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El-Sayed GM, Emam MTH, Hammad MA, Mahmoud SH. Gene Cloning, Heterologous Expression, and In Silico Analysis of Chitinase B from Serratia marcescens for Biocontrol of Spodoptera frugiperda Larvae Infesting Maize Crops. Molecules 2024; 29:1466. [PMID: 38611746 PMCID: PMC11012731 DOI: 10.3390/molecules29071466] [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: 02/18/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Spodoptera frugiperda, the fall armyworm (FAW), is a highly invasive polyphagous insect pest that is considered a source of severe economic losses to agricultural production. Currently, the majority of chemical insecticides pose tremendous threats to humans and animals besides insect resistance. Thus, there is an urgent need to develop new pest management strategies with more specificity, efficiency, and sustainability. Chitin-degrading enzymes, including chitinases, are promising agents which may contribute to FAW control. Chitinase-producing microorganisms are reported normally in bacteria and fungi. In the present study, Serratia marcescens was successfully isolated and identified from the larvae of Spodoptera frugiperda. The bacterial strain NRC408 displayed the highest chitinase enzyme activity of 250 units per milligram of protein. Subsequently, the chitinase gene was cloned and heterologously expressed in E. coli BL21 (DE3). Recombinant chitinase B was overproduced to 2.5-fold, driven by the T7 expression system. Recombinant chitinase B was evaluated for its efficacy as an insecticidal bioagent against S. frugiperda larvae, which induced significant alteration in subsequent developmental stages and conspicuous malformations. Additionally, our study highlights that in silico analyses of the anticipated protein encoded by the chitinase gene (ChiB) offered improved predictions for enzyme binding and catalytic activity. The effectiveness of (ChiB) against S. frugiperda was evaluated in laboratory and controlled field conditions. The results indicated significant mortality, disturbed development, different induced malformations, and a reduction in larval populations. Thus, the current study consequently recommends chitinase B for the first time to control FAW.
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Affiliation(s)
- Ghada M. El-Sayed
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo 12622, Egypt
| | - Maha T. H. Emam
- Genetics & Cytology Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo 12622, Egypt;
| | - Maher A. Hammad
- Department of Plant Protection, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
| | - Shaymaa H. Mahmoud
- Zoology Department, Faculty of Science, Menoufia University, Shibin El Kom 32511, Egypt;
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K S R, Varghese S, M S J. Sequence analysis and docking performance of extracellular chitinase from Bacillus pumilus MCB-7, a novel mangrove isolate. Enzyme Microb Technol 2020; 140:109624. [PMID: 32912684 DOI: 10.1016/j.enzmictec.2020.109624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/11/2020] [Indexed: 10/24/2022]
Abstract
Bacterial chitinases has a major role in chitinaceous waste management, biological control of pests and phytopathogens. In the present study, exochitinase gene ChitA encoding extracellular chitinase from the mangrove bacteria Bacillus pumilus MCB-07 was genetically characterized. Oligonucleotide primers specific to chitinase gene of Bacillus pumilus were designed and amplified by PCR. The purified PCR product was successfully cloned in pGEM-T vector and transformed into Escherichia coli DH5-α competent cells. Nucleotide sequence alignment of the chitinase gene revealed 96 % similarity whereas 94 % of the catalytic domain of 598 amino acids is conserved with protein family GH18 chitinases, which is a novel report for Bacillus pumilus. The insert also showed a number of substitutions (mutations) with other sp. of Bacillus which demonstrated that chitinase of Bacillus pumilus MCB-07 is a novel gene. Multiple sequence alignment of chitinase gene sequences and its predicted amino acid sequences were also evaluated and the sequence was deposited in GenBank with accession number KT966736.1. Homology modeling of the chitinase depicted the typical (α/β) 8 TIM barrel structure. Molecular docking of the protein was performed by Autodock 4.2.6 and the docked pocket contained Val 113, Met 114, Gln 99, Ala 75 and Cys 98 as the key binding residues. The molecular docking of Bacillus pumilus chitinase, revealed the involvement of a phenylalanine of the catalytic domain in the catalytic process of chitin to mono and oligomers of NAG. The amino acid exhibited both hydrophobic and hydrogen bond interactions of chitin molecules with phenylalanine.
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Affiliation(s)
- Rishad K S
- UniBiosys Biotech Research Labs, Cochin, Kerala, India
| | - Sherin Varghese
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, India
| | - Jisha M S
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, India.
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Amelia K, Singh J, Shah FH, Bhore SJ. Analysis of common bean (Phaseolus vulgaris L., genotype BAT93) calmodulin cDNA using computational tools. Pharmacognosy Res 2015; 7:209-12. [PMID: 25829797 PMCID: PMC4357974 DOI: 10.4103/0974-8490.150536] [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: 06/14/2014] [Revised: 08/12/2014] [Accepted: 02/02/2015] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Common bean (Phaseolus vulgaris L.) is an important part of the human diet and serves as a source of natural products. Identification and understanding of genes in P. vulgaris is important for its improvement. Characterization of expressed sequence tags (ESTs) is one of the approaches in understanding the expressed genes. For the understanding of genes expression in P. vulgaris pod-tissue, research work of ESTs generation was initiated by constructing cDNA libraries using 5-day and 20-day old bean-pod-tissues. Altogether, 5972 cDNA clones were isolated to have ESTs. While processing ESTs, we found a transcript for calmodulin (CaM) gene. It is an important gene that encodes for a calcium-binding protein and known to express in all eukaryotic cells. Hence, this study was undertaken to analyse and annotate it. OBJECTIVE The objective of this study was to analyze and annotate P. vulgaris CaM (PvCaM) gene cDNA and its deduced protein (amino acids) sequence. MATERIALS AND METHODS Both strands of PvCaM cDNA clone were sequenced using M13 forward and reverse primer to elucidate the nucleotide sequence. The cDNA sequence and deduced protein sequence were analyzed and annotated using bioinformatics tools available online. The secondary structures and three-dimensional (3D) structure of PvCaM protein were predicted using the Phyre automatic fold recognition server. RESULTS Results showed that PvCaM cDNA is 818 bp in length. The cDNA analysis results showed that it contains an open reading frame that encodes for 149 amino acid residues. The deduced protein sequence analysis results showed the presence of conserved domains required for CaM function. The predicted secondary structures and 3D structure are analogous to the Solanum tuberosum CaM. CONCLUSIONS This study analyzed and annotated PvCaM cDNA and protein. However, in order to obtain a complete understanding of PvCaM protein, further study on its expression, structure and regulation is essential.
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Affiliation(s)
- Kassim Amelia
- Department of Molecular Biology, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka ; Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling 08100, Kedah, Malaysia
| | - Jasvin Singh
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling 08100, Kedah, Malaysia
| | - Farida Habib Shah
- Department of Molecular Biology, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka ; Department of Research and Development, Novel Plants Sdn. Bhd., 27C Jln Petaling Utama 12, 7.5 Miles Old Klang Road, 46000 Petaling Jaya, Malaysia
| | - Subhash J Bhore
- Department of Molecular Biology, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka ; Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling 08100, Kedah, Malaysia
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Amelia K, Khor CY, Shah FH, Bhore SJ. Nucleotide sequence of Phaseolus vulgaris L. alcohol dehydrogenase encoding cDNA and three-dimensional structure prediction of the deduced protein. Pharmacognosy Res 2015; 7:203-8. [PMID: 25829796 PMCID: PMC4357973 DOI: 10.4103/0974-8490.150532] [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: 06/14/2014] [Revised: 08/10/2014] [Accepted: 02/02/2015] [Indexed: 11/24/2022] Open
Abstract
Background: Common beans (Phaseolus vulgaris L.) are widely consumed as a source of proteins and natural products. However, its yield needs to be increased. In line with the agenda of Phaseomics (an international consortium), work of expressed sequence tags (ESTs) generation from bean pods was initiated. Altogether, 5972 ESTs have been isolated. Alcohol dehydrogenase (AD) encoding gene cDNA was a noticeable transcript among the generated ESTs. This AD is an important enzyme; therefore, to understand more about it this study was undertaken. Objective: The objective of this study was to elucidate P. vulgaris L. AD (PvAD) gene cDNA sequence and to predict the three-dimensional (3D) structure of deduced protein. Materials and Methods: positive and negative strands of the PvAD cDNA clone were sequenced using M13 forward and M13 reverse primers to elucidate the nucleotide sequence. Deduced PvAD cDNA and protein sequence was analyzed for their basic features using online bioinformatics tools. Sequence comparison was carried out using bl2seq program, and tree-view program was used to construct a phylogenetic tree. The secondary structures and 3D structure of PvAD protein were predicted by using the PHYRE automatic fold recognition server. Results: The sequencing results analysis showed that PvAD cDNA is 1294 bp in length. It's open reading frame encodes for a protein that contains 371 amino acids. Deduced protein sequence analysis showed the presence of putative substrate binding, catalytic Zn binding, and NAD binding sites. Results indicate that the predicted 3D structure of PvAD protein is analogous to the experimentally determined crystal structure of s-nitrosoglutathione reductase from an Arabidopsis species. Conclusions: The 1294 bp long PvAD cDNA encodes for 371 amino acid long protein that contains conserved domains required for biological functions of AD. The predicted deduced PvAD protein's 3D structure reflects the analogy with the crystal structure of Arabidopsis thaliana s-nitrosoglutathione reductase. Further study is required to validate the predicted structure.
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Affiliation(s)
- Kassim Amelia
- Department of Molecular Biology, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka, Malaysia ; Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Semeling 08100, Kedah
| | - Chin Yin Khor
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Semeling 08100, Kedah
| | - Farida Habib Shah
- Department of Research and Development, Novel Plants Sdn. Bhd., 27C Jln Petaling Utama 12, 7.5 Miles Old Klang Road, 46000 Petaling Jaya, Malaysia
| | - Subhash J Bhore
- Department of Molecular Biology, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka, Malaysia ; Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Semeling 08100, Kedah
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Pradeepkiran JA, Sainath SB, Kumar KK, Bhaskar M. Complete genome-wide screening and subtractive genomic approach revealed new virulence factors, potential drug targets against bio-war pathogen Brucella melitensis 16M. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:1691-706. [PMID: 25834405 PMCID: PMC4371898 DOI: 10.2147/dddt.s76948] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Brucella melitensis 16M is a Gram-negative coccobacillus that infects both animals and humans. It causes a disease known as brucellosis, which is characterized by acute febrile illness in humans and causes abortions in livestock. To prevent and control brucellosis, identification of putative drug targets is crucial. The present study aimed to identify drug targets in B. melitensis 16M by using a subtractive genomic approach. We used available database repositories (Database of Essential Genes, Kyoto Encyclopedia of Genes and Genomes Automatic Annotation Server, and Kyoto Encyclopedia of Genes and Genomes) to identify putative genes that are nonhomologous to humans and essential for pathogen B. melitensis 16M. The results revealed that among 3 Mb genome size of pathogen, 53 putative characterized and 13 uncharacterized hypothetical genes were identified; further, from Basic Local Alignment Search Tool protein analysis, one hypothetical protein showed a close resemblance (50%) to Silicibacter pomeroyi DUF1285 family protein (2RE3). A further homology model of the target was constructed using MODELLER 9.12 and optimized through variable target function method by molecular dynamics optimization with simulating annealing. The stereochemical quality of the restrained model was evaluated by PROCHECK, VERIFY-3D, ERRAT, and WHATIF servers. Furthermore, structure-based virtual screening was carried out against the predicted active site of the respective protein using the glycerol structural analogs from the PubChem database. We identified five best inhibitors with strong affinities, stable interactions, and also with reliable drug-like properties. Hence, these leads might be used as the most effective inhibitors of modeled protein. The outcome of the present work of virtual screening of putative gene targets might facilitate design of potential drugs for better treatment against brucellosis.
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Affiliation(s)
| | - Sri Bhashyam Sainath
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, Porto, Portugal ; Department of Biotechnology, Vikrama Simhapuri University, Nellore, Andhra Pradesh, India
| | - Konidala Kranthi Kumar
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati, India
| | - Matcha Bhaskar
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati, India
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Khan SH, Javed MR, Qasim M, Shahzadi S, Jalil A, Rehman SU. Domain analyses of Usher syndrome causing Clarin-1 and GPR98 protein models. Bioinformation 2014; 10:491-5. [PMID: 25258483 PMCID: PMC4166767 DOI: 10.6026/97320630010491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 11/23/2022] Open
Abstract
Usher syndrome is an autosomal recessive disorder that causes hearing loss, Retinitis Pigmentosa (RP) and vestibular dysfunction. It is clinically and genetically heterogeneous disorder which is clinically divided into three types i.e. type I, type II and type III. To date, there are about twelve loci and ten identified genes which are associated with Usher syndrome. A mutation in any of these genes e.g. CDH23, CLRN1, GPR98, MYO7A, PCDH15, USH1C, USH1G, USH2A and DFNB31 can result in Usher syndrome or non-syndromic deafness. These genes provide instructions for making proteins that play important roles in normal hearing, balance and vision. Studies have shown that protein structures of only seven genes have been determined experimentally and there are still three genes whose structures are unavailable. These genes are Clarin-1, GPR98 and Usherin. In the absence of an experimentally determined structure, homology modeling and threading often provide a useful 3D model of a protein. Therefore in the current study Clarin-1 and GPR98 proteins have been analyzed for signal peptide, domains and motifs. Clarin-1 protein was found to be without any signal peptide and consists of prokar lipoprotein domain. Clarin-1 is classified within claudin 2 super family and consists of twelve motifs. Whereas, GPR98 has a 29 amino acids long signal peptide and classified within GPCR family 2 having Concanavalin A-like lectin/glucanase superfamily. It was found to be consists of GPS and G protein receptor F2 domains and twenty nine motifs. Their 3D structures have been predicted using I-TASSER server. The model of Clarin-1 showed only α-helix but no beta sheets while model of GPR98 showed both α-helix and β sheets. The predicted structures were then evaluated and validated by MolProbity and Ramachandran plot. The evaluation of the predicted structures showed 78.9% residues of Clarin-1 and 78.9% residues of GPR98 within favored regions. The findings of present study has resulted in the three dimensional structure prediction and conserved domain analysis which will be quite beneficial in better understanding of molecular components, protein-protein interaction, clinical heterogeneity and pathophysiology of Usher syndrome.
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Affiliation(s)
- Sehrish Haider Khan
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Allama Iqbal Road 38000, Faisalabad, Pakistan
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Allama Iqbal Road 38000, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Allama Iqbal Road 38000, Faisalabad, Pakistan
| | - Samar Shahzadi
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Allama Iqbal Road 38000, Faisalabad, Pakistan
| | - Asma Jalil
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Allama Iqbal Road 38000, Faisalabad, Pakistan
| | - Shahid ur Rehman
- Department of Poultry Husbandry, University of Agriculture, Faisalabad, Pakistan
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Sehar U, Mehmood MA, Hussain K, Nawaz S, Nadeem S, Siddique MH, Nadeem H, Gull M, Ahmad N, Sohail I, Gill SS, Majeed S. Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4. Bioinformation 2013; 9:901-7. [PMID: 24307767 PMCID: PMC3842575 DOI: 10.6026/97320630009901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 10/19/2013] [Indexed: 11/23/2022] Open
Abstract
This paper presents an in silico characterization of the chitin binding protein CBP50 from B. thuringiensis serovar konkukian S4 through homology modeling and molecular docking. The CBP50 has shown a modular structure containing an N-terminal CBM33 domain, two consecutive fibronectin-III (Fn-III) like domains and a C-terminal CBM5 domain. The protein presented a unique modular structure which could not be modeled using ordinary procedures. So, domain wise modeling using MODELLER and docking analyses using Autodock Vina were performed. The best conformation for each domain was selected using standard procedure. It was revealed that four amino acid residues Glu-71, Ser-74, Glu-76 and Gln-90 from N-terminal domain are involved in protein-substrate interaction. Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding. Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.
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Affiliation(s)
- Ujala Sehar
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University Faisalabad, Faisalabad, Pakistan
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