Displaying publications 1 - 20 of 62 in total

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  1. Hamdan SH, Maiangwa J, Ali MSM, Normi YM, Sabri S, Leow TC
    Appl Microbiol Biotechnol, 2021 Oct;105(19):7069-7094.
    PMID: 34487207 DOI: 10.1007/s00253-021-11520-7
    Thermal stability is one of the most desirable characteristics in the search for novel lipases. The search for thermophilic microorganisms for synthesising functional enzyme biocatalysts with the ability to withstand high temperature, and capacity to maintain their native state in extreme conditions opens up new opportunities for their biotechnological applications. Thermophilic organisms are one of the most favoured organisms, whose distinctive characteristics are extremely related to their cellular constituent particularly biologically active proteins. Modifications on the enzyme structure are critical in optimizing the stability of enzyme to thermophilic conditions. Thermostable lipases are one of the most favourable enzymes used in food industries, pharmaceutical field, and actively been studied as potential biocatalyst in biodiesel production and other biotechnology application. Particularly, there is a trade-off between the use of enzymes in high concentration of organic solvents and product generation. Enhancement of the enzyme stability needs to be achieved for them to maintain their enzymatic activity regardless the environment. Various approaches on protein modification applied since decades ago conveyed a better understanding on how to improve the enzymatic properties in thermophilic bacteria. In fact, preliminary approach using advanced computational analysis is practically conducted before any modification is being performed experimentally. Apart from that, isolation of novel extremozymes from various microorganisms are offering great frontier in explaining the crucial native interaction within the molecules which could help in protein engineering. In this review, the thermostability prospect of lipases and the utility of protein engineering insights into achieving functional industrial usefulness at their high temperature habitat are highlighted. Similarly, the underlying thermodynamic and structural basis that defines the forces that stabilize these thermostable lipase is discussed. KEY POINTS: • The dynamics of lipases contributes to their non-covalent interactions and structural stability. • Thermostability can be enhanced by well-established genetic tools for improved kinetic efficiency. • Molecular dynamics greatly provides structure-function insights on thermodynamics of lipase.
  2. Obeng EM, Brossette T, Ongkudon CM, Budiman C, Maas R, Jose J
    Appl Microbiol Biotechnol, 2018 Jun;102(11):4829-4841.
    PMID: 29675801 DOI: 10.1007/s00253-018-8987-4
    This article comparatively reports the workability of Escherichia coli BL21(DE3) and Pseudomonas putida KT2440 cell factories for the expression of three model autodisplayed cellulases (i.e., endoglucanase, BsCel5A; exoglucanase, CelK; β-glucosidase, BglA). The differentiation of the recombinant cells was restricted to their cell growth and enzyme expression/activity attributes. Comparatively, the recombinant E. coli showed higher cell growth rates but lower enzyme activities than the recombinant P. putida. However, the endo-, exoglucanase, and β-glucosidase on the surfaces of both cell factories showed activity over a broad range of pH (4-10) and temperature (30-100 °C). The pH and temperature optima were pH 6, 60 °C (BsCel5A); pH 6, 60-70 °C (CelK); and pH 6, 50 °C (BglA). Overall, the P. putida cell factory with autodisplayed enzymes demonstrated higher bioactivity and remarkable biochemical characteristics and thus was chosen for the saccharification of filter paper. A volumetric blend of the three cellulases with P. putida as the host yielded a ratio of 1:1:1.5 of endoglucanase, exoglucanase, and β-glucosidase, respectively, as the optimum blend composition for filter paper degradation. At an optical density (578 nm) of 50, the blend generated a maximum sugar yield of about 0.7 mg/ml (~ 0.08 U/g) from Whatman filter paper (Ø 6 mm, ~ 2.5 mg) within 24 h.
  3. Gantait S, El-Dawayati MM, Panigrahi J, Labrooy C, Verma SK
    Appl Microbiol Biotechnol, 2018 Oct;102(19):8229-8259.
    PMID: 30054703 DOI: 10.1007/s00253-018-9232-x
    Date palm (Phoenix dactylifera L.) is one of the most important fruit trees that contribute a major part to the economy of Middle East and North African countries. It is quintessentially called "tree of life" owing to its resilience to adverse climatic conditions, along with manifold nutritional-cum-medicinal attributes that comes from its fruits and other plant parts. Being a tree with such immense utility, it has gained substantial attention of tree breeders for its genetic advancement via in vitro biotechnological interventions. Herein, an extensive review of biotechnological research advances in date palm has been consolidated as one of the major research achievements during the past two decades. This article compares the different biotechnological techniques used in this species such as: tissue and organ culture, bioreactor-mediated large-scale propagation, cell suspension culture, embryogenic culture, protoplast culture, conservation (for short- and long-term) of germplasms, in vitro mutagenesis, in vitro selection against biotic and abiotic stresses, secondary metabolite production in vitro, and genetic transformation. This review provides an insight on crop improvement and breeding programs for improved yield and quality fruits; besides, it would undeniably facilitate the tissue culture-based research on date palm for accelerated propagation and enhanced production of quality planting materials, along with conservation and exchange of germplasms, and genetic engineering. In addition, the unexplored research methodologies and major bottlenecks identified in this review should be contemplated on in near future.
  4. Moi IM, Roslan NN, Leow ATC, Ali MSM, Rahman RNZRA, Rahimpour A, et al.
    Appl Microbiol Biotechnol, 2017 Jun;101(11):4371-4385.
    PMID: 28497204 DOI: 10.1007/s00253-017-8300-y
    Photobacterium species are Gram-negative coccobacilli which are distributed in marine habitats worldwide. Some species are unique because of their capability to produce luminescence. Taxonomically, about 23 species and 2 subspecies are validated to date. Genomes from a few Photobacterium spp. have been sequenced and studied. They are considered a special group of bacteria because some species are capable of producing essential polyunsaturated fatty acids, antibacterial compounds, lipases, esterases and asparaginases. They are also used as biosensors in food and environmental monitoring and detectors of drown victim, as well as an important symbiont.
  5. Naz S, Gul A, Zia M, Javed R
    Appl Microbiol Biotechnol, 2023 Feb;107(4):1039-1061.
    PMID: 36635395 DOI: 10.1007/s00253-023-12364-z
    Versatile nature of copper oxide nanoparticles (CuO NPs) has made them an imperative nanomaterial being employed in nanomedicine. Various physical, chemical, and biological methodologies are in use for the preparation of CuO NPs. The physicochemical and biological properties of CuO NPs are primarily affected by their method of fabrication; therefore, selectivity of a synthetic technique is immensely important that makes these NPs appropriate for a specific biomedical application. The deliberate use of CuO NPs in biomedicine questions their biocompatible nature. For this reason, the present review has been designed to focus on the approaches employed for the synthesis of CuO NPs; their biomedical applications highlighting antimicrobial, anticancer, and antioxidant studies; and most importantly, the in vitro and in vivo toxicity associated with these NPs. This comprehensive overview of CuO NPs is unique and novel as it emphasizes on biomedical applications of CuO NPs along with its toxicological assessments which would be useful in providing core knowledge to researchers working in these domains for planning and conducting futuristic studies. KEY POINTS: • The recent methods for fabrication of CuO nanoparticles have been discussed with emphasis on green synthesis methods for different biomedical approaches. • Antibacterial, antioxidant, anticancer, antiparasitic, antidiabetic, and antiviral properties of CuO nanoparticles have been explained. • In vitro and in vivo toxicological studies of CuO nanoparticles exploited along with their respective mechanisms.
  6. Sudesh K, Bhubalan K, Chuah JA, Kek YK, Kamilah H, Sridewi N, et al.
    Appl Microbiol Biotechnol, 2011 Mar;89(5):1373-86.
    PMID: 21279347 DOI: 10.1007/s00253-011-3098-5
    Polyhydroxyalkanoate (PHA) is a potential substitute for some petrochemical-based plastics. This biodegradable plastic is derived from microbial fermentation using various carbon substrates. Since carbon source has been identified as one of the major cost-absorbing factors in PHA production, cheap and renewable substrates are currently being investigated as substitutes for existing sugar-based feedstock. Plant oils have been found to result in high-yield PHA production. Malaysia, being the world's second largest producer of palm oil, is able to ensure continuous supply of palm oil products for sustainable PHA production. The biosynthesis and characterization of various types of PHA using palm oil products have been described in detail in this review. Besides, by-products and waste stream from palm oil industry have also demonstrated promising results as carbon sources for PHA biosynthesis. Some new applications in cosmetic and wastewater treatment show the diversity of PHA usage. With proper management practices and efficient milling processes, it may be possible to supply enough palm oil-based raw materials for human consumption and other biotechnological applications such as production of PHA in a sustainable manner.
  7. Packiam KAR, Ramanan RN, Ooi CW, Krishnaswamy L, Tey BT
    Appl Microbiol Biotechnol, 2020 Apr;104(8):3253-3266.
    PMID: 32076772 DOI: 10.1007/s00253-020-10454-w
    Over the past few decades, Escherichia coli (E. coli) remains the most favorable host among the microbial cell factories for the production of soluble recombinant proteins. Recombinant protein production (RPP) via E. coli is optimized at the level of gene expression (expression level) and the process condition of fermentation (process level). Presently, the reported studies do not give a clear view on the selection of methods employed in the optimization of RPP. Here, we have reviewed various optimization methods and their preferences with respect to the factors at expression and process levels to achieve the optimal levels of soluble RPP. With a greater understanding of these optimization methods, we proposed a stepwise methodology linking the factors from both levels for optimizing the production of soluble recombinant protein in E. coli. The proposed methodology is further explained through five sets of examples demonstrating the optimization of RPP at both expression and process levels.Key Points• Stepwise methodology of optimizing recombinant protein production is proposed.• In silico tools can facilitate the optimization of gene- and protein-based factors.• Optimization of gene- and protein-based factors aids host-vector selection.• Statistical optimization is preferred for achieving optimal levels of process factors.
  8. Mustapha NA, Hu A, Yu CP, Sharuddin SS, Ramli N, Shirai Y, et al.
    Appl Microbiol Biotechnol, 2018 Jun;102(12):5323-5334.
    PMID: 29696331 DOI: 10.1007/s00253-018-9003-8
    Efficient approaches for the utilization of waste sewage sludge have been widely studied. One of them is to use it for the bioenergy production, specifically methane gas which is well-known to be driven by complex bacterial interactions during the anaerobic digestion process. Therefore, it is important to understand not only microorganisms for producing methane but also those for controlling or regulating the process. In this study, azithromycin analogs belonging to macrolide, ketolide, and lincosamide groups were applied to investigate the mechanisms and dynamics of bacterial community in waste sewage sludge for methane production. The stages of anaerobic digestion process were evaluated by measuring the production of intermediate substrates, such as protease activity, organic acids, the quantification of bacteria and archaea, and its community dynamics. All azithromycin analogs used in this study achieved a high methane production compared to the control sample without any antibiotic due to the efficient hydrolysis process and the presence of important fermentative bacteria and archaea responsible in the methanogenesis stage. The key microorganisms contributing to the methane production may be Clostridia, Cladilinea, Planctomycetes, and Alphaproteobacteria as an accelerator whereas Nitrosomonadaceae and Nitrospiraceae may be suppressors for methane production. In conclusion, the utilization of antibiotic analogs of macrolide, ketolide, and lincosamide groups has a promising ability in finding the essential microorganisms and improving the methane production using waste sewage sludge.
  9. Doni F, Mispan MS, Suhaimi NSM, Ishak N, Uphoff N
    Appl Microbiol Biotechnol, 2019 Jul;103(13):5131-5142.
    PMID: 31101941 DOI: 10.1007/s00253-019-09879-9
    The system of rice intensification (SRI) is an agroecological approach to rice cultivation that seeks to create optimal conditions for healthy plant growth by minimizing inter-plant competition, transplanting widely spaced young single seedlings, and optimizing favorable soil conditions with organic amendments, increased soil aeration by weeding, and controlled water management. These practices improve rice plant growth with yields up to three times more than with conventional cultivation methods, and increase crop resilience under biotic and abiotic stresses. This review discusses the roles of beneficial microbes in improving rice plant growth, yield, and resilience when SRI practices are used, and how these modifications in plant, soil, water, and nutrient management affect the populations and diversity of soil microorganisms. Mechanisms whereby symbiotic microbes support rice plants' growth and performance are also discussed.
  10. Goh KM, Kahar UM, Chai YY, Chong CS, Chai KP, Ranjani V, et al.
    Appl Microbiol Biotechnol, 2013 Feb;97(4):1475-88.
    PMID: 23324802 DOI: 10.1007/s00253-012-4663-2
    The Bacillaceae family members are a good source of bacteria for bioprocessing and biotransformation involving whole cells or enzymes. In contrast to Bacillus and Geobacillus, Anoxybacillus is a relatively new genus that was proposed in the year 2000. Because these bacteria are alkali-tolerant thermophiles, they are suitable for many industrial applications. More than a decade after the first report of Anoxybacillus, knowledge accumulated from fundamental and applied studies suggests that this genus can serve as a good alternative in many applications related to starch and lignocellulosic biomasses, environmental waste treatment, enzyme technology, and possibly bioenergy production. This current review provides the first summary of past and recent discoveries regarding the isolation of Anoxybacillus, its medium requirements, its proteins that have been characterized and cloned, bioremediation applications, metabolic studies, and genomic analysis. Comparisons to some other members of Bacillaceae and possible future applications of Anoxybacillus are also discussed.
  11. Akhtar J, Idris A, Abd Aziz R
    Appl Microbiol Biotechnol, 2014 Feb;98(3):987-1000.
    PMID: 24292125 DOI: 10.1007/s00253-013-5319-6
    Production of succinic acid via separate enzymatic hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) are alternatives and are environmentally friendly processes. These processes have attained considerable positions in the industry with their own share of challenges and problems. The high-value succinic acid is extensively used in chemical, food, pharmaceutical, leather and textile industries and can be efficiently produced via several methods. Previously, succinic acid production via chemical synthesis from petrochemical or refined sugar has been the focus of interest of most reviewers. However, these expensive substrates have been recently replaced by alternative sustainable raw materials such as lignocellulosic biomass, which is cheap and abundantly available. Thus, this review focuses on succinic acid production utilizing lignocellulosic material as a potential substrate for SSF and SHF. SSF is an economical single-step process which can be a substitute for SHF - a two-step process where biomass is hydrolyzed in the first step and fermented in the second step. SSF of lignocellulosic biomass under optimum temperature and pH conditions results in the controlled release of sugar and simultaneous conversion into succinic acid by specific microorganisms, reducing reaction time and costs and increasing productivity. In addition, main process parameters which influence SHF and SSF processes such as batch and fed-batch fermentation conditions using different microbial strains are discussed in detail.
  12. Yip CH, Yarkoni O, Ajioka J, Wan KL, Nathan S
    Appl Microbiol Biotechnol, 2019 Feb;103(4):1667-1680.
    PMID: 30637495 DOI: 10.1007/s00253-018-09611-z
    Prodigiosin, a red linear tripyrrole pigment and a member of the prodiginine family, is normally secreted by the human pathogen Serratia marcescens as a secondary metabolite. Studies on prodigiosin have received renewed attention as a result of reported immunosuppressive, antimicrobial and anticancer properties. High-level synthesis of prodigiosin and the bioengineering of strains to synthesise useful prodiginine derivatives have also been a subject of investigation. To exploit the potential use of prodigiosin as a clinical drug targeting bacteria or as a dye for textiles, high-level synthesis of prodigiosin is a prerequisite. This review presents an overview on the biosynthesis of prodigiosin from its natural host Serratia marcescens and through recombinant approaches as well as highlighting the beneficial properties of prodigiosin. We also discuss the prospect of adopting a synthetic biology approach for safe and cost-effective production of prodigiosin in a more industrially compliant surrogate host.
  13. Mathew S, Zakaria ZA
    Appl Microbiol Biotechnol, 2015 Jan;99(2):611-22.
    PMID: 25467926 DOI: 10.1007/s00253-014-6242-1
    Pyroligneous acid (PA) is a complex highly oxygenated aqueous liquid fraction obtained by the condensation of pyrolysis vapors, which result from the thermochemical breakdown or pyrolysis of plant biomass components such as cellulose, hemicellulose, and lignin. PA produced by the slow pyrolysis of plant biomass is a yellowish brown or dark brown liquid with acidic pH and usually comprises a complex mixture of guaiacols, catechols, syringols, phenols, vanillins, furans, pyrans, carboxaldehydes, hydroxyketones, sugars, alkyl aryl ethers, nitrogenated derivatives, alcohols, acetic acid, and other carboxylic acids. The phenolic components, namely guaiacol, alkyl guaiacols, syringol, and alkyl syringols, contribute to the smoky odor of PA. PA finds application in diverse areas, as antioxidant, antimicrobial, antiinflammatory, plant growth stimulator, coagulant for natural rubber, and termiticidal and pesticidal agent; is a source for valuable chemicals; and imparts a smoky flavor for food.
  14. Parvizpour S, Hussin N, Shamsir MS, Razmara J
    Appl Microbiol Biotechnol, 2021 Feb;105(3):899-907.
    PMID: 33427934 DOI: 10.1007/s00253-020-11074-0
    Psychrophiles are cold-living microorganisms synthesizing enzymes that are permanently active at almost near-zero temperatures. Psychrozymes are supposed to be structurally more flexible than their homologous proteins. This structural flexibility enables these proteins to undergo conformational changes during catalysis and improve catalytic efficiency at low temperatures. The outstanding characteristics of the psychrophilic enzymes have attracted the attention of the scientific community to utilize them in a wide variety of industrial and pharmaceutical applications. In this review, we first highlight the current knowledge of the cold-adaptation mechanisms of the psychrophiles. In the sequel, we describe the potential applications of the enzymes in different biotechnological processes specifically, in the production of industrial and pharmaceutical products. KEY POINTS: • Methods that organisms have evolved to survive and proliferate at cold environments. • The economic benefits due to their high activity at low and moderate temperatures. • Applications of the psychrophiles in biotechnological and pharmaceutical industry.
  15. Muhammad Nasir I, Mohd Ghazi TI, Omar R
    Appl Microbiol Biotechnol, 2012 Jul;95(2):321-9.
    PMID: 22622840 DOI: 10.1007/s00253-012-4152-7
    Anaerobic digestion treatments have often been used for biological stabilization of solid wastes. These treatment processes generate biogas which can be used as a renewable energy sources. Recently, anaerobic digestion of solid wastes has attracted more interest because of current environmental problems, most especially those concerned with global warming. Thus, laboratory-scale research on this area has increased significantly. In this review paper, the summary of the most recent research activities covering production of biogas from solid wastes according to its origin via various anaerobic technologies was presented.
  16. Phan CW, Sabaratnam V
    Appl Microbiol Biotechnol, 2012 Nov;96(4):863-73.
    PMID: 23053096 DOI: 10.1007/s00253-012-4446-9
    Mushroom industries generate a virtually in-exhaustible supply of a co-product called spent mushroom substrate (SMS). This is the unutilised substrate and the mushroom mycelium left after harvesting of mushrooms. As the mushroom industry is steadily growing, the volume of SMS generated annually is increasing. In recent years, the mushroom industry has faced challenges in storing and disposing the SMS. The obvious solution is to explore new applications of SMS. There has been considerable discussion recently about the potentials of using SMS for production of value-added products. One of them is production of lignocellulosic enzymes such as laccase, xylanase, lignin peroxidase, cellulase and hemicellulase. This paper reviews scientific research and practical applications of SMS as a readily available and cheap source of enzymes for bioremediation, animal feed and energy feedstock.
  17. Moi IM, Leow ATC, Ali MSM, Rahman RNZRA, Salleh AB, Sabri S
    Appl Microbiol Biotechnol, 2018 Jul;102(14):5811-5826.
    PMID: 29749565 DOI: 10.1007/s00253-018-9063-9
    Polyunsaturated fatty acids (PUFAs) play an important role in human diet. Despite the wide-ranging importance and benefits from heart health to brain functions, humans and mammals cannot synthesize PUFAs de novo. The primary sources of PUFA are fish and plants. Due to the increasing concerns associated with food security as well as issues of environmental contaminants in fish oil, there has been considerable interest in the production of polyunsaturated fatty acids from alternative resources which are more sustainable, safer, and economical. For instance, marine bacteria, particularly the genus of Shewanella, Photobacterium, Colwellia, Moritella, Psychromonas, Vibrio, and Alteromonas, are found to be one among the major microbial producers of polyunsaturated fatty acids. Recent developments in the area with a focus on the production of polyunsaturated fatty acids from marine bacteria as well as the metabolic engineering strategies for the improvement of PUFA production are discussed.
  18. Chek MF, Hiroe A, Hakoshima T, Sudesh K, Taguchi S
    Appl Microbiol Biotechnol, 2019 Feb;103(3):1131-1141.
    PMID: 30511262 DOI: 10.1007/s00253-018-9538-8
    Polyhydroxyalkanoates (PHAs) are biopolymers synthesized by a wide range of bacteria, which serve as a promising candidate in replacing some conventional petrochemical-based plastics. PHA synthase (PhaC) is the key enzyme in the polymerization of PHA, and the crystal structures were successfully determined using the catalytic domain of PhaC from Cupriavidus necator (PhaCCn-CAT) and Chromobacterium sp. USM2 (PhaCCs-CAT). Here, we review the beneficial mutations discovered in PhaCs from a structural perspective. The structural comparison of the residues involved in beneficial mutation reveals that the residues are near to the catalytic triad, but not inside the catalytic pocket. For instance, Ala510 of PhaCCn is near catalytic His508 and may be involved in the open-close regulation, which presumably play an important role in substrate specificity and activity. In the class II PhaC1 from Pseudomonas sp. 61-3 (PhaC1Ps), Ser325 stabilizes the catalytic cysteine through hydrogen bonding. Another residue, Gln508 of PhaC1Ps is located in a conserved hydrophobic pocket which is next to the catalytic Asp and His. A class I, II-conserved Phe420 of PhaCCn is one of the residues involved in dimerization and its mutation to serine greatly reduced the lag phase. The current structural analysis shows that the Phe362 and Phe518 of PhaC from Aeromonas caviae (PhaCAc) are assisting the dimer formation and maintaining the integrity of the core beta-sheet, respectively. The structure-function relationship of PhaCs discussed in this review will serve as valuable reference for future protein engineering works to enhance the performance of PhaCs and to produce novel biopolymers.
  19. Low KO, Muhammad Mahadi N, Md Illias R
    Appl Microbiol Biotechnol, 2013 May;97(9):3811-26.
    PMID: 23529680 DOI: 10.1007/s00253-013-4831-z
    Escherichia coli-the powerhouse for recombinant protein production-is rapidly gaining status as a reliable and efficient host for secretory expression. An improved understanding of protein translocation processes and its mechanisms has inspired and accelerated the development of new tools and applications in this field and, in particular, a more efficient secretion signal. Several important characteristics and requirements are summarised for the design of a more efficient signal peptide for the production of recombinant proteins in E. coli. General approaches and strategies to optimise the signal peptide, including the selection and modification of the signal peptide components, are included. Several challenges in the secretory production of recombinant proteins are discussed, and research approaches designed to meet these challenges are proposed.
  20. Yahaya RSR, Normi YM, Phang LY, Ahmad SA, Abdullah JO, Sabri S
    Appl Microbiol Biotechnol, 2021 May;105(10):3955-3969.
    PMID: 33937928 DOI: 10.1007/s00253-021-11321-y
    Keratinase is an important enzyme that can degrade recalcitrant keratinous wastes to form beneficial recyclable keratin hydrolysates. Keratinase is not only important as an alternative to reduce environmental pollution caused by chemical treatments of keratinous wastes, but it also has industrial significance. Currently, the bioproduction of keratinase from native keratinolytic host is considered low, and this hampers large-scale usage of the enzyme. Straightforward approaches of cloning and expression of recombinant keratinases from native keratinolytic host are employed to elevate the amount of keratinase produced. However, this is still insufficient to compensate for the lack of its large-scale production to meet the industrial demands. Hence, this review aimed to highlight the various sources of keratinase and the strategies to increase its production in native keratinolytic hosts. Molecular strategies to increase the production of recombinant keratinase such as plasmid selection, promoter engineering, chromosomal integration, signal peptide and propeptide engineering, codon optimization, and glycoengineering were also described. These mentioned strategies have been utilized in heterologous expression hosts, namely, Escherichia coli, Bacillus sp., and Pichia pastoris, as they are most widely used for the heterologous propagations of keratinases to further intensify the production of recombinant keratinases adapted to better suit the large-scale demand for them. KEY POINTS: • Molecular strategies to enhance keratinase production in heterologous hosts. • Construction of a prominent keratinolytic host from a native strain. • Patent analysis of keratinase production shows rapid high interest in molecular field.
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