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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences
Oyewusi, Habeebat Adekilekun
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Agriculture, Biological Sciences & Forestry Environmental Science

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Dehalogenases for pollutant degradation in brief: A mini review Zakary, sefatullah; Oyewusi, Habeebat Adekilekun; Huyop, Fahrul
Journal of Tropical Life Science Vol 11, No 1 (2021)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.11.01.03

Abstract

Dehalogenases are microbial enzyme catalysed the cleavage of carbon-halogen bond of halogenated organic compounds. It has potential use in the area of biotechnology such as bioremediation and chemical industry. Halogenated organic compounds can be found in a considerable amount in the environment due to utilization in agriculture and industry, such as pesticides and herbicides. The presence of halogenated compound in the environment have been implicated on the health and natural ecosystem. Microbial dehalogenation is a significant method to tackle this problem. This review intends to briefly describe the microbial dehalogenases in relation to the environment where they are isolated. The basic information about dehalogenases in relation to dehalogenation mechanisms, classification, sources and the transportation of these pollutants into bacterial cytoplasm will be described. We also summarised readily available synthetic halogenated organic compound in the environment.
Genomic Analysis of Mesorhizobium loti Strain TONO Reveals Dehalogenases for Bioremediation Zakary, Sefatullah; Oyewusi, Habeebat Adekilekun; Huyop, Fahrul
Journal of Tropical Life Science Vol 11, No 1 (2021)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.11.01.09

Abstract

Halogenated compounds are extensively utilized in different industrial applications such as pesticides and herbicides and cause severe environmental problems because of their toxicity and persistence. Degradation of these compounds by the biological method is a significant method to reduce these recalcitrant. Mesorhizobium loti is important for nitrogen fixation in legume roots. Up to now, there is no report to indicate M. loti can produce dehalogenase enzymes. Thus, a total of twenty-five genomes of M. loti strains from the National Center for Biotechnology Information (NCBI) were analyzed. These strains notably carry dehalogenase genes and were further investigated. The relative ratio of haloalkane and haloacid dehalogenase type II or L-type from all twenty-five genomes was 26% and 74%, respectively, suggesting type II dehalogenase is common. Surprisingly, only M. loti strain TONO carries four dehalogenases and therefore it was further characterized. The chromosome of M. loti strain TONO contains four haloacid dehalogenase type II genes namely, dehLt1 (MLTONO_2099), dehLt2 (MLTONO_3660), dehLt3 (MLTONO_4143), and dehLt4 (MLTONO_6945), and their corresponding enzymes were designated as DehLt1, DehLt2, DehLt3, and DehLt4, respectively. The only haloalkane dehalogenase gene (MLTONO_4828) was located upstream of the dehLt3 gene and its amino acid share 88% identity with DmlA of Mesorhizobium japonicum MAFF 303099. The putative haloacid permease gene designated as dehrPt (MLTONO_0284) was located downstream of the dehLt1 and its amino acids show 69% identity with haloacid permease of Rhizobium sp. RC1. The gene encoding helix-turn-helix (HTH) motif family DNA-binding protein regulator and LysR family transcriptional regulator genes were also identified, possibly for regulatory functions. The genomic studies as such, have good potential to be screened for ne
A Review on Enzymatic Response to Salt Stress and Genomic/Metagenomic Analysis of Adaptation Protein in Hypersaline Environment Oyewusi, Habeebat Adekilekun; Muhammad, Muhammad; Wahab, Roswanira Abdul; Huyop, Fahrul
Journal of Tropical Life Science Vol 11, No 3 (2021)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.11.03.11

Abstract

Microorganisms adapted to conditions of high salinity (low water activity) provide an understanding on how the problem of maintaining an efficient cell integrity under high osmotic stress conditions that had been tackled naturally. Almost all microbes adapting to extreme situations either by intracellularly amass inorganic ions (K+) to counterbalance high salt concentration or by synthesizing and accumulating certain organic solutes called compatible solutes that confer protection without affecting cell functions and this process may be chloride ion dependent in some microorganisms. However, the use of culture-independent method like genomic or metagenomics shields more light on the microbial diversity, gene structure and regulation as well as discovery of novel genes that led to understanding of their adaptation mechanism and roles in extreme environments. Therefore, microbes that survive this natural attenuation aimed at acclimatizing with the extreme environments could serve as the sources of biotechnologically essential molecules with an extensive array of uses.
In silico Characterization of Poly (ethylene) Terephthalate (PET): Degrading Enzymes from Rhizobacter sp. for Enzymatic Degradation Mechanisms: Characterization of Rhizobacter sp. PET Hydrolases Damuri, Nur Wahida; Mohd Rozdhi, Amira Azawani; Tirmizhi Abubakar, Munkaila; Wayan Gunam, Ida Bagus; Huyop, Fahrul; Oyewusi, Habeebat Adekilekun
Journal of Tropical Life Science Vol. 15 No. 1 (2025)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/

Abstract

Dienelactone hydrolase (DHL) from Rhizobacter sp. is an enzyme from the β‐ketoadipate pathway that belongs to the α/β hydrolase family. It involves the conversion of chloroaromatics, such as nitrophenols and hydrocarbons, into harmless metabolites. The sequence-based analysis of Dienelactone hydrolase from Rhizobacter sp. shows significant homology to the extensively studied polyethylene terephthalate hydrolase of Ideonella sakaiensis (IsPETase). IsPETase can degrade the polymer, polyethylene terephthalate (PET), at room temperature. It was chosen as a template for dienelactone hydrolase from Rhizobacter sp. that was studied as a putative PET hydrolase. This study employs bioinformatics tools such as Expasy Protparam, Clustal Omega, SWISS-MODEL, GROMACS and Autodock vina to analyse the amino acid sequence of this enzyme, predict its three-dimensional structure and study its binding interaction. The structure of the putative PET hydrolase has been determined with 0.9 GMQE value and an overall quality factor of 96%. The residues responsible in substrate binding interactions are Leu88, Ser160 and Trp185. Thus, this in silico analysis depicts the ability of the putative PET hydrolase to bind to the polymer polyethylene terephthalate.
Structural Comparison of α-agarase (α-AgaD) from Thalassomonas sp. LD5: An in-silico study: Structural Comparison of α-agarase (α-AgaD) from Thalassomonas sp. LD5 Oyewusi, Habeebat Adekilekun; Oladipo, Oluwatosin; Abdul Wahab, Roswanira; Adekilekun , Habeebulahi Ajibola; Wayan Gunam, Ida Bagus; Huyop, Fahrul
Journal of Tropical Life Science Vol. 15 No. 2
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/

Abstract

The significance of agarase enzymes spans various high-value industries, including food, cosmetics, and medicine. These enzymes play a crucial role in the hydrolysis of agar to produce bioactive oligosaccharides, enabling wide-ranging applications across multiple fields. Among them, α-AgaD is a novel α-agarase enzyme produced by the Thalassomonas sp. LD5 strain. However, the structural and functional characteristics of α-AgaD within biological systems remain largely unexplored. This study therefore aims to provide a comprehensive in silico analysis of α-AgaD, focusing on its physicochemical properties, phylogenetic relationships, secondary structure composition, and 3D homology modelling. A range of computational tools was employed to validate the findings and enhance the structural understanding of this newly identified α-AgaD enzyme. The α-AgaD protein consists of 1,466 amino acids with a molecular weight of 158,787.82 Da. It has a theoretical isoelectric point (pI) of 4.14, indicating an overall acidic nature. Structural analysis revealed that alpha helices and random coils are the predominant secondary structures. Hydrophobic amino acids were more abundant than hydrophilic ones, with glycine accounting for approximately 10.4% of the total residues. The protein's aliphatic index was 72.05, and the instability index was 28.28, suggesting that α-AgaD is stable and likely to maintain its structure across a wide temperature range. Three-dimensional models of α-AgaD were constructed using I-TASSER, NCBI-PDB, SWISS-MODEL, and AlphaFold2, and subsequently validated using ERRAT, Verify3D, and PROCHECK. Among the models generated, AlphaFold2 produced the most accurate prediction, with nearly all amino acid residues located in the preferred regions of the Ramachandran plot. This further confirmed the reliability and quality of the refined models. The in silico structural analysis of α-AgaD offers valuable insights into the enzyme’s primary sequence, functional domains, and overall structural architecture, enhancing our understanding of α-agarase from Thalassomonas sp. LD5.
Concerted Structural analysis predictions of an organohalide pollutants uptake enzyme, putative permease protein (DehHsAADcPt) from Halomonas smyrnensis AAD6T.: Comparative Structural Prediction of putative permease protein (DehHsAADcPt) Oyewusi, Habeebat Adekilekun; Oladipo, Oluwatosin; Adekilekun, Habeebulahi; Abdul Wahab, Roswanira; Akinyede, Kolajo; Oladimeji Tugbobo, Samuel; Wayan Gunam, Ida Bagus; Huyop, Fahrul
Journal of Tropical Life Science Vol. 15 No. 3
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.15.03.07

Abstract

Halomonas smyrnensis AAD6T is a halophilic bacterium capable of utilizing haloalkanoic acid and possessing a specific gene for the uptake of organohalide pollutants. This distinctive characteristic has garnered the attention of researchers who seek to understand the underlying mechanisms. Among its genome, a putative permease protein known as DehHsAADcPt has been identified as a potential candidate for facilitating the uptake of these pollutants. Structural predictions of DehHsAADcPt have been conducted to gain a better understanding of its potential role in pollutant uptake. The predictions of DehHsAADcPt's structural characteristics, presented in this study, shed light on its potential application in bioremediation efforts. The implications of these findings are discussed in detail. The in-silico characterization and functional analysis of DehHsAADcPt was carried out with different bio-computational tools or servers. DehHsAADcPt belongs to the ABC inner membrane transporter permease family protein that is highly basic, hydrophobic, and thermostable having a molecular weight of 58,885.47Da as revealed from ExPASy server. The DehHsAADcPt compost mostly alpha helix structure and functional motif belongs to the binding-protein-dependent transport system inner membrane components and phage shock protein family. The 3-D structure obtained by AlphaFold2 homology modeling program and verified by Ramachandran plot revealed that most of the residues are in the allowed or favored regions of the plot. Likewise, several amino acid residues are predicted as ligand binding residues and most of them are highly conserved. The different computational tools used have proven to give holistic structural analysis predictions of DehHsAADcPt and revealed the concerted nature of these tools in elucidation. This study provides valuable insights into the structural and functional properties of DehHsAADcPt protein, which could pave the way for its potential application in the bioremediation of halogenated organic pollutants.
Co-Authors Abdul Wahab, Roswanira Adekilekun , Habeebulahi Ajibola Adekilekun, Habeebulahi Akinyede, Kolajo Damuri, Nur Wahida Huyop, Fahrul Ida Bagus Wayan Gunam Mohd Rozdhi, Amira Azawani Muhammad Muhammad Oladimeji Tugbobo, Samuel Oladipo, Oluwatosin Tirmizhi Abubakar, Munkaila Wahab, Roswanira Abdul Zakary, sefatullah