Current Biotechnology - Volume 7, Issue 2, 2018

Background: Contamination of soil with heavy metal is a major problem for developed and developing countries. Therefore, different approaches including bioremediation has been applied for remediation of metal contaminated sites. Biological approaches offer efficient and better way to remediate pollution in the air, soil and water. The plant-microbe interaction for remediation of polluted site is attracting interests and attentions, due to its high effectiveness and low cost. Therefore, in this review, mechanisms involved in removal of heavy metals like metal accumulation, enzymatic transformation and metal precipitation, and how plant-microbe interations can uplift the success rate of the process has been discussed. Approach of using plant-microbe interactions for the remediation of heavy metal contaminated soil, along with the roles of bacterial metabolites like siderophores, organic ligands and biosurfactants have been critically elaborated. Methods: A planned study was conducted for search of bibliographic databases of scientific studies of heavy metal remediaton and plant-microbe interactions for bioremediation. The chracteristics of the screened papers are described and the findings to conceptual framework critically analysed. Results: Different conventional methods have been used for remediation of heavy metals from contaminated sites. But bioremediation using plant-microbe interactions seems to be efficient and low cost alternate to such conventional remediation technologies. Rhizoremediation performance is based on the interactions of plant and microorganisms in the rhizoremediation. Rhizospheric microorganisms and their metabolites (e.g. siderophore, organic acids, IAA, etc.) have been suggested to be involved in (1) plant growth promotion through nutrient acquirement, alleviation of biotic/abiotic stress and (2) detoxification of metals through altering its mobility and bioavailability. Conclusion: Although bioremediation through rhizosphere has been promoted as an effective technique for bioremediation of heavy metal contamination, yet its applications has not been exploited much, and there is an urgent need to identify the lacunae to be addressed for success of this strategy.

Background: Despite the recognition that endophytic fungi are an important source of diverse and unique natural bioactive products, there are no reviews outlining how African researchers have been tapping into this bioresource. Objective: This review aims to consolidate and provide insights into the research on fungal endophytes in Africa during the period 1994-2014. Methods: A predefined search protocol was used to undertake a structured search of the bibliographic databases for peer-reviewed research literature. Literature that met the inclusion criteria was then analysed using semi-quantitative and qualitative techniques. Results: One hundred and thirty-nine papers from only 20 African countries met the inclusion criteria, with Egypt (35 papers) and South Africa (31 papers) being the leading countries. The main areas of research were biology and diversity determination (38.1%), bioprospecting for compounds with pharmaceutical potential (35.3%) and assessment of the ability of endophytic fungi to act as biopesticides (21.6%). A diversity of new and known compounds were shown to be secondary metabolites produced by the endophytic fungi and most of these compounds were investigated for their potential as antimicrobial and anticancer agents. Research was observed to have evolved from a focus on endophyte diversity in the 1990s and early 2000s to exploring the possibility of using endophyte fungi as sources of compounds with pharmaceutical and other commercial applications post 2005. Conclusion: In Africa, whilst fungal endophytes remain largely an untapped reservoir of potentially useful natural products, research on the fungal endophytes has also evolved in line with trends elsewhere.

Background: The design of microbial mediated remediation strategies for hydrocarbon polluted sites requires understanding of the microbial community structure pre and post contamination. This research is focused on investigating fungal community succession before and after crude oil contamination and nutrient amendment. Objective: To examine fungal community response to crude oil contamination, following biostimulation with various organic and inorganic nutrients. Method: A portion of the internal transcribed spacer (ITS) gene sequence of the total soil fungal DNA extracted from each treatment was subjected to polymerase chain reaction using the primer pair ITS1 and ITS4. Denaturing gradient gel electrophoresis of the ITS-PCR amplicons was done to elucidate community succession and diversity of fungal species associated with crude oil degradation. Results: Sequencing of excised bands and pairwise comparison using BLAST showed close affiliation of the ITS sequences with Diutina catenulata, Trichosporon asahii, T. posorum, T. japonicum, T. coremiiforme, Candida sp., Candida neorugosa, Candida rugosa, Meyerozyma guilliermondii, Candida sp., Geomyces destructans, Exophiala sp., Aphelenchoides arachidis and several uncultured fungal clones. The percentage similarity of the recovered fungal isolates with those deposited in GenBank ranged from 85%-100% indicating the presence of some well-established hydrocarbon degraders and some potential novel fungal species. As natural attenuation progressed following nutrient amendments, there was a shift in dominance of the samples from mostly uncultured fungal species to dominance by fungal species that have previously been implicated in hydrocarbons degradation. Conclusion: This report on fungal dynamics during bioremediation will be vital in designing environmental recovery strategies for crude oil polluted sites.

Background: Proper understanding of the true microbial diversity of cassava waste (CW) and their technological significance is critical for efficient utilization of the waste for value addition. Objective: In this study, technologically relevant characteristics of bacterial species associated with cassava peel waste (CPW) and cassava wastewater (CWW) were investigated with a view to identifying their industrial potential. Methods: Genotypic method involving sequencing of the 16S rRNA gene was used for identification of the bacterial species. Bacteriocin, H2O2, organic acid, linamarase, α-amylase and tannase production were determined using standard methods. Results: Twenty four bacterial species were isolated from CPW. The predominant species were Bacillus licheniformis (11.3%) and B. subtilis (11.3%). In CWW, 26 bacterial species were isolated. Lactobacillus fermentum (11.1%) was the most abundant species, followed by Lactobacillus plantarum (10.7%). Bacteriocin production was more common among L. fallax and L. fermentum from CWW and Bacillus species from CPW while H2O2 was more common among L. fermentum, L. delbrueckii and Leucoostoc fallax from CWW. L. plantarum from CWW were better acid producers and capable of faster acid production than L. fermentum and Leuconostoc fallax. Linamarase activity was highest in Bacillus coagulans, B. licheniformis, L. plantarum and L. fermentum from CPW. However, appreciable activity was also observed in L. plantarum, L. fermentum and Leuconostoc fallax from CWW. Bacillus species from CPW also showed α-amylase and tannase activities. Conclusion: This study showed that CW, on account of its rich bacterial diversity and techno-functional properties, has great potential for the food industry.

Background: Biotransformation and enzymatic methods of ester synthesis are more effective when performed in non-aqueous media. The aim of this work was to prepare reusable and more effective biocatalyst to catalyze the synthesis of pentyl valerate by esterification reaction. Method: Silane modified CdS nanoparticles were prepared and used for lipase immobilization. Characterization study was carried out using Infrared spectroscopy (FT-IR), Transmission electron microscopy (TEM), Fluorescence microscopy and Thermal gravimetric analysis (TGA). The effects of the reaction parameters such as pH, temperature, and molar ratio of the substrate to the solvent, acid to alcohol chain length was scrutinized in order to get enhanced esterification activity. Results: Upon optimization, the highest yield obtained for ester synthesis was 86% for immobilized lipase, whereas with free lipase only 52% yield was obtain. The immobilized biocatalyst showed higher catalytic activity (1.6 folds) than crude lipase. Immobilized lipase was recycled for 15 times retaining 80% of its initial activity. Km and Vmax for immobilized lipase are 0.38mM and 205μmoles/mg/min whereas for free lipase Km was 1.4mM and Vmax was 25 μmoles/mg/min. Conclusion: The application of enzyme immobilized on functionalized CdS verifies to be the promising system for ester synthesis in non-aqueous environment. In addition, nanobioconjugant system proves better for improving catalytic performance of lipase when exploited into organic solvents.

Background: Telomerase is a reverse transcriptase that maintains the length of telomere in cells. Human telomerase reverse transcriptase (hTERT) is one of the two basic components of telomere, consists of four domains and is an important target for inhibiting cell proliferation in malignant tumours. Human telomerase reverse transcriptase consists of 1132 amino acids that form four different domains. Amino acid residue from position 58 to 197 represents the GQ motif of Telomerase Essential N-Terminal domain (TEN) domain of hTERT. GQ governs the interaction between hTR and TERT. Similarly, CP motif present in TRBD domain is made of helix α3 followed by a loop. CP together with T motif ensures proper assembly of telomerase ribonucleotide complex. Controlling telomerase can help in ceasing cell proliferation in cancerous tissue. Thus, identifying hTERT inhibitory molecules can be used to design anticancer drugs. Objective: The main purpose of the study is to identify molecules that can inhibit motifs present in domains of hTERT. Method: The 3D structure of hTERT was modeled using I-TASSER server and the energy minimized structure was validated using overall quality factor (ERRAT) and Ramachandran plot. Using hierarchical virtual screening, zinc natural database was screened against Telomerase Essential N-Terminal domain (TEN) and Telomerase RNA Binding Domain (TRBD) domains of modeled hTERT, ADME filtering, DFT analysis and molecular dynamics Studies. Results: The molecule ZINC13142555 had the best glide score and energy and was chosen for density functional analysis to study its electronic properties. The stability of hTERT- ZINC13142555 was studied through molecular dynamics simulation for a period of 10ns. The identified compounds show interaction with GQ and CP motifs and hence it can be further proceeded to drug discovery process.

Background: Enzyme cycling is a sensitive assay method that exploits amplification techniques. We recently developed a novel enzymatic cycling method, which utilizes both the forward and reverse reactions of creatine kinase (CK), for the quantitative determination of creatine. Objective: Our aim was to develop a novel enzymatic cycling method to measure pyruvate or phosphoenolpyruvate using pyruvate kinase (PK), which exploits a similar principle to that of the CK assay. Methods: The method was developed by utilizing the reversibility of the PK reaction, in which the forward (pyruvate forming) and reverse reactions are catalyzed in the presence of an excess amount of IDP and ATP. Spectrophotometric real-time detection was accomplished by coupling the reaction to ADPdependent glucokinase (ADP-GK) together with glucose-6-phosphate dehydrogenase (G6PD). The rate of increase in absorbance of NADH at 340 nm was monitored. Results: When using PK from rabbit muscle (RMPK), we observed that the efficiency of the cycling reaction was markedly enhanced when Mg²⁺ was replaced with Mn²⁺. Unexpectedly, steady-state kinetic analysis of the reverse reaction alone coupled with ADP-GK and G6PD revealed the initial velocity was accelerated by approximately three-fold upon addition of IDP or GDP. This activation was not observed when Mg²⁺ was used as the divalent cation. Conclusion: We have developed a novel enzymatic cycling method mediated by RMPK, which utilizes the reversibility of the reaction in the presence of an excess amount of ATP and IDP with Mn²⁺. The limit of detection was estimated to be 12 nM.

Background: Mediator complex subunit 23 (MED23) is a transcriptional mediator of RNA polymerase II and essential for heat-shock-specific gene expression in humans. Mutations in MED23 gene cause neural diseases. Therefore, prior to a population study, it is important to uncover different deleterious single nucleotide polymorphisms (SNPs) structural and functional effects within MED23 encoded protein. Methods: The present study identified functional nsSNPs in MED23 and its effect on protein signaling cascade. The SNPs were retrieved from a dbSNP database and potentially deleteriousness SNPs were identified through in-silico screening with SIFT, the Polyphen server and PANTHER. Furthermore, protein structural prediction & validation of wild-type and mutated proteins were achieved through ITASSER and ProsA. At the end, protein-protein interactions and pathway analysis were conducted through STRING and literature review to uncover the effects of deleterious nsSNP to the MED23 protein biological function in the body. Results: The current approach predicted, the most pathogenic nsSNP is rs104893948 G235R exhibit position- specific evolutionary preservation induces the major damage to protein stability by disturbing its natural function and amino acid interactions. Destabilized MED23 protein provoked transcriptional dysregulation of enhancer based transcriptional factors presenting neurologic disorders and impaired brain development. Conclusion: In the future, mapping of G235R nsSNPs in MED23 gene would provide valuable information about population study and can apply as diagnostic markers for neural deformities and vascular diseases. Tumor suppressor in-vitro role of MED23 is needed to be explored among individuals carrying these polymorphisms to enhance our knowledge about complex mechanisms of this protein in several congenital human diseases.