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Identification and characterization of a 2,2-dichloropropionic acid (2,2-DCP) degrading alkalotorelant bacterium strain BHS1 isolated from Blue Lake, Turkey Abdul Wahhab, Batool Hazim; Khairul Anuar, Nurul Fatin Syamimi; Abdul Wahab, Roswanira; Al Nimer, Marwan S.M.; Samsulrizal, Nurul HIdayah; Abdul Hamid, Azzmer Azzar; Edbeib, Mohamed Faraj; Kaya, Yilmaz; Huyop, Fahrul
Journal of Tropical Life Science Vol 10, No 3 (2020)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.10.03.08

An acid, 2,2-dichloropropionic acid (2,2-DCP) is an active ingredient in herbicide (DalaponÂ®). Using 2,2-DCP as a model substrate, an alkalotolerant bacterium was successfully isolated from the Blue Lake, Turkey. This bacterium is a potential bioremediation agent of recalcitrant xenobiotic halogenated compounds. This study aimed to prove the efficacy of the alkalotolerance Bacillus megaterium BHS1 in degrading 2,2-DCP as the sole source of carbon. Biolog GEN III system and 16S rRNA analysis were used for the identification of the bacterium. It was discovered that the strain BHS1 is Bacillus megaterium, and the bacterium that was observed to thrive in alkaline conditions (pH 7.0âˆ’14.0), supplemented with varying concentrations of 2,2-DCP (from 20 to 60 mM). Growth of strain BHS1 was exceptional in 40 mM of 2,2-DCP at pH 9, corresponding to a cell doubling time of 17.7 hour, whereas was fully inhibited at 50 mM 2,2-DCP. Since halogenated pollutants can make their way into highly alkaline environments, therefore, identifying threshold levels of strain BHS1 with respect to alkaline-tolerance and maximum level of 2,2-DCP may prove pertinent. This is to ensure that an optimal environment is created for the bacteria to degrade 2,2-DCP-contaminated water. In addition, this is the first study exploring a Bacillus species isolated from an alkaline environment adept in utilizing 2,2-DCP as a sole source of carbon. Hence, the ability of this strain to degrade other types of haloalkanoic acids constitutes a worthy future study.

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

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

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

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.

Exploring Microbial Diversity in Green Honey from Pulau Banggi Sabah: A Preliminary Study: Microbial Diversity in Green Honey from Pulau Banggi Sabah Rajindran, Nanthini; Ab Wahabb, Roswanira; Huda , Nurul; Adekilekun Oyewusi, Habeebat; Wayan Gunam, Ida Bagus; Mohd Shariff , Amir Husni; Izzah Ismail, Norjihada; Huyop, Fahrul
Journal of Tropical Life Science Vol. 14 No. 1 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.01.02

The microbiological composition of honey can include microorganisms that are beneficial or harmful to human health. Therefore, it is essential to investigate the microbiological quality of different honey types available in the market. However, there is limited information available on the analysis, isolation, and characterization of honey-associated microbes, especially for green honey from Banggi Island. Green honey is sourced from underground areas within the island's forest. This study aimed to assess the microbiological quality of raw (freshly collected) and processed green honey by examining the presence of bacteria, yeast, molds, and pathogens. The results revealed that raw green honey had a slightly higher total plate count (770 ± 0.03 cfu/g) compared to processed green honey (640 ± 0.02 cfu/g). Both raw and processed green honey contained Lactobacillus spp. with counts of 350 ± 0.02 cfu/g and 160 ± 0.02 cfu/g, respectively. Bacillus count was higher in raw green honey (110 ± 0.01 cfu/g) compared to processed green honey (5 ± 0.01 cfu/g). Molds were only detected in raw green honey, while osmophilic yeast counts were higher in raw green honey (16000 ± 0.03 cfu/g) compared to processed green honey (120 ± 0.02 cfu/g). Mesophilic bacteria, thermophilic bacteria, coliforms, E. coli, and Staphylococcus aureus were not detected in either raw or processed green honey. Furthermore, green honey was free from pathogenic bacteria such as Salmonella spp., Listeria spp., and Shigella spp. Bacteria isolated from green honey included Lysinibacillus macrolides, Lysinibacillus boronitolerans, Paenibacillus cineris, Paenibacillus favisporus, and Bacillus oleronius, none of which were pathogenic. This study identified important microorganisms present in green honey, which have the potential to provide beneficial effects without posing any harm to human health.

Exploring Microbial Diversity in Green Honey from Pulau Banggi Sabah: A Preliminary Study: Microbial Diversity in Green Honey from Pulau Banggi Sabah Rajindran, Nanthini; Ab Wahabb, Roswanira; Huda , Nurul; Adekilekun Oyewusi, Habeebat; Wayan Gunam, Ida Bagus; Mohd Shariff , Amir Husni; Izzah Ismail, Norjihada; Huyop, Fahrul
Journal of Tropical Life Science Vol. 14 No. 1 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.01.02

The microbiological composition of honey can include microorganisms that are beneficial or harmful to human health. Therefore, it is essential to investigate the microbiological quality of different honey types available in the market. However, there is limited information available on the analysis, isolation, and characterization of honey-associated microbes, especially for green honey from Banggi Island. Green honey is sourced from underground areas within the island's forest. This study aimed to assess the microbiological quality of raw (freshly collected) and processed green honey by examining the presence of bacteria, yeast, molds, and pathogens. The results revealed that raw green honey had a slightly higher total plate count (770 ± 0.03 cfu/g) compared to processed green honey (640 ± 0.02 cfu/g). Both raw and processed green honey contained Lactobacillus spp. with counts of 350 ± 0.02 cfu/g and 160 ± 0.02 cfu/g, respectively. Bacillus count was higher in raw green honey (110 ± 0.01 cfu/g) compared to processed green honey (5 ± 0.01 cfu/g). Molds were only detected in raw green honey, while osmophilic yeast counts were higher in raw green honey (16000 ± 0.03 cfu/g) compared to processed green honey (120 ± 0.02 cfu/g). Mesophilic bacteria, thermophilic bacteria, coliforms, E. coli, and Staphylococcus aureus were not detected in either raw or processed green honey. Furthermore, green honey was free from pathogenic bacteria such as Salmonella spp., Listeria spp., and Shigella spp. Bacteria isolated from green honey included Lysinibacillus macrolides, Lysinibacillus boronitolerans, Paenibacillus cineris, Paenibacillus favisporus, and Bacillus oleronius, none of which were pathogenic. This study identified important microorganisms present in green honey, which have the potential to provide beneficial effects without posing any harm to human health.

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/

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 (2025): In Press
Publisher : Journal of Tropical Life Science

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

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.

Medicines in medicines: Challenges and Prospects in Drug Discovery from Fungal Endophytes of Medicinal Plants in Southeast Asia: Challenges and Prospects in Drug Discovery from Fungal Endophytes of Medicinal Plants Guerrero, Jonathan Jaime G.; General, Mheljor; Balendres, Mark Angelo; Tan, Mario; Buiza, Marielle; Huyop, Fahrul
Journal of Tropical Life Science Vol. 15 No. 2 (2025): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/xvfdnn97

Fungal endophytes engage in a balanced symbiotic continuum with their host plants, from mutualism to commensalism and parasitism. These host-endophyte interactions play a pivotal role in shaping the biosynthetic and chemical space of the host plants and their associated mycobiomes, resulting in a wealth of biologically active natural products that are attractive for drug discovery. Endophytic fungi in medicinal plants continue to attract attention, highlighting a holistic view of plant-based therapeutics that considers the plant and its endophytic partners as sources of medicinal compounds. In this review, we assembled recent Southeast Asian studies related to fungal endophytes from plants with traditional medicinal uses and their potential biomedical applications. Here, we present a comprehensive analysis of the interactions within the region, identifying prolific fungal classes that produce compounds of biomedical significance. This analysis is based on a consolidated dataset of over 1,300 interactions. We noted an association between plant-endophyte-synthesized compounds and their related chemistry. However, the majority are preliminary and lack comprehensive follow-through research. While fungal endophytes in the region produce important compounds, their applicability in drug discovery necessitates extensive long-term studies.

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