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Math RK, Bharatham N, Javaregowda PK, Yun HD. Role of Cel5H protein surface amino acids in binding with clay minerals and measurements of its forces. Appl Microsc 2021; 51:17. [PMID: 34762191 PMCID: PMC8586110 DOI: 10.1186/s42649-021-00066-7] [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: 09/20/2021] [Accepted: 10/27/2021] [Indexed: 11/10/2022] Open
Abstract
Our previous study on the binding activity between Cel5H and clay minerals showed highest binding efficiency among other cellulase enzymes cloned. Here, based on previous studies, we hypothesized that the positive amino acids on the surface of Cel5H protein may play an important role in binding to clay surfaces. To examine this, protein sequences of Bacillus licheniformis Cel5H (BlCel5H) and Paenibacillus polymyxa Cel5A (PpCel5A) were analyzed and then selected amino acids were mutated. These mutated proteins were investigated for binding activity and force measurement via atomic force microscopy (AFM). A total of seven amino acids which are only present in BlCel5H but not in PpCel5A were selected for mutational studies and the positive residues which are present in both were omitted. Of the seven selected surface lysine residues, only three mutants K196A(M2), K54A(M3) and K157T(M4) showed 12%, 7% and 8% less clay mineral binding ability, respectively compared with wild-type. The probable reason why other mutants did not show altered binding efficiency might be due to relative location of amino acids on the protein surface. Meanwhile, measurement of adhesion forces on mica sheets showed a well-defined maximum at 69 ± 19 pN for wild-type, 58 ± 19 pN for M2, 53 ± 19 pN for M3, and 49 ± 19 pN for M4 proteins. Hence, our results demonstrated that relative location of surface amino acids of Cel5H protein especially positive charged amino acids are important in the process of clay mineral-protein binding interaction through electrostatic exchange of charges.
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Affiliation(s)
- Renukaradhya K Math
- SDM Research Institute for Biomedical Sciences, 5th Floor, Manjushree Building, SDM College of Medical Sciences & Hospital Campus, Shri Dharmasthala Manjunatheshwara University, Dharwad, Sattur, 580009, India. .,Division of Applied Life Sciences, Gyeongsang National University, Chinju, 660701, Republic of Korea.
| | - Nagakumar Bharatham
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka, 560064, India
| | - Palaksha K Javaregowda
- SDM Research Institute for Biomedical Sciences, 5th Floor, Manjushree Building, SDM College of Medical Sciences & Hospital Campus, Shri Dharmasthala Manjunatheshwara University, Dharwad, Sattur, 580009, India
| | - Han Dae Yun
- Division of Applied Life Sciences, Gyeongsang National University, Chinju, 660701, Republic of Korea
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Math RK, Kambiranda D, Yun HD, Ghebreiyessus Y. Binding of cloned Cel enzymes on clay minerals related to the pI of the enzymes and database survey of cellulases of soil bacteria for pI. Biosci Biotechnol Biochem 2019; 84:238-246. [PMID: 31625450 DOI: 10.1080/09168451.2019.1679613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The Cel genes from Bacillus licheniformis MSB03 were cloned and expressed to investigate binding ability on clay minerals and sea sand at pH ranging 3 to 9. FTIR analysis has been done to characterize bound enzymes on clay minerals. Subsequent, surveying of NCBI database for extracellular enzymes of soil bacteria was carried out. Among the five cloned Cel enzymes assayed for binding to clay minerals, only Cel5H enzyme had the binding ability. Enzyme Cel5H exhibited highest binding to montmorillonite followed by kaolinite and sea sand. Interestingly, Cel5H had higher pI value of 9.24 than other proteins (5.2-5.7). Cel5H binding to montmorillonite was shown to be negatively affected below pH 3 and above pH 9. Infrared absorption spectra of the Cel5H-montmorillonite complexes showed distinct peaks for clay minerals and bound proteins. Furthermore, database survey of soil bacterial extracellular enzymes revealed that Bacillus species enzymes had higher pI than other soil bacterial enzymes.
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Affiliation(s)
- Renukaradhya K Math
- Research Institute of Agriculture and Life Science, Gyeongsang National University, Chinju, Republic of Korea
| | - Devaiah Kambiranda
- Department of Agricultural Sciences, Southern University Agriculture Research and Extension Center, Baton Rouge, LA, USA
| | - Han Dae Yun
- Research Institute of Agriculture and Life Science, Gyeongsang National University, Chinju, Republic of Korea
| | - Yemane Ghebreiyessus
- Department of Agricultural Sciences, Southern University Agriculture Research and Extension Center, Baton Rouge, LA, USA
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Islam SMA, Yeasmin S, Islam MS, Islam MS. Binding affinity and adhesion force of organophosphate hydrolase enzyme with soil particles related to the isoelectric point of the enzyme. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 141:85-92. [PMID: 28319863 DOI: 10.1016/j.ecoenv.2017.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 02/07/2017] [Accepted: 03/07/2017] [Indexed: 06/06/2023]
Abstract
The binding affinity of organophosphate hydrolase enzyme (OphB) with soil particles in relation to the isoelectric point (pI) was studied. Immobilization of OphB with soil particles was observed by confocal microscopy, Fourier transform infrared spectroscopy (FT-IR), and Atomic force microscopy (AFM). The calculated pI of OphB enzyme was increased from 8.69 to 8.89, 9.04 and 9.16 by the single, double and triple mutant of OphB enzyme, respectively through the replacement of negatively charged aspartate with positively charged histidine. Practically, the binding affinity was increased to 5.30%, 11.50%, and 16.80% for single, double and triple mutants, respectively. In contrast, enzyme activity of OphB did not change by the mutation of the enzyme. On the other hand, adhesion forces were gradually increased for wild type OphB enzyme (90 pN) to 96, 100 and 104 pN for single, double and triple mutants of OphB enzyme, respectively. There was an increasing trend of binding affinity and adhesion force by the increase of isoelectric point (pI) of OphB enzyme.
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Affiliation(s)
- Shah Md Asraful Islam
- Department of Plant Pathology, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh.
| | - Shabina Yeasmin
- Department of Forest Products, IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Md Saiful Islam
- Department of Soil Science, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Md Shariful Islam
- Department of Agricultural Chemistry, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
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Barman DN, Haque MA, Islam SMA, Yun HD, Kim MK. Cloning and expression of ophB gene encoding organophosphorus hydrolase from endophytic Pseudomonas sp. BF1-3 degrades organophosphorus pesticide chlorpyrifos. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2014; 108:135-141. [PMID: 25062445 DOI: 10.1016/j.ecoenv.2014.06.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 06/08/2014] [Accepted: 06/19/2014] [Indexed: 06/03/2023]
Abstract
Chlorpyrifos is an organophosphate pesticide that has adverse effect on animals and plants. We isolated endophytic bacterial strain, Pseudomonas sp. BF1-3, from balloon flower root which can hydrolyze chlorpyrifos. A gene (ophB) encoding a protein involved in chlorpyrifos degradation from this strain was cloned into Escherichia coli DH5α for confirming enzyme activity. After sequencing, total 1024bp nucleotide sequences were found in the open reading frame of ophB. The chlorpyrifos degradation patterns by E. coli DH5α (ophB) were observed. During incubation in minimal salt (M9) medium supplemented with chlorpyrifos (100mgL(-1)), the E. coli DH5α harboring ophB degraded about 97% initial chlorpyrifos (100mgL(-1)) and accumulated 86mgL(-1) 3,5,6-trichloro-2-pyridinol (TCP) within 9 days. In addition, optical density (OD) of E. coli DH5α (ophB) culture at 600nm was increased from 0.172 to 1.118 within 2 days of inoculation in the chlorpyrifos supplemented M9 medium. The estimated molecular weight of purified OphB protein was determined to be 31.4kDa by SDS-PAGE. The OphB enzyme was most active at pH 8 and an optimal temperature around 35°C. These results indicate that endophytic bacteria are supposed to be useful for biological control of environments contaminated with pesticides.
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Affiliation(s)
- Dhirendra Nath Barman
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Chinju 660-701, Republic of Korea
| | - Md Azizul Haque
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Chinju 660-701, Republic of Korea
| | - Shah Md Asraful Islam
- Department of Plant Pathology, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Han Dae Yun
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Chinju 660-701, Republic of Korea; Research Institute of Agriculture and Life Science, Gyeongsang National University, Chinju 660-701, Republic of Korea
| | - Min Keun Kim
- Gyeongsangnam-do Agricultural Research and Extension Service, Chinju 660-360, Republic of Korea.
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Kim MK, Kang TH, Kim J, Kim H, Yun HD. Evidence Showing Duplication and Recombination of cel Genes in Tandem from Hyperthermophilic Thermotoga sp. Appl Biochem Biotechnol 2012; 168:1834-48. [DOI: 10.1007/s12010-012-9901-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 09/10/2012] [Indexed: 12/01/2022]
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An CL, Kim MK, Kang TH, Kim J, Kim H, Yun HD. Cloning and biochemical analysis of β-glucoside utilization (bgl) operon without phosphotransferase system in Pectobacterium carotovorum subsp. carotovorum LY34. Microbiol Res 2012; 167:461-9. [DOI: 10.1016/j.micres.2012.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/06/2012] [Accepted: 03/11/2012] [Indexed: 10/28/2022]
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Yeasmin S, Kim CH, Park HJ, Sheikh MI, Lee JY, Kim JW, Back KK, Kim SH. Cell Surface Display of Cellulase Activity–Free Xylanase Enzyme on Saccharomyces Cerevisiae EBY100. Appl Biochem Biotechnol 2010; 164:294-304. [DOI: 10.1007/s12010-010-9135-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 11/19/2010] [Indexed: 11/29/2022]
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Islam SMA, Math RK, Cho KM, Lim WJ, Hong SY, Kim JM, Yun MG, Cho JJ, Yun HD. Organophosphorus hydrolase (OpdB) of Lactobacillus brevis WCP902 from kimchi is able to degrade organophosphorus pesticides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:5380-5386. [PMID: 20405842 DOI: 10.1021/jf903878e] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Lactobacillus brevis WCP902 that is capable of biodegrading chlorpyrifos was isolated from kimchi. The opdB gene cloned from this strain revealed 825 bp, encoding 274 aa, and an enzyme molecular weight of about 27 kDa. OpdB contains the same Gly-X-Ser-X-Gly motif found in most bacterial and eukaryotic esterase, lipase, and serine hydrolases, yet it is a novel member of the GDSVG family of esterolytic enzymes. Its conserved serine residue, Ser82, is significantly involved with enzyme activity that may have application for removing some pesticides. Optimum organophosphorus hydrolase (OpdB) activity appeared at pH 6.0 and 35 degrees C and during degradation of chlorpyrifos, coumaphos, diazinon, methylparathion, and parathion.
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Affiliation(s)
- Shah Md Asraful Islam
- Division of Applied Life Science (BK21 Program), Gyeongsang National University, Chinju, Korea
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Zhang LQ, Zhang HJ, Guo P, Xue P, Xie ZS, Chen Z, Jing GZ. C-terminal effect of Thermoanaerobacter tengcongensis ribosome recycling factor on its activity and conformation changes. Arch Biochem Biophys 2007; 466:211-20. [PMID: 17697668 DOI: 10.1016/j.abb.2007.06.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 06/22/2007] [Accepted: 06/27/2007] [Indexed: 11/24/2022]
Abstract
The in vivo activities and conformational changes of ribosome recycling factor from Thermoanaerobacter tengcongensis (TteRRF) with 12 successive C-terminal deletions were compared. The results showed that TteRRF mutants lacking one to four amino acid residues are inactive, those lacking five to nine are reactivated to a similar or a little higher level than wild-type TteRRF, and those lacking ten to twelve are inactivated again gradually. Conformational studies indicated that only the ANS binding fluorescence change is correlated well with the RRF in vivo activity change, while the secondary structure and local structure at the aromatic residues are not changed significantly. Trypsin cleavage site identification and protein stability measurement suggested that mutation only induced subtle conformation change and increased flexibility of the protein. Our results indicated that the ANS-detected local conformation changes of TteRRF and mutants are one verified direct reason of the in vivo inactivation and reactivation in Escherichia coli.
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Affiliation(s)
- Li-Qiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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Zhang L, Guo P, Zhang H, Jing G. Cooperative unfolding of Escherichia coli ribosome recycling factor originating from its domain-domain interaction and its implication for function. Arch Biochem Biophys 2006; 450:191-202. [PMID: 16684502 DOI: 10.1016/j.abb.2006.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Revised: 03/24/2006] [Accepted: 03/27/2006] [Indexed: 11/27/2022]
Abstract
Cooperative unfolding of Escherichia coli ribosome recycling factor (RRF) and its implication for function were investigated by comparing the in vitro unfolding and the in vivo activity of wild-type E. coli RRF and its temperature-sensitive mutant RRF(V117D). The experiments show that mutation V117D at domain I could perturb the domain II structure as evidenced in the near-UV CD and tyrosine fluorescence spectra though no significant globular conformation change occurred. Both equilibrium unfolding induced by heat or denaturant and kinetic unfolding induced by denaturant obey the two-state transition model, indicating V117D mutation does not perturb the efficient interdomain interaction, which results in cooperative unfolding of the RRF protein. However, the mutation significantly destabilizes the E. coli RRF protein, moving the thermal unfolding transition temperature range from 50-65 to 35-50 degrees C, which spans the non-permissive temperature for the growth of E. coli LJ14 strain (frr(ts)). The in vivo activity assays showed that although V117D mutation results in a temperature sensitive phenotype of E. coli LJ14 strain (frr(ts)), over-expression of mutant RRF(V117D) can eliminate the temperature sensitive phenotype at the non-permissive temperature (42 degrees C). Taking all the results into consideration, it can be suggested that the mechanism of the temperature sensitive phenotype of the E. coli LJ14 cells is due to inactivation of mutant RRF(V117D) caused by unfolding at the non-permissive temperatures.
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Affiliation(s)
- Liqiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, China
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Guo P, Zhang L, Zhang H, Feng Y, Jing G. Domain II plays a crucial role in the function of ribosome recycling factor. Biochem J 2006; 393:767-77. [PMID: 16262604 PMCID: PMC1360730 DOI: 10.1042/bj20050780] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RRF (ribosome recycling factor) consists of two domains, and in concert with EF-G (elongation factor-G), triggers dissociation of the post-termination ribosomal complex. However, the function of the individual domains of RRF remains unclear. To clarify this, two RRF chimaeras, EcoDI/TteDII and TteDI/EcoDII, were created by domain swaps between the proteins from Escherichia coli and Thermoanaerobacter tengcongensis. The ribosome recycling activity of the RRF chimaeras was compared with their wild-type RRFs by using in vivo and in vitro activity assays. Like wild-type TteRRF (T. tengcongensis RRF), the EcoDI/TteDII chimaera is non-functional in E. coli, but both wild-type TteRRF, and EcoDI/TteDII can be activated by coexpression of T. tengcongensis EF-G in E. coli. By contrast, like wild-type E. coli RRF (EcoRRF), TteDI/EcoDII is fully functional in E. coli. These findings suggest that domain II of RRF plays a crucial role in the concerted action of RRF and EF-G for the post-termination complex disassembly, and the specific interaction between RRF and EF-G on ribosomes mainly depends on the interaction between domain II of RRF and EF-G. This study provides direct genetic and biochemical evidence for the function of the individual domains of RRF.
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Affiliation(s)
- Peng Guo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China
| | - Liqiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China
| | - Hongjie Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China
| | - Yanming Feng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China
| | - Guozhong Jing
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China
- To whom correspondence should be addressed (email )
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