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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] [Grants] [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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2
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McClure R, Garcia M, Couvillion S, Farris Y, Hofmockel KS. Removal of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancy. Front Microbiol 2023; 13:1046661. [PMID: 36762098 PMCID: PMC9902710 DOI: 10.3389/fmicb.2022.1046661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/21/2022] [Indexed: 01/25/2023] Open
Abstract
Introduction Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here, we used a model substrate, chitin, and a synthetic Model Soil Consortium (MSC-2) to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent. Methods To characterize specific roles within this synthetic community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members. Results Our results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed, as well as alterations in the metabolic profile, especially when Streptomyces was lacking. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration. Discussion Our findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.
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Affiliation(s)
- Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Marci Garcia
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sneha Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kirsten S. Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
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Akram F, Jabbar Z, Aqeel A, Haq IU, Tariq S, Malik K. A Contemporary Appraisal on Impending Industrial and Agricultural Applications of Thermophilic-Recombinant Chitinolytic Enzymes from Microbial Sources. Mol Biotechnol 2022; 64:1055-1075. [PMID: 35397055 DOI: 10.1007/s12033-022-00486-0] [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: 12/18/2021] [Accepted: 03/25/2022] [Indexed: 01/09/2023]
Abstract
The ability of chitinases to degrade the second most abundant polymer, chitin, into potentially useful chitooligomers and chitin derivatives has not only rendered them fit for chitinous waste management but has also made them important from industrial point of view. At the same time, they have also been recognized to have an imperative role as promising biocontrol agents for controlling plant diseases. As thermostability is an important property for an industrially important enzyme, various bacterial and fungal sources are being exploited to obtain such stable enzymes. These stable enzymes can also play a role in agriculture by maintaining their stability under adverse environmental conditions for longer time duration when used as biocontrol agent. Biotechnology has also played its role in the development of recombinant chitinases with enhanced activity, thermostability, fungicidal and insecticidal activity via recombinant DNA techniques. Furthermore, a relatively new approach of generating pathogen-resistant transgenic plants has opened new ways for sustainable agriculture by minimizing the yield loss of valuable crops and plants. This review focuses on the potential applications of thermostable and recombinant microbial chitinases in industry and agriculture.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Zuriat Jabbar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.,Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Shahbaz Tariq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Kausar Malik
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Gaona-Mendoza AS, Bravo Rivas MC, Barboza-Corona JE, Massange-Sánchez JA, Casados-Vázquez LE. Expression of thurincin H, ChiA74 and Cry proteins at the sporulation phase in Bacillus thuringiensis HD1. J Appl Microbiol 2021; 132:3049-3057. [PMID: 34967963 DOI: 10.1111/jam.15434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/03/2021] [Accepted: 12/28/2021] [Indexed: 11/29/2022]
Abstract
AIMS The objective of this study was to produce thurincin H, ChiA74 and Cry proteins together using B. thuringiensis subsp. kurstaki HD1 as a heterologous host. METHODS AND RESULTS pSTAB-ThurH and pSTAB-ChiA74 constructs were designed to produce thurincin H and chitinase respectively, at the sporulation phase. They were transformed into Bt HD1 generating the recombinant strains HD1/pSTAB-ThurH and HD1/pSTAB-ThurH/pSTAB-ChiA74. Antimicrobial and chitinolytic activity tests were performed with recombinant strains. Both strains were able to produce thurincin H up to 72 h with antibacterial activity of ~ 4000 U mg-1 . The HD1/pSTAB-ThurH/pSTAB-ChiA74 strain also showed chitinolytic activity of ~ 23 mU mg-1 at 72 h. All B. thuringiensis strains exhibited crystal formation at 72, and 96 h. In addition, the application of thurincin H in corn seeds increased the germination percentage and root length by 7 % and 10 %, respectively. CONCLUSIONS We showed that is possible to produce three proteins of biotechnological interest at the sporulation stage in B. thuringiensis, which two of them (thurincin H, and ChiA74) are naturally expressed in the vegetative stage. SIGNIFICANCE AND IMPACT OF THE STUDY These results form the basis for developing of a biocontrol and biostimulator product that can be used as an alternative for chemical application.
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Affiliation(s)
- America S Gaona-Mendoza
- Universidad de Guanajuato Campus Irapuato-Salamanca, Life Science Division, Graduate Program in Biosciences.,Food Department, Irapuato, Guanajuato, Mexico, 36500
| | - Martha C Bravo Rivas
- Universidad de Guanajuato Campus Irapuato-Salamanca, Life Science Division, Graduate Program in Biosciences.,Food Department, Irapuato, Guanajuato, Mexico, 36500
| | - José E Barboza-Corona
- Universidad de Guanajuato Campus Irapuato-Salamanca, Life Science Division, Graduate Program in Biosciences.,Food Department, Irapuato, Guanajuato, Mexico, 36500
| | - Julio A Massange-Sánchez
- Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología, Diseño del Estado de Jalisco A.C. (CIATEJ), Guadalajara, 44270, Mexico
| | - Luz E Casados-Vázquez
- Universidad de Guanajuato Campus Irapuato-Salamanca, Life Science Division, Graduate Program in Biosciences.,Food Department, Irapuato, Guanajuato, Mexico, 36500.,Cátedra Conacyt-Universidad de Guanajuato
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Abady SM, M Ghanem K, Ghanem NB, Embaby AM. Molecular cloning, heterologous expression, and in silico sequence analysis of Enterobacter GH19 class I chitinase (chiRAM gene). Mol Biol Rep 2021; 49:951-969. [PMID: 34773550 DOI: 10.1007/s11033-021-06914-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/30/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Using in silico sequence analyses, the present study aims to clone and express the gene-encoding sequence of a GH19 chitinase from Enterobacter sp. in Escherichia coli. METHODS AND RESULTS The putative open reading frame of a GH19 chitinase from Enterobacter sp. strain EGY1 was cloned and expressed into pGEM®-T and pET-28a (+) vectors, respectively using a degenerate primer. The isolated nucleotide sequence (1821 bp, GenBank accession no.: MK533791.2) was translated to a chiRAM protein (606 amino acids, UniProt accession no.: A0A4D6J2L9). The in silico protein sequence analysis of chiRAM revealed a class I GH19 chitinase: an N-terminus signal peptide (Met1-Ala23), a catalytic domain (Val83-Glu347 and the catalytic triad Glu149, Glu171, and Ser218), a proline-rich hinge region (Pro414 -Pro450), a polycystic kidney disease protein motif (Gly 465-Ser 533), a C-terminus chitin-binding domain (Ala553- Glu593), and conserved class I motifs (NYNY and AQETGG). A three-dimensional model was constructed by LOMETS MODELLER of PDB template: 2dkvA (class I chitinase of Oryza sativa L. japonica). Recombinant chiRAM was overexpressed as inclusion bodies (IBs) (~ 72 kDa; SDS-PAGE) in 1.0 mM IPTG induced E. coli BL21 (DE3) Rosetta strain at room temperature 18 h after induction. Optimized expression yielded active chiRAM with 1.974 ± 0.0002 U/mL, on shrimp colloidal chitin (SCC), in induced E. coli BL21 (DE3) Rosetta cells growing in SB medium. LC-MS/MS identified a band of 72 kDa in the soluble fraction with a 52.3% coverage sequence exclusive to the GH19 chitinase of Enterobacter cloacae (WP_063869339.1). CONCLUSIONS Although chiRAM of Enterobacter sp. was successfully cloned and expressed in E. coli with appreciable chitinase activity, future studies should focus on minimizing IBs to facilitate chiRAM purification and characterization.
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Affiliation(s)
- Shahinaz M Abady
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, 1 Baghdad Street-Moharam Bek, Alexandria, 21568, Egypt
| | - Khaled M Ghanem
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, 1 Baghdad Street-Moharam Bek, Alexandria, 21568, Egypt
| | - Nevine B Ghanem
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, 1 Baghdad Street-Moharam Bek, Alexandria, 21568, Egypt
| | - Amira M Embaby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, P.O.Box 832, 163 Horreya Avenue, Chatby, Alexandria, 21526, Egypt.
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Bartholomai BM, Gladfelter AS, Loros JJ, Dunlap JC. Quantitative single molecule RNA-FISH and RNase-free cell wall digestion in Neurospora crassa. Fungal Genet Biol 2021; 156:103615. [PMID: 34425213 PMCID: PMC8463489 DOI: 10.1016/j.fgb.2021.103615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 10/20/2022]
Abstract
Single molecule RNA-FISH (smFISH) is a valuable tool for analysis of mRNA spatial patterning in fixed cells that is underutilized in filamentous fungi. A primary complication for fixed-cell imaging in filamentous fungi is the need for enzymatic cell wall permeabilization, which is compounded by considerable variability in cell wall composition between species. smFISH adds another layer of complexity due to a requirement for RNase free conditions. Here, we describe the cloning, expression, and purification of a chitinase suitable for supplementation of a commercially available RNase-free enzyme preparation for efficient permeabilization of the Neurospora cell wall. We further provide a method for smFISH in Neurospora which includes a tool for generating numerical data from images that can be used in downstream customized analysis protocols.
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Affiliation(s)
- Bradley M Bartholomai
- Geisel School of Medicine at Dartmouth, Department of Molecular and Systems Biology, Hanover, NH, USA
| | - Amy S Gladfelter
- University of North Carolina, Department of Biology, Chapel Hill, NC, USA
| | - Jennifer J Loros
- Geisel School of Medicine at Dartmouth, Department of Biochemistry and Cell Biology, Hanover, NH, USA
| | - Jay C Dunlap
- Geisel School of Medicine at Dartmouth, Department of Molecular and Systems Biology, Hanover, NH, USA.
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7
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Menghiu G, Ostafe V, Prodanović R, Fischer R, Ostafe R. A High-Throughput Screening System Based on Fluorescence-Activated Cell Sorting for the Directed Evolution of Chitinase A. Int J Mol Sci 2021; 22:ijms22063041. [PMID: 33809788 PMCID: PMC8002391 DOI: 10.3390/ijms22063041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/13/2022] Open
Abstract
Chitinases catalyze the degradation of chitin, a polymer of N-acetylglucosamine found in crustacean shells, insect cuticles, and fungal cell walls. There is great interest in the development of improved chitinases to address the environmental burden of chitin waste from the food processing industry as well as the potential medical, agricultural, and industrial uses of partially deacetylated chitin (chitosan) and its products (chito-oligosaccharides). The depolymerization of chitin can be achieved using chemical and physical treatments, but an enzymatic process would be more environmentally friendly and more sustainable. However, chitinases are slow-acting enzymes, limiting their biotechnological exploitation, although this can be overcome by molecular evolution approaches to enhance the features required for specific applications. The two main goals of this study were the development of a high-throughput screening system for chitinase activity (which could be extrapolated to other hydrolytic enzymes), and the deployment of this new method to select improved chitinase variants. We therefore cloned and expressed the Bacillus licheniformis DSM8785 chitinase A (chiA) gene in Escherichia coli BL21 (DE3) cells and generated a mutant library by error-prone PCR. We then developed a screening method based on fluorescence-activated cell sorting (FACS) using the model substrate 4-methylumbelliferyl β-d-N,N′,N″-triacetyl chitotrioside to identify improved enzymes. We prevented cross-talk between emulsion compartments caused by the hydrophobicity of 4-methylumbelliferone, the fluorescent product of the enzymatic reaction, by incorporating cyclodextrins into the aqueous phases. We also addressed the toxicity of long-term chiA expression in E. coli by limiting the reaction time. We identified 12 mutants containing 2–8 mutations per gene resulting in up to twofold higher activity than wild-type ChiA.
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Affiliation(s)
- Gheorghita Menghiu
- Institute for Biology VII, Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (G.M.); (R.F.)
- Advanced Environmental Research Laboratories, Department of Biology–Chemistry, West University of Timisoara, Oituz 4, 300086 Timisoara, Romania;
| | - Vasile Ostafe
- Advanced Environmental Research Laboratories, Department of Biology–Chemistry, West University of Timisoara, Oituz 4, 300086 Timisoara, Romania;
| | - Radivoje Prodanović
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia;
| | - Rainer Fischer
- Institute for Biology VII, Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (G.M.); (R.F.)
- Departments of Biological Sciences and Chemistry, Purdue University, 207 S. Martin Jischke Dr., West Lafayette, IN 47907, USA
| | - Raluca Ostafe
- Institute for Biology VII, Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (G.M.); (R.F.)
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Molecular Evolution, Protein Engineering and Production, Purdue University, 207 S. Martin Jischke Dr., West Lafayette, IN 47907, USA
- Correspondence: ; Tel.: +1-317-765-496-4012
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Secretory production in Escherichia coli of a GH46 chitosanase from Chromobacterium violaceum, suitable to generate antifungal chitooligosaccharides. Int J Biol Macromol 2020; 165:1482-1495. [PMID: 33017605 DOI: 10.1016/j.ijbiomac.2020.09.221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 01/23/2023]
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Oliveira ST, Azevedo MIG, Cunha RMS, Silva CFB, Muniz CR, Monteiro-Júnior JE, Carneiro RF, Nagano CS, Girão MS, Freitas CDT, Grangeiro TB. Structural and functional features of a class VI chitinase from cashew (Anacardium occidentale L.) with antifungal properties. PHYTOCHEMISTRY 2020; 180:112527. [PMID: 33007618 DOI: 10.1016/j.phytochem.2020.112527] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/25/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
A partial cDNA sequence from Anacardium occidentale CCP 76 was obtained, encoding a GH19 chitinase (AoChi) belonging to class VI. AoChi exhibits distinct structural features in relation to previously characterized plant GH19 chitinases from classes I, II, IV and VII. For example, a conserved Glu residue at the catalytic center of typical GH19 chitinases, which acts as the proton donor during catalysis, is replaced by a Lys residue in AoChi. To verify if AoChi is a genuine chitinase or is a chitinase-like protein that has lost its ability to degrade chitin and inhibit the growth of fungal pathogens, the recombinant protein was expressed in Pichia pastoris, purified and biochemically characterized. Purified AoChi (45 kDa apparent molecular mass) was able to degrade colloidal chitin, with optimum activity at pH 6.0 and at temperatures from 30 °C to 50 °C. AoChi activity was completely lost when the protein was heated at 70 °C for 1 h or incubated at pH values of 2.0 or 10.0. Several cation ions (Al3+, Cd2+, Ca2+, Pb2+, Cu2+, Fe3+, Mn2+, Rb+, Zn2+ and Hg2+), chelating (EDTA) and reducing agents (DTT, β-mercaptoethanol) and the denaturant SDS, drastically reduced AoChi enzymatic activity. AoChi chitinase activity fitted the classical Michaelis-Menten kinetics, although turnover number and catalytic efficiency were much lower in comparison to typical GH19 plant chitinases. Moreover, AoChi inhibited in vitro the mycelial growth of Lasiodiplodia theobromae, causing several alterations in hyphae morphology. Molecular docking of a chito-oligosaccharide in the substrate-binding cleft of AoChi revealed that the Lys residue (theoretical pKa = 6.01) that replaces the catalytic Glu could act as the proton donor during catalysis.
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Affiliation(s)
- Simone T Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Mayara I G Azevedo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Rodrigo M S Cunha
- Centro de Ciências Agrárias e Biológicas, Universidade do Vale do Acaraú, Sobral, Ceará, Brazil
| | | | - Celli R Muniz
- Embrapa Agroindústria Tropical, Fortaleza, Ceará, Brazil
| | - José E Monteiro-Júnior
- Laboratório de Genética Molecular, Departamento de Biologia, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Rômulo F Carneiro
- Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Celso S Nagano
- Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Matheus S Girão
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Cleverson D T Freitas
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Thalles B Grangeiro
- Laboratório de Genética Molecular, Departamento de Biologia, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil.
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Mathew GM, Madhavan A, Arun KB, Sindhu R, Binod P, Singhania RR, Sukumaran RK, Pandey A. Thermophilic Chitinases: Structural, Functional and Engineering Attributes for Industrial Applications. Appl Biochem Biotechnol 2020; 193:142-164. [PMID: 32827066 DOI: 10.1007/s12010-020-03416-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
Chitin is the second most widely found natural polymer next to cellulose. Chitinases degrade the insoluble chitin to bioactive chitooligomers and monomers for various industrial applications. Based on their function, these enzymes act as biocontrol agents against pathogenic fungi and invasive pests compared with conventional chemical fungicides and insecticides. They have other functional roles in shellfish waste management, fungal protoplast generation, and Single-Cell Protein production. Among the chitinases, thermophilic and thermostable chitinases are gaining popularity in recent years, as they can withstand high temperatures and maintain the enzyme stability for longer periods. Not all chitinases are thermostable; hence, tailor-made thermophilic chitinases are designed to enhance their thermostability by direct evolution, genetic engineering involving mutagenesis, and proteomics approach. Although research has been done extensively on cloning and expression of thermophilic chitinase genes, there are only few papers discussing on the mechanism of chitin degradation using thermophiles. The current review discusses the sources of thermophilic chitinases, improvement of protein stability by gene manipulation, metagenomics approaches, chitin degradation mechanism in thermophiles, and their prospective applications for industrial, agricultural, and pharmaceutical purposes.
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Affiliation(s)
- Gincy M Mathew
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - K B Arun
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | | | - Rajeev K Sukumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR - Indian Institute of Toxicology Research, Lucknow, 226 001, India.
- Frontier Research Lab, Yonsei University, Seoul, South Korea.
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Li RK, Hu YJ, Ng TB, Guo BQ, Zhou ZH, Zhao J, Ye XY. Expression and biochemical characterization of a novel chitinase ChiT-7 from the metagenome in the soil of a mangrove tidal flat in China. Int J Biol Macromol 2020; 158:1125-1134. [PMID: 32360969 DOI: 10.1016/j.ijbiomac.2020.04.242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 12/18/2022]
Abstract
Chitinases play an important role in the process of chitin bioavailability. In this study, we cloned a new chitinase gene and characterized its recombinant protein. The new 1251 bp gene of chitinase (ChiT-7) was cloned from the metagenome of the mangrove tidal flat soil in the city of Zhangzhou in Fujian Province (China) by genome walking. The gene encoded a mature protein with 381 amino acids, which manifested certain sequence similarity (59% identity) to characterized GH18 chitinases. The mature protein of ChiT-7 was successfully expressed in E. coli BL21 (DE3). After purification, the specific activity of the recombinant enzyme was 0.63 U/mg at the optimal pH of 6.0 and the optimal temperature of 45 °C. The rChiT-7 was active over a wide pH range, and the residual enzyme activity reached 80% or higher at 30 °C-50 °C. rChiT-7 hydrolyzed colloidal chitin with (GlcNAc)2 and GlcNAc as the main final products. Structural analysis of ChiT-7 indicated that ChiT-7 could be a processive chitinase. rChiT-7 manifested characteristics analogous to those of fungi and actinomycetes and exhibited sequence homology.
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Affiliation(s)
- Ren Kuan Li
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, PR China; National Engineering Laboratory for High-efficient Enzyme Expression, PR China
| | - Ya Juan Hu
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, PR China
| | - Tzi Bun Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Bing Qi Guo
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, PR China
| | - Zi He Zhou
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, PR China
| | - Jing Zhao
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, PR China
| | - Xiu Yun Ye
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, PR China; National Engineering Laboratory for High-efficient Enzyme Expression, PR China.
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12
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Ma X, Gözaydın G, Yang H, Ning W, Han X, Poon NY, Liang H, Yan N, Zhou K. Upcycling chitin-containing waste into organonitrogen chemicals via an integrated process. Proc Natl Acad Sci U S A 2020; 117:7719-7728. [PMID: 32213582 PMCID: PMC7149430 DOI: 10.1073/pnas.1919862117] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chitin is the most abundant renewable nitrogenous material on earth and is accessible to humans in the form of crustacean shell waste. Such waste has been severely underutilized, resulting in both resource wastage and disposal issues. Upcycling chitin-containing waste into value-added products is an attractive solution. However, the direct conversion of crustacean shell waste-derived chitin into a wide spectrum of nitrogen-containing chemicals (NCCs) is challenging via conventional catalytic processes. To address this challenge, in this study, we developed an integrated biorefinery process to upgrade shell waste-derived chitin into two aromatic NCCs that currently cannot be synthesized from chitin via any chemical process (tyrosine and l-DOPA). The process involves a pretreatment of chitin-containing shell waste and an enzymatic/fermentative bioprocess using metabolically engineered Escherichia coli The pretreatment step achieved an almost 100% recovery and partial depolymerization of chitin from shrimp shell waste (SSW), thereby offering water-soluble chitin hydrolysates for the downstream microbial process under mild conditions. The engineered E. coli strains produced 0.91 g/L tyrosine or 0.41 g/L l-DOPA from 22.5 g/L unpurified SSW-derived chitin hydrolysates, demonstrating the feasibility of upcycling renewable chitin-containing waste into value-added NCCs via this integrated biorefinery, which bypassed the Haber-Bosch process in providing a nitrogen source.
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Affiliation(s)
- Xiaoqiang Ma
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-Massachusetts Institute of Technology Alliance for Research and Technology, Singapore 138602, Singapore
| | - Gökalp Gözaydın
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Huiying Yang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Wenbo Ning
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Xi Han
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Nga Yu Poon
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-Massachusetts Institute of Technology Alliance for Research and Technology, Singapore 138602, Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Hong Liang
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-Massachusetts Institute of Technology Alliance for Research and Technology, Singapore 138602, Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Ning Yan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Kang Zhou
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-Massachusetts Institute of Technology Alliance for Research and Technology, Singapore 138602, Singapore;
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
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13
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Martínez-Zavala SA, Barboza-Pérez UE, Hernández-Guzmán G, Bideshi DK, Barboza-Corona JE. Chitinases of Bacillus thuringiensis: Phylogeny, Modular Structure, and Applied Potentials. Front Microbiol 2020; 10:3032. [PMID: 31993038 PMCID: PMC6971178 DOI: 10.3389/fmicb.2019.03032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/17/2019] [Indexed: 01/09/2023] Open
Abstract
The most important bioinsecticide used worldwide is Bacillus thuringiensis and its hallmark is a rich variety of insecticidal Cry protein, many of which have been genetically engineered for expression in transgenic crops. Over the past 20 years, the discovery of other insecticidal proteins and metabolites synthesized by B. thuringiensis, including chitinases, antimicrobial peptides, vegetative insecticidal proteins (VIP), and siderophores, has expanded the applied value of this bacterium for use as an antibacterial, fungicidal, and nematicidal resource. These properties allow us to view B. thuringiensis not only as an entity for the production of a particular metabolite, but also as a multifaceted microbial factory. In particular, chitinases of B. thuringiensis are secreted enzymes that hydrolyze chitin, an abundant molecule in the biosphere, second only to cellulose. The observation that chitinases increase the insecticidal activity of Cry proteins has stimulated further study of these enzymes produced by B. thuringiensis. Here, we provide a review of a subset of our knowledge of B. thuringiensis chitinases as it relates to their phylogenetic relationships, regulation of expression, biotechnological potential for controlling entomopathogens, fungi, and nematodes, and their use in generating chitin-derived oligosaccharides (ChOGs) that possess antibacterial activities against a number of clinically significant bacterial pathogens. Recent advances in the structural organization of these enzymes are also discussed, as are our perspective for future studies.
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Affiliation(s)
- Sheila A Martínez-Zavala
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Guanajuato, Mexico
| | - Uriel E Barboza-Pérez
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Gustavo Hernández-Guzmán
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Guanajuato, Mexico.,Department of Biological Sciences, California Baptist University, Riverside, CA, United States
| | - Dennis K Bideshi
- Department of Entomology, University of California, Riverside, Riverside, CA, United States.,Food Department, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Guanajuato, Mexico
| | - José E Barboza-Corona
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Guanajuato, Mexico.,Department of Biological Sciences, California Baptist University, Riverside, CA, United States
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14
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Li Z, Xia C, Wang Y, Li X, Qiao Y, Li C, Zhou J, Zhang L, Ye X, Huang Y, Cui Z. Identification of an endo-chitinase from Corallococcus sp. EGB and evaluation of its antifungal properties. Int J Biol Macromol 2019; 132:1235-1243. [PMID: 30980875 DOI: 10.1016/j.ijbiomac.2019.04.056] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/18/2022]
Abstract
As the main component of the fungal cell wall, chitin has been regarded as an optimal molecular target for the biocontrol of plant-pathogenic fungi. In this study, the chitin hydrolase CcCti1, which belongs to the glycoside hydrolase family 18 (GH 18) and exhibits potential antifungal activity, was identified from Corallococcus sp. EGB. CcCti1 lacks a fibronectin type-III (FN3) domain that is present in similar enzymes from most genera of myxobacteria, indicating that CcCti1 may have acquired chitinase activity due to the FN3 domain deletion during myxobacterial evolution. CcCti1 was expressed in Escherichia coli BL21 (DE3) with a specific activity of up to 10.5 U/μmol with colloidal chitin as the substrate. Product analysis showed that CcCti1 could hydrolyze chitin into N-acetylated chitohexaose (GlcNAc)6 as the major product, in addition to chitooligosaccharides. The analysis of biochemical properties indicated that the CBD and FN3 domains in CcCti1 determine the substrate affinity and pH stability. Otherwise, CcCti1 exhibited efficient biocontrol activity against the plant pathogen Magnaporthe oryzae in a dose-dependent manner, inhibiting the conidia germination and appressoria formation at a concentration of 0.08 mg/mL. Overall, the chitohexaose-producing chitinase CcCti1 with hydrolytic features may find potential application in chitin conversion and biocontrol of fungal plant diseases.
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Affiliation(s)
- Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chengyao Xia
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yanxin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xu Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yan Qiao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chenyu Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Lei Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China.
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15
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Sousa AJS, Silva CFB, Sousa JS, Monteiro JE, Freire JEC, Sousa BL, Lobo MDP, Monteiro-Moreira ACO, Grangeiro TB. A thermostable chitinase from the antagonistic Chromobacterium violaceum that inhibits the development of phytopathogenic fungi. Enzyme Microb Technol 2019; 126:50-61. [PMID: 31000164 DOI: 10.1016/j.enzmictec.2019.03.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/30/2019] [Accepted: 03/30/2019] [Indexed: 01/19/2023]
Abstract
The biocontrol activity of some soil strains of Chromobacterium sp. against pathogenic fungi has been attributed to secreted chitinases. The aim of this work was to characterize biochemically a recombinant chitinase (CvChi47) from C. violaceum ATCC 12472 and to investigate its effects on phytopathogenic fungi. CvChi47 is a modular enzyme with 450 amino acid residues, containing a type I signal peptide at the N-terminal region, followed by one catalytic domain belonging to family 18 of the glycoside hydrolases, and two type-3 chitin-binding domains at the C-terminal end. The recombinant enzyme was expressed in Escherichia coli as a His-tagged protein and purified to homogeneity. The native signal peptide of CvChi47 was used to direct its secretion into the culture medium, from where the recombinant product was purified by affinity chromatography on chitin and immobilized metal. The purified protein showed an apparent molecular mass of 46 kDa, as estimated by denaturing polyacrylamide gel electrophoresis, indicating the removal of the signal peptide. CvChi47 was a thermostable protein, retaining approximately 53.7% of its activity when heated at 100 °C for 1 h. The optimum hydrolytic activity was observed at 60 °C and pH 5. The recombinant chitinase inhibited the conidia germination of the phytopathogenic fungi Fusarium oxysporum and F. guttiforme, hence preventing mycelial growth. Furthermore, atomic force microscopy experiments revealed a pronounced morphological alteration of the cell surface of conidia incubated with CvChi47 in comparison to untreated cells. Taken together, these results show the potential of CvChi47 as a molecular tool to control plant diseases caused by these Fusarium species.
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Affiliation(s)
- Antônio J S Sousa
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências, Universidade Federal do Ceará (UFC), Fortaleza, CE, Brazil
| | - Christiana F B Silva
- Embrapa Agroindústria Tropical, Laboratório de Patologia Pós-colheita, Fortaleza, CE, Brazil
| | - Jeanlex S Sousa
- Departamento de Física, Centro de Ciências, UFC, Fortaleza, CE, Brazil
| | - José E Monteiro
- Laboratório de Genética Molecular, Departamento de Biologia, Centro de Ciências, UFC, Fortaleza, CE, Brazil
| | - José E C Freire
- Laboratório de Genética Molecular, Departamento de Biologia, Centro de Ciências, UFC, Fortaleza, CE, Brazil
| | - Bruno L Sousa
- Faculdade de Filosofia Dom Aureliano Matos, Universidade Estadual do Ceará, Av. Dom Aureliano Matos, 2060, Limoeiro do Norte, CE, 62930-000, Brazil
| | - Marina D P Lobo
- Núcleo de Biologia Experimental (Nubex), Universidade de Fortaleza (UNIFOR), Fortaleza, CE, Brazil
| | - Ana C O Monteiro-Moreira
- Núcleo de Biologia Experimental (Nubex), Universidade de Fortaleza (UNIFOR), Fortaleza, CE, Brazil
| | - Thalles B Grangeiro
- Laboratório de Genética Molecular, Departamento de Biologia, Centro de Ciências, UFC, Fortaleza, CE, Brazil.
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16
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Rocha AJ, Sousa BL, Girão MS, Barroso-Neto IL, Monteiro-Júnior JE, Oliveira JT, Nagano CS, Carneiro RF, Monteiro-Moreira AC, Rocha BA, Freire VN, Grangeiro TB. Cloning of cDNA sequences encoding cowpea (Vigna unguiculata) vicilins: Computational simulations suggest a binding mode of cowpea vicilins to chitin oligomers. Int J Biol Macromol 2018; 117:565-573. [DOI: 10.1016/j.ijbiomac.2018.05.197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 11/24/2022]
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17
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Oyeleye A, Normi YM. Chitinase: diversity, limitations, and trends in engineering for suitable applications. Biosci Rep 2018; 38:BSR2018032300. [PMID: 30042170 PMCID: PMC6131217 DOI: 10.1042/bsr20180323] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/07/2018] [Accepted: 12/07/2018] [Indexed: 01/09/2023] Open
Abstract
Chitinases catalyze the degradation of chitin, a ubiquitous polymer generated from the cell walls of fungi, shells of crustaceans, and cuticles of insects. They are gaining increasing attention in medicine, agriculture, food and drug industries, and environmental management. Their roles in the degradation of chitin for the production of industrially useful products and in the control of fungal pathogens and insect pests render them attractive for such purposes. However, chitinases have diverse sources, characteristics, and mechanisms of action that seem to restrain optimization procedures and render standardization techniques for enhanced practical applications complex. Hence, results of laboratory trials are not usually consistent with real-life applications. With the growing field of protein engineering, these complexities can be overcome by modifying or redesigning chitinases to enhance specific features required for specific applications. In this review, the variations in features and mechanisms of chitinases that limit their exploitation in biotechnological applications are compiled. Recent attempts to engineer chitinases for improved efficiency are also highlighted.
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Affiliation(s)
- Ayokunmi Oyeleye
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia
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18
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Acidic Chitinase-Chitin Complex Is Dissociated in a Competitive Manner by Acetic Acid: Purification of Natural Enzyme for Supplementation Purposes. Int J Mol Sci 2018; 19:ijms19020362. [PMID: 29370114 PMCID: PMC5855584 DOI: 10.3390/ijms19020362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/10/2018] [Accepted: 01/22/2018] [Indexed: 01/09/2023] Open
Abstract
Acidic chitinase (Chia) has been implicated in asthma, allergic inflammations, and food processing. We have purified Chia enzymes with striking acid stability and protease resistance from chicken and pig stomach tissues using a chitin column and 8 M urea (urea-Chia). Here, we report that acetic acid is a suitable agent for native Chia purification from the stomach tissues using a chitin column (acetic acid-Chia). Chia protein can be eluted from a chitin column using 0.1 M acetic acid (pH 2.8), but not by using Gly-HCl (pH 2.5) or sodium acetate (pH 4.0 or 5.5). The melting temperatures of Chia are not affected substantially in the elution buffers, as assessed by differential scanning fluorimetry. Interestingly, acetic acid appears to be more effective for Chia-chitin dissociation than do other organic acids with similar structures. We propose a novel concept of this dissociation based on competitive interaction between chitin and acetic acid rather than on acid denaturation. Acetic acid-Chia also showed similar chitinolytic activity to urea-Chia, indicating that Chia is extremely stable against acid, proteases, and denaturing agents. Both acetic acid- and urea-Chia seem to have good potential for supplementation or compensatory purposes in agriculture or even biomedicine.
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19
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Monteiro Júnior JE, Valadares NF, Pereira HD, Dyszy FH, da Costa Filho AJ, Uchôa AF, de Oliveira AS, da Silveira Carvalho CP, Grangeiro TB. Expression in Escherichia coli of cysteine protease inhibitors from cowpea (Vigna unguiculata): The crystal structure of a single-domain cystatin gives insights on its thermal and pH stability. Int J Biol Macromol 2017; 102:29-41. [DOI: 10.1016/j.ijbiomac.2017.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/26/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
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20
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Landim PGC, Correia TO, Silva FD, Nepomuceno DR, Costa HP, Pereira HM, Lobo MD, Moreno FB, Brandão-Neto J, Medeiros SC, Vasconcelos IM, Oliveira JT, Sousa BL, Barroso-Neto IL, Freire VN, Carvalho CP, Monteiro-Moreira AC, Grangeiro TB. Production in Pichia pastoris, antifungal activity and crystal structure of a class I chitinase from cowpea (Vigna unguiculata): Insights into sugar binding mode and hydrolytic action. Biochimie 2017; 135:89-103. [DOI: 10.1016/j.biochi.2017.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/27/2017] [Indexed: 02/02/2023]
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21
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Paulsen SS, Andersen B, Gram L, Machado H. Biological Potential of Chitinolytic Marine Bacteria. Mar Drugs 2016; 14:md14120230. [PMID: 27999269 PMCID: PMC5192467 DOI: 10.3390/md14120230] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 12/26/2022] Open
Abstract
Chitinolytic microorganisms secrete a range of chitin modifying enzymes, which can be exploited for production of chitin derived products or as fungal or pest control agents. Here, we explored the potential of 11 marine bacteria (Pseudoalteromonadaceae, Vibrionaceae) for chitin degradation using in silico and phenotypic assays. Of 10 chitinolytic strains, three strains, Photobacterium galatheae S2753, Pseudoalteromonas piscicida S2040 and S2724, produced large clearing zones on chitin plates. All strains were antifungal, but against different fungal targets. One strain, Pseudoalteromonas piscicida S2040, had a pronounced antifungal activity against all seven fungal strains. There was no correlation between the number of chitin modifying enzymes as found by genome mining and the chitin degrading activity as measured by size of clearing zones on chitin agar. Based on in silico and in vitro analyses, we cloned and expressed two ChiA-like chitinases from the two most potent candidates to exemplify the industrial potential.
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Affiliation(s)
- Sara Skøtt Paulsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Birgitte Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Henrique Machado
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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22
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Khan FI, Bisetty K, Gu KR, Singh S, Permaul K, Hassan MI, Wei DQ. Molecular dynamics simulation of chitinase I from Thermomyces lanuginosus SSBP to ensure optimal activity. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1237024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Faez Iqbal Khan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, South Africa
| | - Ke-Ren Gu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| | - Suren Singh
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Kugen Permaul
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Dong-Qing Wei
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
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23
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Dhar H, Kasana RC, Dutt S, Gulati A. Cloning and expression of low temperature active endoglucanase EG5C from Paenibacillus sp. IHB B 3084. Int J Biol Macromol 2015; 81:259-66. [DOI: 10.1016/j.ijbiomac.2015.07.060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 07/25/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
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24
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Yan Q, Fong SS. Bacterial chitinase: nature and perspectives for sustainable bioproduction. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-015-0057-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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25
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Cretoiu MS, Berini F, Kielak AM, Marinelli F, van Elsas JD. A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil. Appl Microbiol Biotechnol 2015; 99:8199-215. [PMID: 26040993 PMCID: PMC4561078 DOI: 10.1007/s00253-015-6639-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/21/2015] [Accepted: 04/24/2015] [Indexed: 12/04/2022]
Abstract
Here, we report on the construction of a metagenomic library from a chitin-amended disease-suppressive agricultural soil and its screening for genes that encode novel chitinolytic enzymes. The library, constructed in fosmids in an Escherichia coli host, comprised 145,000 clones containing inserts of sizes of 21 to 40 kb, yielding a total of approximately 5.8 GB of cloned soil DNA. Using genetic screenings by repeated PCR cycles aimed to detect gene sequences of the bacterial chitinase A-class (hereby named chi A genes), we identified and characterized five fosmids carrying candidate genes for chitinolytic enzymes. The analysis thus allowed access to the genomic (fosmid-borne) context of these genes. Using the chiA-targeted PCR, which is based on degenerate primers, the five fosmids all produced amplicons, of which the sequences were related to predicted chitinolytic enzyme-encoding genes of four different host organisms, including Stenotrophomonas maltophilia. Sequencing and de novo annotation of the fosmid inserts confirmed that each one of these carried one or more open reading frames that were predicted to encode enzymes active on chitin, including one for a chitin deacetylase. Moreover, the genetic contexts in which the putative chitinolytic enzyme-encoding genes were located were unique per fosmid. Specifically, inserts from organisms related to Burkholderia sp., Acidobacterium sp., Aeromonas veronii, and the chloroflexi Nitrolancetus hollandicus and/or Ktedonobacter racemifer were obtained. Remarkably, the S. maltophilia chiA-like gene was found to occur in two different genetic contexts (related to N. hollandicus/K. racemifer), indicating the historical occurrence of genetic reshufflings in this part of the soil microbiota. One fosmid containing the insert composed of DNA from the N. hollandicus-like organism (denoted 53D1) was selected for further work. Using subcloning procedures, its putative gene for a chitinolytic enzyme was successfully brought to expression in an E. coli host. On the basis of purified protein preparations, the produced protein was characterized as a chitobiosidase of 43.6 kDa, with a pI of 4.83. Given its activity spectrum, it can be typified as a halotolerant chitobiosidase.
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Affiliation(s)
- Mariana Silvia Cretoiu
- />Department of Microbial Ecology, CEES, University of Groningen, Groningen, The Netherlands
- />Department of Marine Microbiology, Royal Netherlands Institute for Sea Research, Yerseke, The Netherlands
| | - Francesca Berini
- />Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- />“The Protein Factory” Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, Varese, Italy
| | - Anna Maria Kielak
- />Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO), Wageningen, The Netherlands
| | - Flavia Marinelli
- />Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- />“The Protein Factory” Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, Varese, Italy
| | - Jan Dirk van Elsas
- />Department of Microbial Ecology, CEES, University of Groningen, Groningen, The Netherlands
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26
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Khan FI, Govender A, Permaul K, Singh S, Bisetty K. Thermostable chitinase II from Thermomyces lanuginosus SSBP: Cloning, structure prediction and molecular dynamics simulations. J Theor Biol 2015; 374:107-14. [PMID: 25861869 DOI: 10.1016/j.jtbi.2015.03.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/02/2015] [Accepted: 03/27/2015] [Indexed: 01/02/2023]
Abstract
Thermomyces lanuginosus is a thermophilic fungus that produces large number of industrially-significant enzymes owing to their inherent stability at high temperatures and wide range of pH optima, including thermostable chitinases that have not been fully characterized. Here, we report cloning, characterization and structure prediction of a gene encoding thermostable chitinase II. Sequence analysis revealed that chitinase II gene encodes a 343 amino acid protein of molecular weight 36.65kDa. Our study reports that chitinase II exhibits a well-defined TIM-barrel topology with an eight-stranded α/β domain. Structural analysis and molecular docking studies suggested that Glu176 is essential for enzyme activity. Folding studies of chitinase II using molecular dynamics simulations clearly demonstrated that the stability of the protein was evenly distributed at 350K.
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Affiliation(s)
- Faez Iqbal Khan
- Department of Chemistry, Durban, Steve Biko Campus, Durban University of Technology, Durban, South Africa; Department of Biotechnology and Food Technology, Steve Biko Campus, Durban University of Technology, Durban, South Africa
| | - Algasan Govender
- Department of Biotechnology and Food Technology, Steve Biko Campus, Durban University of Technology, Durban, South Africa
| | - Kugen Permaul
- Department of Biotechnology and Food Technology, Steve Biko Campus, Durban University of Technology, Durban, South Africa
| | - Suren Singh
- Department of Biotechnology and Food Technology, Steve Biko Campus, Durban University of Technology, Durban, South Africa
| | - Krishna Bisetty
- Department of Chemistry, Durban, Steve Biko Campus, Durban University of Technology, Durban, South Africa.
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