Physiology and molecular biology of plants : an international journal of functional plant biology, 2021
The amino acid, proline, is utilized by different organisms to offset cellular imbalances caused ... more The amino acid, proline, is utilized by different organisms to offset cellular imbalances caused by environmental stresses. The wide use of proline as a stress adaptor molecule indicates that proline has a fundamental biological role in stress response. A comprehensive analysis of the transcript abundance of proline metabolizing genes is fundamental for the assessment of function and regulation of each gene. Using available microarray data and quantitative real-time RT-PCR, the expression profiles of gene encoding key proline biosynthesis and degradation enzymes i.e., OAT, P5CS, P5CR and PDH were examined. Interestingly, validation of candidate genes in rice using in-silico data provided strong evidence for their involvement in stress response. Note that, OsOAT, OsP5CS1, OsP5CS2, OsP5CR showed similar expression pattern in quantitative real-time RT-PCR results as compared to microarray data. However, OsPDH showed a different expression pattern which may be due to the genotypic varia...
The Aldehyde dehydrogenase (ALDH) superfamily comprises a group of enzymes involved in the scaven... more The Aldehyde dehydrogenase (ALDH) superfamily comprises a group of enzymes involved in the scavenging of toxic aldehyde molecules by converting them into their corresponding non-toxic carboxylic acids. A genome-wide study in potato identified a total of 22 ALDH genes grouped into ten families that are presented unevenly throughout all the 12 chromosomes. Based on the evolutionary analysis of ALDH proteins from different plant species, ALDH2 and ALDH3 were found to be the most abundant families in the plant, while ALDH18 was found to be the most distantly related one. Gene expression analysis revealed that the expression of StALDH genes is highly tissue-specific and divergent in various abiotic, biotic, and hormonal treatments. Structural modelling and functional analysis of selected StALDH members revealed conservancy in their secondary structures and cofactor binding sites. Taken together, our findings provide comprehensive information on the ALDH gene family in potato that will he...
Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L
PLOS ONE
Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant e... more Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant enzyme superfamily that has great importance on cellular detoxification against abiotic and biotic stresses as well as plant development and growth. The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants—Medicago truncatula. Here, we have identified a total of ninety-two putative MtGST genes that code for 120 proteins. All these members were classified into twelve classes based on their phylogenetic relationship and the presence of structural conserved domain/motif. Among them, 7 MtGST gene pairs were identified to have segmental duplication. Expression profiling of MtGST transcripts revealed their high level of organ/tissue-specific expression in most of the developmental stages and anatomical tissues. The transcripts of MtGSTU5, MtGSTU8, MtGSTU17, MtGSTU46, and MtGSTU47 showed...
An analysis for the abundance and diversity of amylolytic bacteria of two different soil types vi... more An analysis for the abundance and diversity of amylolytic bacteria of two different soil types viz. garbage and garden soil was carried out. pH of the garbage and garden soil samples ranged between 7.73 and 9.84, 6.88 and 7.93, respectively. Average bacterial load on both NA and PYG agar media was found to be higher in garbage than garden soils. Bacterial load of garbage soil samples ranged from 2.08 × 108 to 3.79 ×108 cfu/g and 1.45 × 108 to 2.74 × 108 cfu/g on NA and PYG agar, respectively. On the other hand, bacterial load of the garden soil samples ranged from 3.3×106 to 9.7 ×106 cfu/g on NA and 2.9 × 106 to 9.35 × 106 cfu/g on PYG agar. A total of 200 bacterial isolates (100 from each soil type) were primarily selected for their amylolytic potential. Among them, the percentage of amylolytic bacteria was higher in garbage soil (46) than garden soil (38). Finally, a total of 8 (4 from each soil type) amylolytic potential isolates were selected for detailed study and identificatio...
Evolutionary variation and expression profiling of Isopentenyl transferase gene family in Arabidopsis thaliana L. and Oryza sativa L
Plant Gene
Cytokinin is widely known for its critical involvement in various processes of plant growth and d... more Cytokinin is widely known for its critical involvement in various processes of plant growth and development, such as cell division, differentiation, and nutrient metabolism. As a phytohormone, it also plays a vital role in the stress modulation mechanism of the plant. Isopentenyl transferase (IPT) is the key regulatory enzyme of cyto-kinin biosynthesis. In the present study, all the identified members of Arabidopsis and rice IPT family were analyzed in terms of their chromosomal location, exon-intron distribution, and sub-cellular localization. Based on structural variation and evolutionary conservancy, they could be broadly divided into two families-Adenylate IPT and t-RNA IPT. Further, expression of all AtIPT and OsIPT transcripts were analyzed based on publicly available microarray datasets. All AtIPT genes except AtIPT3 and AtIPT6 showed a high level of expression in all the developmental stages of Arabidopsis. Different members of the AtIPT gene family responded differently depending on the type of stress exposure. A high level of expression was observed in the case of OsIPT2 and OsIPT9 in all the developmental stages and tissues of rice, as compared to the other members. In the case of abiotic stresses, OsIPT5 showed significant up-regulation. Transcript abundance of OsIPT2, OsIPT5, OsIPT7-2 and OsIPT9 fluctuated after biotic stress, hormonal imbalance, chemical toxicity, and nutrient deficiency. These members of the OsIPT gene family might be the crucial stress modulators that were validated through semi-quantitative RT-PCR and their role could be explored further for the generation of abiotic stress tolerant plants.
Cymbidium aloifolium (L.) Sw. is an epiphytic orchid distributed locally in Bangladesh. Natural p... more Cymbidium aloifolium (L.) Sw. is an epiphytic orchid distributed locally in Bangladesh. Natural populations of this orchid are under threat due to its high commercial value in the floriculture industry by over exploitation. Mass propagation provides an alternative means of satisfying the demand. In this study, half strength of MS supplemented with BAP or different combinations with NAA was evaluated for seed germination and early protocorm development of C. aloifolium (L.) Sw. The maximum percentage of seed germination (98) was obtained on modified MS (half strength of micro and macro nutrients and full strength of vitamin) supplemented with 0.5 mg/l BAP and 0.5 mg/l NAA after three weeks of culture. Maximum number of shoots (9.6 shoots per single shoot) were developed from shoot tip explants on half strength of MS supplemented with 1.0 mg/l BAP and 0.5 mg/l NAA. The most effective auxin source promoting root production (3.2 roots per shoot) was 1.0 mg/l IBA in combination with 0.5 ...
Attempt was made to isolate and identify poly-β-hydroxybutyrate (PHB) producing bacteria from dif... more Attempt was made to isolate and identify poly-β-hydroxybutyrate (PHB) producing bacteria from different domestic and industrial waste materials from in and around Dhaka Metropolitan city. The bacterial load of the collected samples ranged in between 5.50 ×103 and 2.52 × 107, 3.10 × 104 and 2.23 × 107, 7.50 × 103 and 1.01 × 107 cfu/g or cfu/ml in NAG (nutrient agar glucose), PYG and LB media, respectively. The maximum bacterial count (2.52 × 107 cfu/g) was observed in NAG medium from soil sample of BDR market and the lowest bacterial load (5.5 × 103 cfu/ml) was observed in NAG medium from the garments wastewater. The highest number (33) of PHB producing bacteria was found in the kitchen waste soil and the lowest number (9) was in water sample of the Turag river. All the Sudan Black B positives isolates were tested for positive PHB production. Primarily, 160 PHB positive bacteria were isolated and finally 30 isolates were selected for identification. Provisionally identified potential...
Glutathione S-transferases (GSTs) compose a family of multifunctional enzymes involved in the num... more Glutathione S-transferases (GSTs) compose a family of multifunctional enzymes involved in the numerous aspects of regulating plant growth, development, and stress response. An in silico genomewide analysis of pepper (Capsicum annuum L.) was performed to identify eighty-five GST genes that were annotated according to their chromosomal location. Segmental duplication contributed more than tandem duplication for the expansion of GST gene family in pepper. All the identified members belong to ten different classes which are highly conserved among Arabidopsis, rice, tomato and potato counterparts indicating the pre-dicot-monocot split diversification of GST classes. Gene structure, protein domain, and motif organization were found to be notably conserved over the distinct phylogenetic groups, which demonstrated the evolutionary significant role of each class. Expression of most of the CaGST transcripts as well as the total pepper GST activity was found to be significantly upregulated in response to cold, heat, drought, salinity and osmotic stress conditions. Presence of various hormone and stress-responsive cis-elements on most of the putative CaGST promoter regions could be directly correlated with the alteration of their transcripts. All these findings might provide opportunities for future functional validation of this important gene family in pepper. Cellular detoxification is an elementary biological process in all living organisms including animals, plants, and microorganisms. It provides protection against different environmental noxious agents as well as reactive oxygen species (ROS) formed from different metabolic pathways, to ensure the optimum cellular condition for the growth and survival 1. After the conversion of toxic components into reactive electrophiles by cytochrome P450s, these reactive molecules are subsequently transformed by the exertion of phase II enzymes, namely Glutathione S-transferase (GST) for the final degradation process 2. GSTs are metabolic isozymes that form a complex family with versatile functions in plants 3. Among its myriad functions, this family mainly works as a detoxification route in plants by conjugating glutathione (γ-Glu-Cys-Gly) to a diverse range of hydrophobic, electrophilic, xenobiotic compounds and redox buffering to form a soluble S-glutathionylated (R-SG) products 4. This gene family possesses a high transcript abundance in most of the tissues and thus, act as a biomarker for the detection and monitoring of organ/tissue damage both in plants and animals 1,5. GST genes are abundantly found in animals, plants and even in some prokaryotes 6. The family consists of cytosolic, mitochondrial and microsomal GSTs. Among them, the mitochondrial and microsomal members
The availability of molecular marker systems allowed estimating the relationships among various t... more The availability of molecular marker systems allowed estimating the relationships among various taxa. This study was aimed at assessing the genetic diversity among ten aromatic rice (Oryza sativa L.) pools from Bangladesh by means of randomly amplified polymorphic DNA (RAPD) markers. These varieties were evaluated for polymorphisms after amplification with 10 decamer primers. A total of 60 RAPD fragments were generated among the assessed varieties with a polymorphism percentage of 80. Cluster analysis by the unweighted pair group method of arithmetic means (UPGMA) showed that these 10 varieties could be placed into two groups with a similarity ranging from 65 to 86% depicting adjacent association between Rajbhog and Kalijira‐12, whereas Maloti belongs to a separate group maintaining maximum distance from rest of the varieties. The analysis revealed that the intervarietal genetic relationship of several varieties is related to their center of origin. As expected, most of the varietie...
Molecular evolution of SUN-domain containing proteins in diverse plant species and their expression profiling in response to developmental and perturbation stimuli
Phytochemistry
Genome-wide identification and expression analysis of glutathione S-transferase gene family in tomato: Gaining an insight to their physiological and stress-specific roles
PloS one, 2017
Glutathione S-transferase (GST) refers to one of the major detoxifying enzymes that plays an impo... more Glutathione S-transferase (GST) refers to one of the major detoxifying enzymes that plays an important role in different abiotic and biotic stress modulation pathways of plant. The present study aimed to a comprehensive genome-wide functional characterization of GST genes and proteins in tomato (Solanum lycopersicum L.). The whole genome sequence analysis revealed the presence of 90 GST genes in tomato, the largest GST gene family reported till date. Eight segmental duplicated gene pairs might contribute significantly to the expansion of SlGST gene family. Based on phylogenetic analysis of tomato, rice, and Arabidopsis GST proteins, GST family members could be further divided into ten classes. Members of each orthologous class showed high conservancy among themselves. Tau and lambda are the major classes of tomato; while tau and phi are the major classes for rice and Arabidopsis. Chromosomal localization revealed highly uneven distribution of SlGST genes in 13 different chromosomes,...
Comprehensive genome-wide analysis of Glutathione S-transferase gene family in potato (Solanum tuberosum L.) and their expression profiling in various anatomical tissues and perturbation conditions
Gene, Jan 10, 2018
Glutathione S-transferases (GSTs) are ubiquitous enzymes which play versatile functions including... more Glutathione S-transferases (GSTs) are ubiquitous enzymes which play versatile functions including cellular detoxification and stress tolerance. In this study, a comprehensive genome-wide identification of GST gene family was carried out in potato (Solanum tuberosum L.). The result demonstrated the presence of at least 90 GST genes in potato which is greater than any other reported species. According to the phylogenetic analyses of Arabidopsis, rice and potato GST members, GSTs could be subdivided into ten different classes and each class is found to be highly conserved. The largest class of potato GST family is tau with 66 members, followed by phi and lambda. The chromosomal localization analysis revealed the highly uneven distribution of StGST genes across the potato genome. Transcript profiling of 55 StGST genes showed the tissue-specific expression for most of the members. Moreover, expression of StGST genes were mainly repressed in response to abiotic stresses, while largely ind...
DNA barcoding, based on the sequencing of a short, standardized region of the cytochrome c oxidas... more DNA barcoding, based on the sequencing of a short, standardized region of the cytochrome c oxidase subunit 1 (COI) gene has the potential to be a practical method for fish species identification in raw or processed fish products. The aim of this study was to identify the level of fraudulence in fish marketing particularly in super shops of Bangladesh. Different species of fish as whole or in fillet were collected from different supermarkets and local markets of Dhaka metropolis for examination. COI gene sequence was amplified using random primers (Fish F1, Fish F2, Fish R1 and Fish R2) and then compared with reference sequences from GenBank and BOLD (Barcode of Life Data Systems). The database was able to provide species matches of >85% sequence similarity for ten samples tested. The overall fraudulence was detected 80% but specifically for whole fish it was 85.71% and fraudulence for fish fillet was 66.67%. These naming discrepancies and ambiguities demonstrate that DNA barcoding can be a reliable tool for the detection of fish products mislabeling in Bangladesh. Therefore, it can be a useful tool for fraudulence control, law enforcement and guiding consumers to get rid of fish product fraudulence.
Fertilizers and herbicides are two vital components of modern agriculture. The imminent danger of... more Fertilizers and herbicides are two vital components of modern agriculture. The imminent danger of phosphate reserve depletion and multiple herbicide tolerance casts doubt on agricultural sustainability in the future. Phosphite, a reduced form of phosphorus, has been proposed as an alternative fertilizer and herbicide that would address the above problems to a considerable extent. To assess the suitability of a phosphite-based fertilization and weed control system for rice, we engineered rice plants with a codon-optimized ptxD gene from Pseudomonas stutzeri. Ectopic expression of this gene led to improved root growth, physiology and overall phenotype in addition to normal yield in transgenic plants in the presence of phosphite. Phosphite functioned as a translocative, non-selective, pre- and post-emergent herbicide. Phosphite use as a dual fertilizer and herbicide may mitigate the overuse of phosphorus fertilizers and reduce eutrophication and the development of herbicide resistance,...
Reactive oxygen species (ROS) arise in the plant system due to inevitable influence of various en... more Reactive oxygen species (ROS) arise in the plant system due to inevitable influence of various environmental stimuli. Glutathione peroxidases are one of the important ROS scavengers inside the cell. A glutathione peroxidase (PgGPx) gene was previously found from Pennisetum glauccum abiotic stressed cDNA library. Enzyme kinetics data revealed that PgGPx possessed preference towards thioredoxin rather than glutathione as electron donor and thus belongs to the functional peroxiredoxin group. Moreover, its activity was found to be dependent on divalent cations, especially Cd 2+ and homology model showed the presence of Cd 2+ binding site in the protein. Site directed mutagenesis study of PgGPx protein revealed the vital role of two conserved Cysteine residues for its enzymatic activity and structural folding. Expression analysis suggested that PgGPx transcript is highly upregulated in response to salinity and drought stresses. When expressed ectopically, PgGPx showed enhanced tolerance against multiple abiotic stresses in prokaryotic E. coli and model plant, rice. Transgenic rice plants showed lesser accumulation of MDA and H 2 O 2 ; and higher accumulation of proline as compared to wild type (WT) plants in response to both salinity and drought stresses that clearly indicates suppression of lipid peroxidation and ROS generation in transgenic lines. Moreover, transgenic plants maintained better photosynthesis efficiency and higher level of antioxidant enzyme activity as compared to WT plants under stress conditions. These results clearly indicate the imperative role of PgGPx in cellular redox homeostasis under stress conditions, leading to the maintenance of membrane integrity and increased tolerance towards oxidative stress.
A comparative study of effects of increasing concentrations of phosphate and phosphite on rice seedlings
Acta Physiologiae Plantarum, 2015
In vitro regeneration and characterization of aromatic rice varieties: Application of biotechnology for the improvement of indigenous aromatic rice varieties of Bangladesh
Aromatic rice varieties are of traditional type. These indigenous rice cultivars are low yielding... more Aromatic rice varieties are of traditional type. These indigenous rice cultivars are low yielding but their higher price and low cost of cultivation generate superior profit margins compared to other rice varieties. Several biotic and abiotic factors are believed to be responsible for the low yield potentials of these varieties of Bangladesh. In addition to the conventional breeding methods, biotechnological techniques can be applied in overcoming such constraints. But limited information is available regarding the improvement of these rice varieties through biotechnology. In vitro techniques as well as molecular characterization these varieties may play significant role in their improvement. This book reports about a genotype independent regeneration protocol for six aromatic rice varieties from Bangladesh as well as the diversity of these varieties by RAPD analysis. Moreover possibility of electroporation has been exploited as a transformation protocol using GFP. This book will be...
The generation of excess reactive oxygen species (ROS) is one of the most common consequences of ... more The generation of excess reactive oxygen species (ROS) is one of the most common consequences of abiotic stress on plants. Glutathione reductase (GR, E.C. 1.6.4.2) and allied enzymes of the ascorbate-glutathione cycle play a crucial role to maintain the homeostatic redox balance in the cellular environment. GR plays an essential role in upholding the reduced glutathione pool under stress conditions. In the present study, a full-length GR cDNA and corresponding genomic clone was isolated from Pennisetum glaucum (L.) R. Br. The PgGR cDNA, encodes a 497-amino acid peptide with an estimated molecular mass of *53.5 kDa. The PgGR peptide exhibits 54-89 % sequence homology with GR from other plants and is cytoplasmic in nature. The PgGR enzyme was purified to near homogeneity, the recombinant protein being relatively thermostable and displaying activity in a broad range of temperature, pH and substrate concentrations. The PgGR transcript level was differentially regulated by heat, cold, salinity and methyl viologen-induced oxidative stress. The heterologously expressed PgGR protein in E. coli showed an improved protection against metal-and methyl viologen-induced oxidative stress. Our overall finding underscores the role of PgGR gene that responds to multiple abiotic stresses and provides stress tolerance in the experimental model (E. coli) which can be potentially used for the improvement of crops under abiotic stress conditions.
Excessive generation of reactive oxygen species (ROS) due to environmental stresses critically ef... more Excessive generation of reactive oxygen species (ROS) due to environmental stresses critically effects plant development and productivity. Plants efficiently detoxify ROS by both non-enzymatic and enzymatic mechanisms. Plant glutathione peroxidases (GPXs) are non-haeme thiol peroxidases that catalyze the reduction of H 2 O 2 (or organic hydroperoxides) to water or the respective alcohols using reduced glutathione or thioredoxin. Genome-wide analysis of the known GPXs from rice and Arabidopsis genomes revealed their gene structure, conserved motifs, localization and tissue-specific and/or organ-specific expression profiles in response to various abiotic stresses. Among the eight genes that encoded GPX proteins from Arabidopsis, AtGPX3 showed two alternate spliced forms that spread over four chromosomes. Five genes encoded for rice GPX proteins, while OsGPX1 showed three spliced variants that were distributed on five chromosomes. Utilizing the publicly available microarray and massively parallel signature sequencing (MPSS) data, the GPXs revealed stress-responsive, tissue-specific and/or organspecific expression profiles. Presence of important cisregulatory elements analyzed in the GPX promoter sequences revealed their overlapping or specific responsiveness to different abiotic stresses. Co-expression data of Arabidopsis GPX genes suggested that various protein kinase family members and stress-responsive proteins co-expressed with the GPX proteins. Transcript profile of rice GPX genes by qRT-PCR validated their functional roles in signal transduction and stress pathways. Results revealed that plant GPXs play a crucial role in response to stress and significantly contribute towards their growth and development.
Monellin a sweet-tasting protein exists naturally as a heterodimer of two non-covalently linked s... more Monellin a sweet-tasting protein exists naturally as a heterodimer of two non-covalently linked subunits chain A and B, which loses its sweetness on denaturation. In this study, we validated the expression of a synthetic monellin gene encoding a single polypeptide chain covalently linking the two subunits under T 7 and fruit-ripening-specific promoters in Escherichia coli and tomato fruits, respectively. Purified recombinant monellin protein retained its sweet flavour at 70°C and pH 2. We developed 15 transgenic T 0 tomato plants overexpressing monellin, which were devoid of any growth penalty or phenotypic abnormalities during greenhouse conditions. T-DNA integration and fruit-specific heterologous expression of monellin had occurred in these transgenic tomato lines. ELISA revealed that expression of monellin was 4.5 % of the total soluble fruit protein. Functional analyses of transgenic tomatoes of T 2-5 and T 2-14 lines revealed distinctly strong sweetness compared with wild type. Monellin a potential non-carbohydrate sweetener, if expressed in high amounts in fruits and vegetables, would enhance their flavour and quality.
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