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Rosier A, Pomerleau M, Beauregard PB, Samac DA, Bais HP. Surfactin and Spo0A-Dependent Antagonism by Bacillus subtilis Strain UD1022 against Medicago sativa Phytopathogens. PLANTS (BASEL, SWITZERLAND) 2023; 12:1007. [PMID: 36903868 PMCID: PMC10005099 DOI: 10.3390/plants12051007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) such as the root colonizers Bacillus spp. may be ideal alternatives to chemical crop treatments. This work sought to extend the application of the broadly active PGPR UD1022 to Medicago sativa (alfalfa). Alfalfa is susceptible to many phytopathogens resulting in losses of crop yield and nutrient value. UD1022 was cocultured with four alfalfa pathogen strains to test antagonism. We found UD1022 to be directly antagonistic toward Collectotrichum trifolii, Ascochyta medicaginicola (formerly Phoma medicaginis), and Phytophthora medicaginis, and not toward Fusarium oxysporum f. sp. medicaginis. Using mutant UD1022 strains lacking genes in the nonribosomal peptide (NRP) and biofilm pathways, we tested antagonism against A. medicaginicola StC 306-5 and P. medicaginis A2A1. The NRP surfactin may have a role in the antagonism toward the ascomycete StC 306-5. Antagonism toward A2A1 may be influenced by B. subtilis biofilm pathway components. The B. subtilis central regulator of both surfactin and biofilm pathways Spo0A was required for the antagonism of both phytopathogens. The results of this study indicate that the PGPR UD1022 would be a good candidate for further investigations into its antagonistic activities against C. trifolii, A. medicaginicola, and P. medicaginis in plant and field studies.
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Affiliation(s)
- Amanda Rosier
- Department of Plant and Soil Sciences, University of Delaware, 311 AP Biopharma, 590 Avenue 1743, Newark, DE 19713, USA
| | - Maude Pomerleau
- Département de Biologie, Bureau D8-1014, Université de Sherbrooke, 2500 boul. Université Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Pascale B. Beauregard
- Département de Biologie, Bureau D8-1014, Université de Sherbrooke, 2500 boul. Université Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Deborah A. Samac
- USDA-ARS Plant Science Research Unit, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Harsh P. Bais
- Department of Plant and Soil Sciences, University of Delaware, 311 AP Biopharma, 590 Avenue 1743, Newark, DE 19713, USA
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Sukhanova E, Zimens E, Kaluzhnaya O, Parfenova V, Belykh O. Epilithic Biofilms in Lake Baikal: Screening and Diversity of PKS and NRPS Genes in the Genomes of Heterotrophic Bacteria. Pol J Microbiol 2019; 67:501-516. [PMID: 30550237 PMCID: PMC7256756 DOI: 10.21307/pjm-2018-060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2018] [Indexed: 11/11/2022] Open
Abstract
A collection of heterotrophic bacteria consisting of 167 strains was obtained from microbial communities of biofilms formed on solid substrates in the littoral zone of Lake Baikal. Based on the analysis of 16S rRNA gene fragments, the isolates were classified to four phyla: Proteobacteria , Firmicutes , Actinobacteria , and Bacteroidetes . To assess their biotechnological potential, bacteria were screened for the presence of PKS (polyketide synthase) and NRPS (non-ribosomal peptide synthetases) genes. PKS genes were detected in 41 strains (25%) and NRPS genes in 73 (43%) strains by PCR analysis. The occurrence of PKS genes in members of the phylum Firmicutes (the genera Bacillus and Paenibacillus ) was 34% and NRPS genes were found in 78%. In Proteobacteria , PKS and NRPS genes were found in 20% and 32%, and in 22% and 22% of Actinobacteria , respectively. For further analysis of PKS and NRPS genes, six Bacillus and Paenibacillus strains with antagonistic activity were selected and underwent phylogenetic analysis of 16S rRNA genes. The identification of PKS and NRPS genes in the strains investigated was demonstrated among the homologues the genes involved in the biosynthesis of antibiotics (bacillaene, difficidine, erythromycin, bacitracin, tridecaptin, and fusaricidin), biosurfactants (iturin, bacillomycin, plipastatin, fengycin, and surfactin) and antitumor agents (epothilone, calyculin, and briostatin). Bacillus spp. 9A and 2A strains showed the highest diversity of PKS and NRPS genes. Bacillus and Paenibacillus strains isolated from epilithic biofilms in Lake Baikal are potential producers of antimicrobial compounds and may be of practical interest for biotechnological purposes. A collection of heterotrophic bacteria consisting of 167 strains was obtained from microbial communities of biofilms formed on solid substrates in the littoral zone of Lake Baikal. Based on the analysis of 16S rRNA gene fragments, the isolates were classified to four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. To assess their biotechnological potential, bacteria were screened for the presence of PKS (polyketide synthase) and NRPS (non-ribosomal peptide synthetases) genes. PKS genes were detected in 41 strains (25%) and NRPS genes in 73 (43%) strains by PCR analysis. The occurrence of PKS genes in members of the phylum Firmicutes (the genera Bacillus and Paenibacillus) was 34% and NRPS genes were found in 78%. In Proteobacteria, PKS and NRPS genes were found in 20% and 32%, and in 22% and 22% of Actinobacteria, respectively. For further analysis of PKS and NRPS genes, six Bacillus and Paenibacillus strains with antagonistic activity were selected and underwent phylogenetic analysis of 16S rRNA genes. The identification of PKS and NRPS genes in the strains investigated was demonstrated among the homologues the genes involved in the biosynthesis of antibiotics (bacillaene, difficidine, erythromycin, bacitracin, tridecaptin, and fusaricidin), biosurfactants (iturin, bacillomycin, plipastatin, fengycin, and surfactin) and antitumor agents (epothilone, calyculin, and briostatin). Bacillus spp. 9A and 2A strains showed the highest diversity of PKS and NRPS genes. Bacillus and Paenibacillus strains isolated from epilithic biofilms in Lake Baikal are potential producers of antimicrobial compounds and may be of practical interest for biotechnological purposes.
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Affiliation(s)
- Elena Sukhanova
- Limnological Institute of Siberian Branch of Russian Academy of Sciences , Irkutsk , Russia
| | - Ekaterina Zimens
- Limnological Institute of Siberian Branch of Russian Academy of Sciences , Irkutsk , Russia
| | - Oksana Kaluzhnaya
- Limnological Institute of Siberian Branch of Russian Academy of Sciences , Irkutsk , Russia
| | - Valentina Parfenova
- Limnological Institute of Siberian Branch of Russian Academy of Sciences , Irkutsk , Russia
| | - Olga Belykh
- Limnological Institute of Siberian Branch of Russian Academy of Sciences , Irkutsk , Russia
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Azeem M, Barba-Aliaga M, Borg-Karlson AK, Terenius O, Broberg A, Rajarao GK. Heterobasidion-growth inhibiting Bacillus subtilis A18 exhibits medium- and age-dependent production of lipopeptides. Microbiol Res 2019; 223-225:129-136. [DOI: 10.1016/j.micres.2019.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/14/2019] [Accepted: 04/20/2019] [Indexed: 10/27/2022]
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In Silico Discovery of Novel Ligands for Antimicrobial Lipopeptides for Computer-Aided Drug Design. Probiotics Antimicrob Proteins 2019; 10:129-141. [PMID: 29218506 DOI: 10.1007/s12602-017-9356-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The increase in antibiotic-resistant strains of pathogens has created havoc worldwide. These antibiotic-resistant pathogens require potent drugs for their inhibition. Lipopeptides, which are produced as secondary metabolites by many microorganisms, have the ability to act as potent safe drugs. Lipopeptides are amphiphilic molecules containing a lipid chain bound to the peptide. They exhibit broad-spectrum activities against both bacteria and fungi. Other than their antimicrobial properties, they have displayed anti-cancer properties as well, but their mechanism of action is not understood. In silico drug design uses computer simulation to discover and develop new drugs. This technique reduces the need of expensive and tedious lab work and clinical trials, but this method becomes a challenge due to complex structures of lipopeptides. Specific agonists (ligands) must be identified to initiate a physiological response when combined with a receptor (lipopeptide). In silico drug design and homology modeling talks about the interaction between ligands and the binding sites. This review summarizes the mechanism of selected lipopeptides, their respective ligands, and in silico drug design.
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Yu WQ, Zheng GP, Qiu DW, Yan FC, Liu WZ, Liu WX. Draft genome sequence, disease-resistance genes, and phenotype of a Paenibacillus terrae strain (NK3-4) with the potential to control plant diseases. Genome 2018; 61:725-734. [PMID: 30184440 DOI: 10.1139/gen-2018-0113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Paenibacillus terrae NK3-4 is a plant growth-promoting rhizobacterium that may be useful for controlling plant diseases. We conducted a genomic analysis and identified the genes mediating antimicrobial functions. Additionally, an extracellular antifungal protein component was isolated and identified. The draft genome sequence was assembled into 54 contigs, with 5 458 568 bp and a G+C content of 47%. Moreover, 4 690 015 bp encoded 5090 proteins, 7 rRNAs, and 54 tRNAs. Forty-four genes involved in antimicrobial functions were detected. They mainly encode 19 non-ribosomal peptide synthetases (NRPSs); one polyketide synthase/NRPSs hybrid enzyme; four Zn-dependent metalloproteases; three antilisterial bacteriocin subtilosin biosynthesis proteins (AlbA); four serine proteases; five pectate lyases; three beta-glucanases; and four 1,4-beta-xylanases. These include four novel NRPSs that have not been found in any species of Paenibacillus. Furthermore, five proteins exhibiting antifungal activity were identified from the antifungal extracellular protein component based on MS/MS and the strain NK3-4 predicted protein library. On the basis of these features, we propose that strain NK3-4 represents a promising biocontrol agent for protecting plant from diseases. The draft genome sequence described herein may provide the genetic basis for the characterization of the molecular mechanisms underlying the biocontrol functions. It may also facilitate the development of rational strategies for improving the strain.
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Affiliation(s)
- Wen Qing Yu
- a College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China.,b Heilongjiang Academy of Land Reclamation, Haerbin, Heilongjiang Province, 150038, China.,c Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China
| | - Gui Ping Zheng
- a College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - De Wen Qiu
- c Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China
| | - Feng Chao Yan
- b Heilongjiang Academy of Land Reclamation, Haerbin, Heilongjiang Province, 150038, China
| | - Wen Zhi Liu
- b Heilongjiang Academy of Land Reclamation, Haerbin, Heilongjiang Province, 150038, China
| | - Wan Xue Liu
- c Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China
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Batool M, Shah M, Patra MC, Yesudhas D, Choi S. Structural insights into the Middle East respiratory syndrome coronavirus 4a protein and its dsRNA binding mechanism. Sci Rep 2017; 7:11362. [PMID: 28900197 PMCID: PMC5596018 DOI: 10.1038/s41598-017-11736-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/29/2017] [Indexed: 12/12/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) has evolved to navigate through the sophisticated network of a host's immune system. The immune evasion mechanism including type 1 interferon and protein kinase R-mediated antiviral stress responses has been recently attributed to the involvement of MERS-CoV protein 4a (p4a) that masks the viral dsRNA. However, the structural mechanism of how p4a recognizes and establishes contacts with dsRNA is not well explained. In this study, we report a dynamic mechanism deployed by p4a to engage the viral dsRNA and make it unavailable to the host immune system. Multiple variants of p4a-dsRNA were created and investigated through extensive molecular dynamics procedures to highlight crucial interfacial residues that may be used as potential pharmacophores for future drug development. The structural analysis revealed that p4a exhibits a typical αβββα fold structure, as found in other dsRNA-binding proteins. The α1 helix and the β1-β2 loop play a crucial role in recognizing and establishing contacts with the minor grooves of dsRNA. Further, mutational and binding free energy analyses suggested that in addition to K63 and K67, two other residues, K27 and W45, might also be crucial for p4a-dsRNA stability.
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Affiliation(s)
- Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Masaud Shah
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Mahesh Chandra Patra
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Dhanusha Yesudhas
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, South Korea.
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7
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Fan H, Ru J, Zhang Y, Wang Q, Li Y. Fengycin produced by Bacillus subtilis 9407 plays a major role in the biocontrol of apple ring rot disease. Microbiol Res 2017; 199:89-97. [PMID: 28454713 DOI: 10.1016/j.micres.2017.03.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 02/21/2017] [Accepted: 03/15/2017] [Indexed: 11/26/2022]
Abstract
Apple ring rot, caused by Botryosphaeria dothidea, is a serious apple disease in China. Bacillus subtilis 9407 was isolated from healthy apples and showed strong antifungal activity against B. dothidea. To identify the primary antifungal compound of B. subtilis 9407 and determine its role in controlling apple ring rot, a transposon mutant library was constructed using TnYLB-1, and a mutant completely defective in antifungal activity was obtained. The gene inactivated in the antifungal activity mutant had 98.5% similarity to ppsB in B. subtilis subsp. subtilis str. 168, which encodes one of the five synthetases responsible for synthesizing fengycin. A markerless ppsB deletion mutant was constructed. Compared with the wild-type strain, lipopeptide crude extracts from ΔppsB showed almost no inhibition of B. dothidea mycelial growth. Furthermore, fengycin-like lipopeptides (retention factor 0.1-0.2) that exhibited antifungal activity against B. dothidea were observed in the wild-type strain by thin-layer chromatography (TLC)-bioautography analysis, but not in ΔppsB. Semipreparative reverse-phase high performance liquid chromatography (RP-HPLC) detection revealed that ΔppsB lost the ability to synthesize fengycin. These results suggest that ppsB is responsible for synthesizing fengycin and that fengycin is the major antifungal compound produced by B. subtilis 9407 against B. dothidea. Moreover, a biocontrol assay showed that the control efficacy of ΔppsB was reduced by half compared with the wild-type strain, indicating that fengycin plays a major role in controlling apple ring rot disease. This is the first report on the use of a B. subtilis strain as a potential biological control agent to control apple ring rot disease by the production of fengycin.
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Affiliation(s)
- Haiyan Fan
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Jinjiang Ru
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Yuanyuan Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Qi Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Yan Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
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Liu H, Gao L, Han J, Ma Z, Lu Z, Dai C, Zhang C, Bie X. Biocombinatorial Synthesis of Novel Lipopeptides by COM Domain-Mediated Reprogramming of the Plipastatin NRPS Complex. Front Microbiol 2016; 7:1801. [PMID: 27909427 PMCID: PMC5112269 DOI: 10.3389/fmicb.2016.01801] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/26/2016] [Indexed: 11/25/2022] Open
Abstract
Both donors and acceptors of communication-mediating (COM) domains are essential for coordinating intermolecular communication within nonribosomal peptides synthetases (NRPSs) complexes. Different sets of COM domains provide selectivity, allowing NRPSs to utilize different natural biosynthetic templates. In this study, novel lipopeptides were synthesized by reprogramming the plipastatin biosynthetic machinery. A Thr-to-Asp point mutation was sufficient to shift the selectivity of the donor COM domain of ppsB toward that of ppsD. Deletion and/or interchangeability established donor and acceptor function. Variations in acceptor COM domain did not result in novel product formation in the presence of its partner donor, whereas plipastatin formation was completely abrogated by altering donor modules. Five novel lipopeptides (cyclic pentapeptide, linear hexapeptide, nonapeptide, heptapeptide, and cyclic octapeptide) were identified and verified by high-resolution LC-ESI-MS/MS. In addition, we demonstrated the potential to generate novel strains with the antimicrobial activity by selecting compatible COM domains, and the novel lipopeptides exhibited antimicrobial activity against five of the fungal species at a contention of 31.25–125 μg/ml.
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Affiliation(s)
- Hongxia Liu
- College of Food Science and Technology, Nanjing Agricultural University Nanjing, China
| | - Ling Gao
- College of Food Science and Technology, Nanjing Agricultural University Nanjing, China
| | - Jinzhi Han
- College of Food Science and Technology, Nanjing Agricultural University Nanjing, China
| | - Zhi Ma
- College of Food Science and Technology, Nanjing Agricultural University Nanjing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University Nanjing, China
| | - Chen Dai
- College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Chong Zhang
- College of Food Science and Technology, Nanjing Agricultural University Nanjing, China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University Nanjing, China
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Liu H, Qu X, Gao L, Zhao S, Lu Z, Zhang C, Bie X. Characterization of a Bacillus subtilis surfactin synthetase knockout and antimicrobial activity analysis. J Biotechnol 2016; 237:1-12. [PMID: 27576183 DOI: 10.1016/j.jbiotec.2016.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 11/15/2022]
Abstract
Gene knockout is an important approach to improve the production of antimicrobial compounds. B. subtilis PB2-LS10, derived from B. subtilis PB2-L by a surfactin synthetase (srf) genes knockout, exhibits stronger inhibitory action than its parental strain against all tested pathogenic bacteria and fungi. The antimicrobial extracts produced by B. subtilis PB2-L and B. subtilis PB2-LS10 respectively were characterized by the high-resolution LC-ESI-MS. To provide further insight into the distinct antimicrobial activities, we investigated the impact of the srf genes deletion on the growth and gene transcriptional profile of the strains. The mutant strain grew quickly and reached stationary phase 2h earlier than the wild-type. Prominent expression changes in the modified strain involved genes that were essential to metabolic pathways and processes. Genes related to amino acid transport, ATP-binding cassette (ABC) transporters and protein export were up-regulated in strain PB2-LS10. However, amino acid metabolism, carbohydrate metabolism and fatty acid metabolism were repressed. Because of its excellent antimicrobial activity, strain PB2-LS10 has potential for use in food preservation.
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Affiliation(s)
- Hongxia Liu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Xiaoxu Qu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Ling Gao
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Shengming Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Chong Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China.
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Sarwar MW, Saleem IB, Ali A, Abbas F. insilico Characterization and Homology Modeling of Arabitol Dehydrogenase (ArDH) from Candida albican. Bioinformation 2013; 9:952-7. [PMID: 24391356 PMCID: PMC3867646 DOI: 10.6026/97320630009952] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 11/19/2013] [Indexed: 11/23/2022] Open
Abstract
Background: Arabitol dehydrogenase (ArDH) is involved in the production of different sugar alcohols like arabitol, sorbitol,
mannitol, erythritol and xylitol by using five carbon sugars as substrate. Arabinose, d-ribose, d-ribulose, xylose and d-xylulose are
known substrate of this enzyme. ArDH is mainly produced by osmophilic fungi for the conversion of ribulose to arabitol under
stress conditions. Recently this enzyme has been used by various industries for the production of pharmaceutically important
sugar alcohols form cheap source than glucose. But the information at structure level as well as its binding energy analysis with
different substrates was missing. Results: The present study was focused on sequence analysis, insilico characterization and
substrate binding analysis of ArDH from a fungus specie candida albican. Sequence analysis and physicochemical properties
showed that this protein is highly stable, negatively charged and having more hydrophilic regions, these properties made this
enzyme to bind with number of five carbon sugars as substrate. The predicted 3D model will helpful for further structure based
studies. Docking analysis provided free energies of binding of each substrate from a best pose as arabinose -9.8224calK/mol, dribose
-11.3701Kcal/mol, d-ribulose -8.9230Kcal/mol, xylose -9.7007Kcal/mol and d-xylulose 9.7802Kcal/mol. Conclusion: Our
study provided insight information of structure and interactions of ArDH with its substrate. These results obtained from this study
clearly indicate that d-ribose is best substrate for ArDH for the production of sugar alcohols. This information will be helpful for
better usage of this enzyme for hyper-production of sugar alcohols by different industries.
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Affiliation(s)
- Muhammad Waseem Sarwar
- Department of Bioinformatics and Biotechnology, Government College University (GCU), Faisalabad, Pakistan
| | - Irum Baddisha Saleem
- Department of Bioinformatics and Biotechnology, Government College University (GCU), Faisalabad, Pakistan
| | - Asif Ali
- Department of Bioinformatics and Biotechnology, Government College University (GCU), Faisalabad, Pakistan
| | - Farhat Abbas
- Department of Bioinformatics and Biotechnology, Government College University (GCU), Faisalabad, Pakistan
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Sehar U, Mehmood MA, Nawaz S, Nadeem S, Hussain K, Sohail I, Tabassum MR, Gill SS, Saqib A. Three dimensional (3D) structure prediction and substrate-protein interaction study of the chitin binding protein CBP24 from B. thuringiensis. Bioinformation 2013; 9:725-9. [PMID: 23976829 PMCID: PMC3746096 DOI: 10.6026/97320630009725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 07/25/2013] [Indexed: 12/03/2022] Open
Abstract
Bacillus thuringiensis is an insecticidal bacterium whose chitinolytic system has been exploited to improve insect resistance in crops. In the present study, we studied the CBP24 from B. thuringiensis using homology modeling and molecular docking. The primary and secondary structure analyses showed CBP24 is a positively charged protein and contains single domain that belongs to family CBM33. The 3D model after refinement was used to explore the chitin binding characteristics of CBP24 using AUTODOCK. The docking analyses have shown that the surface exposed hydrophilic amino acid residues Thr-103, Lys-112 and Ser-162 interact with substrate through H-bonding. While, the amino acids resides Glu-39, Tyr-46, Ser-104 and Asn-109 were shown to have polar interactions with the substrate. The binding energy values evaluation of docking depicts a stable intermolecular conformation of the docked complex. The functional characterization of the CBP24 will elucidate the substrate-interaction pathway of the protein in specific and the carbohydrate binding proteins in general leading towards the exploration and exploitation of the prokaryotic substrate utilization pathways.
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Affiliation(s)
- Ujala Sehar
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Salman Nawaz
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Shahid Nadeem
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Khadim Hussain
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Iqra Sohail
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Muhammad Rizwan Tabassum
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Saba Shahid Gill
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Anam Saqib
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
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