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R M, S I, Kv S, Kp S, T R, G S, K R. Genomic characterization of Enterobacter xiangfangensis STP-3: Application to real time petroleum oil sludge bioremediation. Microbiol Res 2021; 253:126882. [PMID: 34619415 DOI: 10.1016/j.micres.2021.126882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Sustainable treatment of petroleum oil sludge still remains as a major challenge to petroleum refineries. Bioremediation is the promising technology involving bacteria for simultaneous production of biosurfactant and followed by degradation of petroleum compounds. Complete genomic knowledge on such potential microbes could accentuate its successful exploitation. The present study discusses the genomic characteristics of novel biosurfactant producing petrophilic/ petroleum hydrocarbon degrading strain, Enterobacter xiangfangensis STP-3, isolated from petroleum refinery oil sludge contaminated soil. The genome has 4,584,462 bp and 4372 protein coding sequences. Functional analysis using the RAST and KEGG databases revealed the presence of biosynthetic gene clusters linked to glycolipid and lipopeptide production and multiple key candidate genes linked with the degradation pathway of petroleum hydrocarbons. Orthology study revealed diversity in gene clusters associated to membrane transport, carbohydrate, amino acid metabolism, virulence and defence mechanisms, and nucleoside and nucleotide synthesis. The comparative analysis with 27 other genomes predicted that the core genome contributes to its inherent bioremediation potential, whereas the accessory genome influences its environmental adaptability in unconventional environmental conditions. Further, experimental results showed that E. xiangfangensis STP-3 was able to degrade PHCs by 82 % in 14 days during the bioremediation of real time petroleum oil sludge with the concomitant production of biosurfactant and metabolic enzymes, To the best of our knowledge, no comprehensive genomic study has been previously reported on the biotechnological prospective of this species.
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Affiliation(s)
- Muneeswari R
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India
| | - Iyappan S
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, Kancheepuram District, Tamil Nadu, India
| | - Swathi Kv
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India
| | - Sudheesh Kp
- Nutrition, Genetics and Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Chennai, 600028, Tamil Nadu, India
| | - Rajesh T
- CSIR-National Environmental Engineering Research Institute, Chennai Zonal Lab, Tamil Nadu, India
| | - Sekaran G
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India
| | - Ramani K
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India.
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Lebedeva J, Jukneviciute G, Čepaitė R, Vickackaite V, Pranckutė R, Kuisiene N. Genome Mining and Characterization of Biosynthetic Gene Clusters in Two Cave Strains of Paenibacillus sp. Front Microbiol 2021; 11:612483. [PMID: 33505378 PMCID: PMC7829367 DOI: 10.3389/fmicb.2020.612483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022] Open
Abstract
The genome sequencing and mining of microorganisms from unexplored and extreme environments has become important in the process of identifying novel biosynthetic pathways. In the present study, the biosynthetic potential of Paenibacillus sp. strains 23TSA30-6 and 28ISP30-2 was investigated. Both strains were isolated from the deep oligotrophic Krubera-Voronja Cave and were found to be highly active against both Gram-positive and Gram-negative bacteria. Genome mining revealed a high number of biosynthetic gene clusters in the cave strains: 21 for strain 23TSA30-6 and 19 for strain 28ISP30-2. Single clusters encoding the biosynthesis of phosphonate, terpene, and siderophore, as well as a single trans-AT polyketide synthase/non-ribosomal peptide synthetase, were identified in both genomes. The most numerous clusters were assigned to the biosynthetic pathways of non-ribosomal peptides and ribosomally synthesized and post-translationally modified peptides. Although four non-ribosomal peptide synthetase gene clusters were predicted to be involved in the biosynthesis of known compounds (fusaricidin, polymyxin B, colistin A, and tridecaptin) of the genus Paenibacillus, discrepancies in the structural organization of the clusters, as well as in the substrate specificity of some adenylation domains, were detected between the reference pathways and the clusters in our study. Among the clusters involved in the biosynthesis of ribosomally synthesized peptides, only one was predicted to be involved in the biosynthesis of a known compound: paenicidin B. Most biosynthetic gene clusters in the genomes of the cave strains showed a low similarity with the reference pathways and were predicted to represent novel biosynthetic pathways. In addition, the cave strains differed in their potential to encode the biosynthesis of a few unique, previously unknown compounds (class II lanthipeptides and three non-ribosomal peptides). The phenotypic characterization of proteinaceous and volatile compounds produced by strains 23TSA30-6 and 28ISP30-2 was also performed, and the results were compared with those of genome mining.
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Affiliation(s)
- Jolanta Lebedeva
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gabriele Jukneviciute
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rimvydė Čepaitė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vida Vickackaite
- Department of Analytical and Environmental Chemistry, Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - Raminta Pranckutė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Nomeda Kuisiene
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Yadav S, Pandey AK, Dubey SK. Molecular modeling, docking and simulation dynamics of β-glucosidase reveals high-efficiency, thermo-stable, glucose tolerant enzyme in Paenibacillus lautus BHU3 strain. Int J Biol Macromol 2020; 168:371-382. [PMID: 33310096 DOI: 10.1016/j.ijbiomac.2020.12.059] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
The enzyme β-glucosidase mediates the rate limiting step of conversion of cellobiose to glucose and thus plays a vital role in the process of cellulose degradation. The present study deals with analysis of the effective novel strain of Paenibacillus lautus BHU3 for identifying high-efficiency thermostable, glucose tolerant β-glucosidases. Seven counterparts with elevated Tm values ranging from 64.6 to 75.8 °C with high thermo-stability, were revealed through this analysis. The blind molecular docking of the model enzymes structures with cellobiose and pNPG gave high negative interaction energies ranging from -11.33 to -13.29 and -6.43 to -9.054 (kcal mol-1), respectively. The enzyme WP_096774744.1 effectively formed 5 hydrogen bonds with the highest interaction energy (-13.29 kcal mol-1) with cellobiose at its catalytic site. Molecular dynamics simulation analysis performed for the WP_096774744.1-pNPG complex predicted Glu5, Arg7, Lue68, Gly69 and Phe325 as the major contributing residues for accomplishing hydrolysis of β-1-4-linkage. Further, the molecular docking of WP_096774744.1 enzyme with glucose revealed a distinct glucose-binding site distant from the substrate-binding site, thus confirming the deficient competitive inhibition by glucose. Hence, WP_096774744.1 β-glucosidase appears to be an efficient enzyme with enhanced activity to biodegrade the cellulosic materials and highly relevant for waste management and various industrial applications.
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Affiliation(s)
- Suman Yadav
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Anand Kumar Pandey
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, 284128, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Xue D, Zeng X, Gong C, Lin D, Yao S. A cold adapt and ethanol tolerant endoglucanase from a marine Bacillus subtilis. Chin J Chem Eng 2018. [DOI: 10.1016/j.cjche.2018.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Manavitehrani I, Fathi A, Schindeler A, Dehghani F. Sustained Protein Release from a Core-Shell Drug Carrier System Comprised of Mesoporous Nanoparticles and an Injectable Hydrogel. Macromol Biosci 2018; 18:e1800201. [PMID: 30395416 DOI: 10.1002/mabi.201800201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/23/2018] [Indexed: 11/11/2022]
Abstract
The manufacture of a biocompatible carrier for controlled delivery of bioactive compounds is described. This carrier is composed of a mesoporous silica nanoparticle as core that is homogenously distributed in an injectable hydrogel. For the synthesis of nanoparticles, a one step sol-gel method is developed to produce pores with the range of 100 nm. BMP2 and Fluorescein-conjugated bovine serum albumin is used as proteinaceous agents for measuring release, and is loaded into mesoporous silica nanoparticles at the optimum conditions of 48 h incubation period using 1:10 ratio of protein to nanoparticles. The release of proteins from either mesoporous nanoparticles or hydrogel individually involves a burst release stage, however the release from the core/shell carrier designed in this study follows a zero order kinetic. In summary, this biomaterial may be favorable for delivery of bioactive compounds such as BMP2 for a range of applications including bone tissue regeneration.
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Affiliation(s)
- Iman Manavitehrani
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, 2006, Australia
| | - Ali Fathi
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, 2006, Australia
| | - Aaron Schindeler
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, 2006, Australia.,Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Westmead, 2145, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, 2006, Australia
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