreased significantly, and the chitin content increased significantly. Some larvae could not molt normally and complete development, leading to certain mortality. Secondly, after RNAi of CHI gene, the content of glucose and glycogen increased first and then decreased, while the content of trehalose decreased significantly or showed a downward trend. The activities of the two types of trehalase and the expression levels of trehalase genes decreased first and then increased, especially the trehalase activities increased significantly at 48 h after dsCHI injection. And trehalose-6-phosphate synthase (TPS), glutamine: fructose-6-phosphate amidotransferase (GFAT), UDP-N-acetylglucosamine pyrophosphorylases (UAP), hexokinase (HK), glucose-6-phosphate isomerase (G6PI) and phosphoacetylglucosamine mutase (PAGM) all decreased significantly at 24 h, and then increased or significantly increased at 48 h. These results indicated that when the expression of chitinase gene of S. frugiperda was inhibited, it affected the degradation of chitin in the old epidermis and the formation of new epidermis, and the content of chitin increased, which led to the failure of larvae to molt normally. Moreover, the chitin synthesis pathway and trehalose metabolism were also regulated. The relevant results provide a theoretical basis for screening target genes and developing green insecticides to control pests by using the chitin metabolism pathway.
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Affiliation(s)
- Xiang-Yu Liu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, China
| | - Sha-Sha Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Fan Zhong
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Min Zhou
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, China
| | - Xin-Yi Jiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yi-Sha Cheng
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, China
| | - Yi-Hao Dan
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, China
| | - Gao Hu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, China
| | - Bin Tang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yan Wu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, China
- *Correspondence: Yan Wu,
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Mikhailov KV, Karpov SA, Letcher PM, Lee PA, Logacheva MD, Penin AA, Nesterenko MA, Pozdnyakov IR, Potapenko EV, Sherbakov DY, Panchin YV, Aleoshin VV. Genomic analysis reveals cryptic diversity in aphelids and sheds light on the emergence of Fungi. Curr Biol 2022; 32:4607-4619.e7. [PMID: 36126656 DOI: 10.1016/j.cub.2022.08.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/26/2022] [Accepted: 08/24/2022] [Indexed: 11/28/2022]
Abstract
Over the past decade, molecular phylogenetics has reshaped our understanding of the fungal tree of life by unraveling a hitherto elusive diversity of the protistan relatives of Fungi. Aphelida constitutes one of these novel deep branches that precede the emergence of osmotrophic fungal lifestyle and hold particular significance as the pathogens of algae. Here, we obtain and analyze the genomes of aphelid species Amoeboaphelidium protococcarum and Amoeboaphelidium occidentale. Genomic data unmask the vast divergence between these species, hidden behind their morphological similarity, and reveal hybrid genomes with a complex evolutionary history in two strains of A. protococcarum. We confirm the proposed sister relationship between Aphelida and Fungi using phylogenomic analysis and chart the reduction of characteristic proteins involved in phagocytic activity in the evolution of Holomycota. Annotation of aphelid genomes demonstrates the retention of actin nucleation-promoting complexes associated with phagocytosis and amoeboid motility and also reveals a conspicuous expansion of receptor-like protein kinases, uncharacteristic of fungal lineages. We find that aphelids possess multiple carbohydrate-processing enzymes that are involved in fungal cell wall synthesis but do not display rich complements of algal cell-wall-processing enzymes, suggesting an independent origin of fungal plant-degrading capabilities. Aphelid genomes show that the emergence of Fungi from phagotrophic ancestors relied on a common cell wall synthetic machinery but required a different set of proteins for digestion and interaction with the environment.
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Affiliation(s)
- Kirill V Mikhailov
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russian Federation; Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russian Federation.
| | - Sergey A Karpov
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russian Federation; Biological Faculty, St. Petersburg State University, St. Petersburg 199034, Russian Federation
| | - Peter M Letcher
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487-0344, USA
| | - Philip A Lee
- Allegheny Science and Technology, Bridgeport, WV 26330, USA
| | - Maria D Logacheva
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russian Federation; Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russian Federation; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russian Federation
| | - Aleksey A Penin
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russian Federation
| | - Maksim A Nesterenko
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russian Federation; Biological Faculty, St. Petersburg State University, St. Petersburg 199034, Russian Federation
| | - Igor R Pozdnyakov
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russian Federation
| | - Evgenii V Potapenko
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Dmitry Y Sherbakov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Yuri V Panchin
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russian Federation; Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russian Federation
| | - Vladimir V Aleoshin
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russian Federation; Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russian Federation
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Ben-Amar A, Allel D, Mliki A. Up-regulation of a stress-responsive endochitinase VvChit-IV in grapevine cell cultures improves in vitro stress tolerance. PROTOPLASMA 2022; 259:1189-1203. [PMID: 34984633 DOI: 10.1007/s00709-021-01733-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Chitinases are pathogenesis-related proteins, which play an important role in plant growth regulation, defense mechanism, and stress tolerance. Embryogenic cultures from Vitis vinifera cv. Tempranillo exposed to in vitro stress exhibited the expression of an extracellular class IV endochitinase VvChit-IV. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationships of chitinases. A computation-based investigation showed conserved domains and illustrated a chitin-binding site for chitin cleavage with a catalytic domain of glycoside hydrolase. Interestingly, gene expression pattern showed a differential expression of VvChit-IV associated with embryonic stress response to in vitro conditions. In response to in vitro stress, transcript level of VvChit-IV increased in embryogenic calli and cell suspensions and peaked at 1.5 and 3 folds, respectively, when compared to an internal reference gene. Evidence of tissue culture stress-induced endochitinase was reported here for the first time indicating that in vitro stress could mitigate elicitor application to induce chitinase expression and can stimulate an immune response against abiotic constraints. Data showed that up-regulation of VvChit-IV was associated with a substantial increase of H2O2 and proline without significant change in malondialdehyde content suggesting that the H2O2 signaling network might trigger a priming effect to boost the defense response against environmental stress. Endochitinase activation in plant stress mitigation was thus highlighted to improve tolerance through attenuation of oxidative stress. This study revealed that the grapevine endochitinase is promising for enhancing coping-oriented adaptation and abiotic stress tolerance, which gives new insights into its feasibility for use in cross-tolerance and crop improvement.
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Affiliation(s)
- Anis Ben-Amar
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia.
| | - Dorsaf Allel
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia
| | - Ahmed Mliki
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia
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42
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Skåne A, Edvardsen PK, Cordara G, Loose JSM, Leitl KD, Krengel U, Sørum H, Askarian F, Vaaje-Kolstad G. Chitinolytic enzymes contribute to the pathogenicity of Aliivibrio salmonicida LFI1238 in the invasive phase of cold-water vibriosis. BMC Microbiol 2022; 22:194. [PMID: 35941540 PMCID: PMC9361615 DOI: 10.1186/s12866-022-02590-2] [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: 03/16/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022] Open
Abstract
Background Aliivibrio salmonicida is the causative agent of cold-water vibriosis in salmonids (Oncorhynchus mykiss and Salmo salar L.) and gadidae (Gadus morhua L.). Virulence-associated factors that are essential for the full spectrum of A. salmonicida pathogenicity are largely unknown. Chitin-active lytic polysaccharide monooxygenases (LPMOs) have been indicated to play roles in both chitin degradation and virulence in a variety of pathogenic bacteria but are largely unexplored in this context. Results In the present study we investigated the role of LPMOs in the pathogenicity of A. salmonicida LFI238 in Atlantic salmon (Salmo salar L.). In vivo challenge experiments using isogenic deletion mutants of the two LPMOs encoding genes AsLPMO10A and AsLPMO10B, showed that both LPMOs, and in particular AsLPMO10B, were important in the invasive phase of cold-water vibriosis. Crystallographic analysis of the AsLPMO10B AA10 LPMO domain (to 1.4 Å resolution) revealed high structural similarity to viral fusolin, an LPMO known to enhance the virulence of insecticidal agents. Finally, exposure to Atlantic salmon serum resulted in substantial proteome re-organization of the A. salmonicida LPMO deletion variants compared to the wild type strain, indicating the struggle of the bacterium to adapt to the host immune components in the absence of the LPMOs. Conclusion The present study consolidates the role of LPMOs in virulence and demonstrates that such enzymes may have more than one function.
Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02590-2.
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Affiliation(s)
- Anna Skåne
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Per Kristian Edvardsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gabriele Cordara
- Department of Chemistry, University of Oslo, Blindern, P.O. Box 1033, NO-0315, Oslo, Norway
| | - Jennifer Sarah Maria Loose
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Kira Daryl Leitl
- Department of Chemistry, University of Oslo, Blindern, P.O. Box 1033, NO-0315, Oslo, Norway
| | - Ute Krengel
- Department of Chemistry, University of Oslo, Blindern, P.O. Box 1033, NO-0315, Oslo, Norway
| | - Henning Sørum
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Fatemeh Askarian
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, San Diego, CA, USA.
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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Liu J, Xu Q, Wu Y, Sun D, Zhu J, Liu C, Liu W. Carbohydrate-binding modules of ChiB and ChiC promote the chitinolytic system of Serratia marcescens BWL1001. Enzyme Microb Technol 2022; 162:110118. [DOI: 10.1016/j.enzmictec.2022.110118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022]
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Speciale I, Notaro A, Abergel C, Lanzetta R, Lowary TL, Molinaro A, Tonetti M, Van Etten JL, De Castro C. The Astounding World of Glycans from Giant Viruses. Chem Rev 2022; 122:15717-15766. [PMID: 35820164 PMCID: PMC9614988 DOI: 10.1021/acs.chemrev.2c00118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Viruses are a heterogeneous ensemble of entities, all
sharing the
need for a suitable host to replicate. They are extremely diverse,
varying in morphology, size, nature, and complexity of their genomic
content. Typically, viruses use host-encoded glycosyltransferases
and glycosidases to add and remove sugar residues from their glycoproteins.
Thus, the structure of the glycans on the viral proteins have, to
date, typically been considered to mimick those of the host. However,
the more recently discovered large and giant viruses differ from this
paradigm. At least some of these viruses code for an (almost) autonomous
glycosylation pathway. These viral genes include those that encode
the production of activated sugars, glycosyltransferases, and other
enzymes able to manipulate sugars at various levels. This review focuses
on large and giant viruses that produce carbohydrate-processing enzymes.
A brief description of those harboring these features at the genomic
level will be discussed, followed by the achievements reached with
regard to the elucidation of the glycan structures, the activity of
the proteins able to manipulate sugars, and the organic synthesis
of some of these virus-encoded glycans. During this progression, we
will also comment on many of the challenging questions on this subject
that remain to be addressed.
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Affiliation(s)
- Immacolata Speciale
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy
| | - Anna Notaro
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy.,Centre National de la Recherche Scientifique, Information Génomique & Structurale, Aix-Marseille University, Unité Mixte de Recherche 7256, IMM, IM2B, 13288 Marseille, Cedex 9, France
| | - Chantal Abergel
- Centre National de la Recherche Scientifique, Information Génomique & Structurale, Aix-Marseille University, Unité Mixte de Recherche 7256, IMM, IM2B, 13288 Marseille, Cedex 9, France
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Napoli, Via Cintia 4, 80126 Napoli, Italy
| | - Todd L Lowary
- Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, Nangang 11529, Taipei, Taiwan
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli, Via Cintia 4, 80126 Napoli, Italy
| | - Michela Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900, United States.,Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, United States
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy
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Jiménez-Ortega E, Kidibule PE, Fernández-Lobato M, Sanz-Aparicio J. Structure-Function Insights into the Fungal Endo-Chitinase Chit33 Depict its Mechanism on Chitinous Material. Int J Mol Sci 2022; 23:ijms23147599. [PMID: 35886948 PMCID: PMC9323625 DOI: 10.3390/ijms23147599] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023] Open
Abstract
Chitin is the most widespread amino renewable carbohydrate polymer in nature and the second most abundant polysaccharide. Therefore, chitin and chitinolytic enzymes are becoming more importance for biotechnological applications in food, health and agricultural fields, the design of effective enzymes being a paramount issue. We report the crystal structure of the plant-type endo-chitinase Chit33 from Trichoderma harzianum and its D165A/E167A-Chit33-(NAG)4 complex, which showed an extended catalytic cleft with six binding subsites lined with many polar interactions. The major trait of Chit33 is the location of the non-conserved Asp117 and Arg274 acting as a clamp, fixing the distorted conformation of the sugar at subsite -1 and the bent shape of the substrate, which occupies the full catalytic groove. Relevant residues were selected for mutagenesis experiments, the variants being biochemically characterized through their hydrolytic activity against colloidal chitin and other polymeric substrates with different molecular weights and deacetylation percentages. The mutant S118Y stands out, showing a superior performance in all the substrates tested, as well as detectable transglycosylation capacity, with this variant providing a promising platform for generation of novel Chit33 variants with adjusted performance by further design of rational mutants'. The putative role of Tyr in binding was extrapolated from molecular dynamics simulation.
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Affiliation(s)
- Elena Jiménez-Ortega
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, 28006 Madrid, Spain;
| | - Peter Elias Kidibule
- Department of Molecular Biology, Centre of Molecular Biology Severo Ochoa, CSIC-UAM, 28049 Madrid, Spain;
| | - María Fernández-Lobato
- Department of Molecular Biology, Centre of Molecular Biology Severo Ochoa, CSIC-UAM, 28049 Madrid, Spain;
- Correspondence: (M.F.-L.); (J.S.-A.)
| | - Julia Sanz-Aparicio
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, 28006 Madrid, Spain;
- Correspondence: (M.F.-L.); (J.S.-A.)
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Kim J, Lee B, Chhetri G, Kim I, So Y, Jang W, Seo T. Identification of Mucilaginibacter conchicola sp. nov., Mucilaginibacter achroorhodeus sp. nov. and Mucilaginibacter pallidiroseus sp. nov. and emended description of the genus Mucilaginibacter. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005431] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three chitinolytic, Gram-negative, light pink, capsule-forming, rod-shaped bacterial strains with gliding motion (MYSH2T, MJ1aT and dk17T) were isolated from seashells, soil and foxtail, respectively. Phylogenetic analysis of the 16S rRNA gene sequences and concatenated alignment of 92 core genes indicated that strains MYSH2T, MJ1aT and dk17T were novel species of the genus
Mucilaginibacter
and exhibited a high 16S rRNA sequence similarity (i.e. more than 97.2 %) among each other. These novel strains contained summed feature 3 (C16:1 ω7c and/or C16:1 ω6), iso-C15:0 and MK-7 as the predominant fatty acids and menaquinone. According to the CAZys coding gene of KAAS, MYSH2T and MJ1aT were interpreted as strains containing both GH18 and 19 family coding genes, except for dk17T, which shows only GH19 family genes. These strains likely degrade chitin to chitobiose or directly to N-acetyl-d-glucosamine, which may enhance their chitinolytic capacity, thus making these stains potentially useful for industrial chitin degradation. Based on distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains MYSH2T, MJ1aT and dk17T represent three novel species in the genus
Mucilaginibacter
, for which the names Mucilaginibacter conchicola sp. nov. (=KACC 19716T=JCM 32787T), Mucilaginibacter achroorhodeus sp. nov. (=KACC 19906T=NBRC 113667T) and Mucilaginibacter pallidiroseus sp. nov. (=KACC 19907T=NBRC 113666T) are proposed. An emended description of the genus
Mucilaginibacter
is proposed.
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Affiliation(s)
- Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Byungjo Lee
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Wonhee Jang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
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47
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Kumari P, Jasrotia P, Kumar D, Kashyap PL, Kumar S, Mishra CN, Kumar S, Singh GP. Biotechnological Approaches for Host Plant Resistance to Insect Pests. Front Genet 2022; 13:914029. [PMID: 35719377 PMCID: PMC9201757 DOI: 10.3389/fgene.2022.914029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/16/2022] [Indexed: 11/14/2022] Open
Abstract
Annually, the cost of insect pest control in agriculture crosses billions of dollars around the world. Until recently, broad-spectrum synthetic pesticides were considered as the most effective means of pest control in agriculture. However, over the years, the overreliance on pesticides has caused adverse effects on beneficial insects, human health and the environment, and has led to the development of pesticide resistant insects. There is a critical need for the development of alternative pest management strategies aiming for minimum use of pesticides and conservation of natural enemies for maintaining the ecological balance of the environment. Host plant resistance plays a vital role in integrated pest management but the development of insect-resistant varieties through conventional ways of host plant resistance takes time, and is challenging as it involves many quantitative traits positioned at various loci. Biotechnological approaches such as gene editing, gene transformation, marker-assisted selection etc. in this direction have recently opened up a new era of insect control options. These could contribute towards about exploring a much wider array of novel insecticidal genes that would otherwise be beyond the scope of conventional breeding. Biotechnological interventions can alter the gene expression level and pattern as well as the development of transgenic varieties with insecticidal genes and can improve pest management by providing access to novel molecules. This review will discuss the emerging biotechnological tools available to develop insect-resistant engineered crop genotypes with a better ability to resist the attack of insect pests.
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Affiliation(s)
- Pritam Kumari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- CCS Haryana Agricultural University, Hisar, India
| | - Poonam Jasrotia
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Deepak Kumar
- CCS Haryana Agricultural University, Hisar, India
| | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
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48
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The Insect Pathogen Photorhabdus luminescens Protects Plants from Phytopathogenic Fusarium graminearum via Chitin Degradation. Appl Environ Microbiol 2022; 88:e0064522. [PMID: 35604230 DOI: 10.1128/aem.00645-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phytopathogens represent a large agricultural challenge. The use of chemical pesticides is harmful to the environment, animals, and humans. Therefore, new sustainable and biological alternatives are urgently needed. The insect-pathogenic bacterium Photorhabdus luminescens, already used in combination with entomopathogenic nematodes (EPNs) as a biocontrol agent, is characterized by two different phenotypic cell forms, called primary (1°) and secondary (2°). The 1° cells are symbiotic with EPNs and are used for biocontrol, and the 2° cells are unable to undergo symbiosis with EPNs, remain in the soil after insect infection, and specifically interact with plant roots. A previous RNA sequencing (RNAseq) analysis showed that genes encoding the exochitinase Chi2A and chitin binding protein (CBP) are highly upregulated in 2° cells exposed to plant root exudates. Here, we investigate Chi2A and CBP functions and demonstrate that both are necessary for P. luminescens 2° cells to inhibit the growth of the phytopathogenic fungus Fusarium graminearum. We provide evidence that Chi2A digests chitin and thereby inhibits fungal growth. Furthermore, we show that 2° cells specifically colonize fungal hyphae as one of the first mechanisms to protect plants from fungal phytopathogens. Finally, soil pot bioassays proved plant protection from F. graminearum by 2° cells, where Chi2A and CPB were essential for this process. This work gives molecular insights into the new applicability of P. luminescens as a plant-growth-promoting and plant-protecting organism in agriculture. IMPORTANCE The enteric enterobacterium Photorhabdus luminescens is already being used as a bioinsecticide since it is highly pathogenic toward a broad range of insects. However, the bacteria exist in two phenotypically different cell types, called 1° and 2° cells. Whereas only 1° cells are symbiotic with their nematode partner to infect insects, 2° cells were shown to remain in the soil after an insect infection cycle. It was demonstrated that 2° cells specifically interact with plant roots. Here, we show that the bacteria are beneficial for the plants by protecting them from phytopathogenic fungi. Specific colonization of the fungus mycelium as well as chitin-degrading activity mediated by the chitin binding protein (CBP) and the chitinase Chi2A are essential for this process. Our data give evidence for the novel future applicability of P. luminescens as a plant-growth-promoting organism and biopesticide.
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Qiu S, Zhou S, Tan Y, Feng J, Bai Y, He J, Cao H, Che Q, Guo J, Su Z. Biodegradation and Prospect of Polysaccharide from Crustaceans. Mar Drugs 2022; 20:310. [PMID: 35621961 PMCID: PMC9146327 DOI: 10.3390/md20050310] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 01/27/2023] Open
Abstract
Marine crustacean waste has not been fully utilized and is a rich source of chitin. Enzymatic degradation has attracted the wide attention of researchers due to its unique biocatalytic ability to protect the environment. Chitosan (CTS) and its derivative chitosan oligosaccharides (COSs) with various biological activities can be obtained by the enzymatic degradation of chitin. Many studies have shown that chitosan and its derivatives, chitosan oligosaccharides (COSs), have beneficial properties, including lipid-lowering, anti-inflammatory and antitumor activities, and have important application value in the medical treatment field, the food industry and agriculture. In this review, we describe the classification, biochemical characteristics and catalytic mechanisms of the major degrading enzymes: chitinases, chitin deacetylases (CDAs) and chitosanases. We also introduced the technology for enzymatic design and modification and proposed the current problems and development trends of enzymatic degradation of chitin polysaccharides. The discussion on the characteristics and catalytic mechanism of chitosan-degrading enzymes will help to develop new types of hydrolases by various biotechnology methods and promote their application in chitosan.
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Affiliation(s)
- Shuting Qiu
- Guangdong Engineering Research Center of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Center of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China; (S.Q.); (S.Z.); (Y.T.); (J.F.)
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Shipeng Zhou
- Guangdong Engineering Research Center of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Center of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China; (S.Q.); (S.Z.); (Y.T.); (J.F.)
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yue Tan
- Guangdong Engineering Research Center of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Center of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China; (S.Q.); (S.Z.); (Y.T.); (J.F.)
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jiayao Feng
- Guangdong Engineering Research Center of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Center of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China; (S.Q.); (S.Z.); (Y.T.); (J.F.)
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yan Bai
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou 510310, China; (Y.B.); (J.H.)
| | - Jincan He
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou 510310, China; (Y.B.); (J.H.)
| | - Hua Cao
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan 528458, China;
| | - Qishi Che
- Guangzhou Rainhome Pharm & Tech Co., Ltd., Science City, Guangzhou 510663, China;
| | - Jiao Guo
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhengquan Su
- Guangdong Engineering Research Center of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Center of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China; (S.Q.); (S.Z.); (Y.T.); (J.F.)
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
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50
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Rajput M, Kumar M, Pareek N. Myco-chitinases as versatile biocatalysts for translation of coastal residual resources to eco-competent chito-bioactives. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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