Sarafat Ali

Fibrosis is a hallmark of progressive kidney diseases. The overexpression of profibrotic cytokine, namely transforming growth factor β (TGF-β) due to excessive inflammation and tissue damage, induces kidney fibrosis. The inhibition of TGF-β signaling is markedly limited in experimental disease models. Targeting TGF-β signaling, therefore, offers a prospective strategy for the management of kidney fibrosis. Presently, the marketed drugs have numerous side effects, but plant-derived compounds are relatively safer and more cost-effective. In this study, TGFβR-1 was targeted to identify the lead compounds among flavonoids using various computational approaches, such as ADME/T (absorption, distribution, metabolism, and excretion/toxicity) analysis, molecular docking, and molecular dynamics simulation. ADME/T screening identified a total of 31 flavonoids with drug-like properties of 31 compounds, a total of 5 compounds showed a higher binding affinity to TGFβR-1, with Epicatechin, Fisetin...

Photosynthesis is the most fundamental and intricate physiological process in all green plants. For the fruitful occurrence of photosynthesis, each plant has certain environmental requirements. They are impacted by the environmental factors and stress during all phases of growth and development. Examples include light availability, water (soil moisture), senescence, carbon strategy and nutrient deficiencies etc. that cause alteration of the net photosynthesis rate of plants. In this study, to determine the effect of different environmental factors on photosynthesis, a number of experiments were conducted where the net photosynthesis, transpirations, water use efficiency and photoinhibition were measured. To study the effect of light intensity, soil moisture, senescence, on net photosynthesis, respectively Ocimum basilicum, Vaccinium vitis-idaea, Cotinus coggygria, were used. To compare carbon strategy, Pisum sativum and Zea mays were grown under similar condition. How variable nutri...

The Clp protease composed of more than 15 proteins, is the central protein degradation machinery in the plastids of a plant cell which plays a similar role as proteasomes in cytoplasm and nucleus. ClpC1 and ClpC2 are two chaperonic proteins for the Clp protease and share more than 90% similarities in the nucleotide and amino acid sequences. In this study, we investigated the functions of ClpC1 and ClpC2 in photosynthesis by co-suppression of both genes (NbClpC1 and NbClpC2, NbClpC1/C2) in Nicotiana benthamiana using virus-induced gene silencing (VIGS) technique. Co-suppression of NbClpC1/C2 in N. benthamiana resulted in aberrant structure with severe chlorotic leaves, stunted growth and reduced numbers of stomata and in lowered photosynthetic capacity. Leaf CO2 assimilation rate, the maximum quantum yield of photosystem II (Fv/Fm), chlorophyll and carotenoid contents were also significantly lower in the leaves of NbClpC1/C2 co-suppressed N. benthamiana than those in the control. Mic...

Phytoene desaturase (PDS) is a rate-limiting enzyme involved in the biosynthesis of carotenoids, which converts phytoene to zeta-carotene in a two-step desaturation reaction. Transiently blocked carotenogenesis by silencing the PDS gene in Nicotiana benthamiana (NbPDS) using the virus-induced gene silencing (VIGS) technique was used. Silencing of NbPDS induced dwarfism and an albino-type leaf trait in N. benthamiana. The NbPDS-silenced leaves accumulated free amino acids in amounts 9.5-folds greater than those of the GFP-silenced control leaves, but contained only 59.6% of total soluble proteins. When treatment with 10 and 100 μM paraquat was carried out to induce oxidative stress, NbPDS-silenced N. benthamiana demonstrated more resistance at both concentrations compared to the control plants. These data strongly suggest that high concentrations of free amino acids occur because they are inadequately incorporated into proteins of the NbPDS-silenced plants, but reduce injury inflicte...

Development of new antibiotic is the prime interest to the researcher now a days as the choice of antibiotic has become limited day by day. Here, we reported the efficacy of methanol extract of Hemigraphis hirta against UTI causing bacteria Escherichia coli and Staphylococcus aureus. Total 10 samples of urine were found positive for UTI. The positive samples were subjected to bacterial identification. Single bacterium as Escherichia coli was found in four samples (isolates as 1a, 3a, 7a and 10a) and Staphylococcus aureus in one (6a). Both the bacteria were found at the same time in three samples (2a and 2b,3a and 3b, 9a and 9b). Ampicillin, Amoxycillin and Cefixime were 100% resistant to all isolates. Total 57.95% isolates showed high level of resistant (Multi drug resistant) against used antibiotics. About 7.95% were found as intermediate resistant and remaining 34.09% were sensitive. All Escherichia coli were sensitive to Ciprofloxacin and all Staphylococcus aureus were sensitive ...

Protein malfunction is typically caused by abiotic stressors. To ensure cell survival during conditions of stress, it is important for plant cells to maintain proteins in their respective functional conformation. Self-compartmentalizing proteases, such as ATP-dependent Clp proteases and proteasomes are designed to act in the crowded cellular environment, and they are responsible for degradation of misfolded or damaged proteins within the cell. During different types of stress conditions, the levels of misfolded or orphaned proteins that are degraded by the 26S proteasome in the cytosol and nucleus and by the Clp proteases in the mitochondria and chloroplasts increase. This allows cells to uphold feedback regulations to cellular-level signals and adjust to altered environmental conditions. In this review, we summarize recent findings on plant proteolytic complexes with respect to their protective functions against abiotic and biotic stressors.

Metabolites in plants are the products of cellular metabolic processes, and their differential amount can be regarded as the final responses of plants to genetic, epigenetic, or environmental stresses. The Clp protease complex, composed of the chaperonic parts and degradation proteases, is the major degradation system for proteins in plastids. ClpC1 and ClpC2 are the two chaperonic proteins for the Clp protease complex and share more than 90% nucleotide and amino acid sequence similarities. In this study, we employed virus-induced gene silencing to simultaneously suppress the expression of ClpC1 and ClpC2 in Nicotiana benthamiana (NbClpC1/C2). The co-suppression of NbClpC1/C2 in N. benthamiana resulted in aberrant development, with severely chlorotic leaves and stunted growth. A comparison of the control and NbClpC1/C2 co-suppressed N. benthamiana metabolomes revealed a total of 152 metabolites identified by capillary electrophoresis time-of-flight mass spectrometry. The co-suppress...

Plants as immovable organisms sense the stressors in their environment and respond to them by means of dedicated stress response pathways. In response to stress, jasmonates (jasmonic acid, its precursors and derivatives), a class of polyunsaturated fatty acid-derived phytohormones, play crucial roles in several biotic and abiotic stresses. As the major immunity hormone, jasmonates participate in numerous signal transduction pathways, including those of gene networks, regulatory proteins, signaling intermediates, and proteins, enzymes, and molecules that act to protect cells from the toxic effects of abiotic stresses. As cellular hubs for integrating informational cues from the environment, jasmonates play significant roles in alleviating salt stress, drought stress, heavy metal toxicity, micronutrient toxicity, freezing stress, ozone stress, CO2 stress, and light stress. Besides these, jasmonates are involved in several developmental and physiological processes throughout the plant ...

Citrus bacterial canker (CBC), caused by the plant pathogenic bacterium Xanthomonas citri subsp. citri (Xcc), is a devastating disease in many commercial citrus cultivars. Every year, CBC causes a substantial reduction in fruit quality and quantity that corresponds to significant economic losses worldwide. Endophytic microorganisms produce numerous bioactive secondary metabolites that can control plant pathogens. We investigated the antagonistic activities of 66 endophytic bacteria isolated from nine citrus cultivars to control streptomycin-resistant Xcc. The suspension of Endophytic Bacteria-39 (EB-39), identified as Bacillus velezensis, exhibited the highest antibacterial activity against three wild-type and six streptomycin-resistant Xcc strains, with the inhibition zones between 39.47 ± 1.6 and 45.31 ± 1.6 mm. The ethyl acetate extract of EB-39 also controlled both wild-type and streptomycin-resistant Xcc strains, with the inhibition zones between 29.28 ± 0.6 and 33.88 ± 1.3 mm....

Co-suppression of chaperonicClpC1andClpC2inNicotiana benthamianasignificantly affect the development and exogenous application of gibberellin partially rescue the developmental defects. Over the past decade, the Clp protease complex has been identified as being implicated in plastid protein quality control in plant cells. CLPC1 and CLPC2 proteins form the chaperone subunits of the Clp protease complex and unfold protein substrates to thread them into the ClpP complex. Here, using the technique of virus-induced gene silencing (VIGS), we suppressed both Nicotiana benthamiana ClpC1 and ClpC2 (NbClpC1/C2) functioning as chaperone subunits in the protease complex. Co-suppression of NbClpC1/C2 caused chlorosis and retarded-growth phenotype with no seed formation and significantly reduced root length. We found that co-suppression of NbClpC1/C2 also affected stomata and trichome formation and vascular bundle differentiation and patterning. Analysis of phytohormones revealed significant alteration and imbalance of major hormones in the leaves of NbClpC1/C2 co-suppressed plant. We also found that application of gibberellin (GA3) partially rescued the developmental defects. Co-suppression of NbClpC1/C2 significantly affected the development of N. benthamiana and exogenous application of GA3 partially rescued the developmental defects. Overall, our findings demonstrate that CLPC1 and CLPC2 proteins have a pivotal role in plant growth and development.

Bacillus velezensis is an aerobic, gram-positive, endospore-forming bacterium that promotes plant growth. Numerous strains of this species have been reported to suppress the growth of microbial pathogens, including bacteria, fungi, and nematodes. Based on recent phylogenetic analysis, several Bacillus species have been reclassified as B. velezensis. However, this information has yet to be integrated into a well-organized resource. Genomic analysis has revealed that B. velezensis possesses strain-specific clusters of genes related to the biosynthesis of secondary metabolites, which play significant roles in both pathogen suppression and plant growth promotion. More specifically, B. velezensis exhibits a high genetic capacity for synthesizing cyclic lipopeptides (i.e., surfactin, bacillomycin-D, fengycin, and bacillibactin) and polyketides (i.e., macrolactin, bacillaene, and difficidin). Secondary metabolites produced by B. velezensis can also trigger induced systemic resistance in pl...

The Clp protease complex, which is the central protein degradation machinery in plastids, plays a role similar to proteasome. ClpC1 and ClpC2 comprise the chaperonic part of the Clp protease and share more than 90% nucleotide sequence similarity with each other. In a previous study, the co-suppression of Nicotiana benthamiana ClpC1 and ClpC2 (NbClpC1/C2) resulted in leaf chlorosis, growth retardation phenotype, disappearance of apical dominance and coarsely packed mesophyll cells. Quantitative real-time PCR analysis revealed that the co-suppression of NbClpC1/C2 upregulated the expression levels of defense-related genes including pathogenesis-related protein 1b (PR1b), glutathione-S-transferase, catalase, ascorbate peroxidase and systemic acquired resistance gene 8.2 (SAR8.2). NbClpC1/C2 co-suppressed leaves accelerated hypersensitive response by the infection with an incompatible pathogen, Pseudomonas syringae pv. tomato T1, but increased susceptibility via the infiltration of a compatible pathogen, P. syringae pv. tabaci. These findings indicate that disruption of the chaperones of ClpC1 and ClpC2 increases the growth of bacterial pathogens and therefore increases hypersensitive response and disease susceptibility.

Paclitaxel (taxol) has long been used as a potent anticancer agent for the treatment of many cancers. Ever since the fungal species Taxomyces andreanae was first shown to produce taxol in 1993, many endophytic fungal species have been recognized as taxol accumulators. In this study, we analyzed the taxol-producing capacity of different Colletotrichum spp. to determine the distribution of a taxol biosynthetic gene within this genus. Distribution of the taxadiene synthase (TS) gene, which cyclizes geranylgeranyl diphosphate to produce taxadiene, was analyzed in 12 Colletotrichum spp., of which 8 were found to contain the unique skeletal core structure of paclitaxel. However, distribution of the gene was not limited to closely related species. The production of taxol by Colletotrichum dematium, which causes pepper anthracnose, depended on the method in which the fungus was stored, with the highest production being in samples stored under mineral oil. Based on its distribution among Col...

Herein, Fe3O4 nanoparticles synthesized using aqueous extract of corn ear leaves were investigated for proteasome inhibitory activity, antioxidant activity, synergistic antibacterial, and anticandidal potential. The UV-Vis spectrum displayed an absorption band at 355 nm that indicated the formation of nano-sized Fe3O4 particles. Vibrating sample magnetometer analysis revealed its superparamagnetic nature. Fe3O4 nanoparticles exhibited strong proteasome inhibitory potential and antioxidant activity and exerted strong synergistic antibacterial and anticandidal activity. Its significant proteasome inhibitory potential could be useful in cancer treatment and drug delivery. Furthermore, strong antioxidant, antibacterial, and anticandidal activity make them a promising candidate for biomedical and pharmaceutical applications.

Genetic transformation system of Gladiolus cv.'Advanced Red' was established based on the regeneration system of embryogenic callus.Several factors were studied such as concentration of the infection,infection time,acetosyringone(AS) concentration,negative pressure and screening methods for genetic transformation of Gladiolus mediated by agrobac-terium tumefaciens(GV3101).The results showed that the highest rate of genetic transformation was obtained under the conditions of non pre-incubation,negative pressure treatment,agrobacterium concentration OD600 = 0.6-0.8,infection time 15-20 min,adding 100 μmol/LAS and 3 ds incuabtion.Following incubation for 3-4 months,the analysis of the resistant plants with PCR and southern blot indicated that the gus had been integrated into the genome of Gladiolus.

Endophytic bacteria (EB) are both a novel source of bioactive compounds that confer phytopathogen resistance and inducers of secondary metabolites in host plants. Twenty-seven EB isolated from various parts of Metasequoia glyptostroboides, Ginkgo biloba, Taxus brevifolia, Pinus densiflora, Salix babylonica, and S. chaenomeloides could produce salicylic acid (SA). The highest producers were isolates EB-44 and EB-47, identified as Pseudomonas tremae and Curtobacterium herbarum, respectively. Nicotiana benthamiana grown from EB-44-soaked seeds exhibited a 2.3-fold higher endogenous SA concentration and increased resistance against P. syringae pv. tabaci, the causative agent of tobacco wildfire disease, than plants grown from water-soaked seeds. N benthamiana and N. tabacum grown from EB-44-treated seeds developed 33% and 54% disease lesions, respectively, when infected with P. syringae pv. tabaci, and showed increased height and weight, in addition to 4.6 and 1.4-fold increases in nico...

We report the significant increase of the content of free amino acids in Nicotiana benthamiana by the co-suppression of the ClpC1 and ClpC2 genes, which are translated to be the chaperonic part in the Clp protease at plastids. Clp protease with ClpC1 and ClpC2 proteins as the chaperonic part degrades denatured or improperly folded protein in plastids. Nicotiana benthamiana ClpC1 and ClpC2 genes (NbClpC1 and NbClpC2: NbClpC1/C2) share 93 % similarities; therefore, co-suppression of the NbClpC1/C2 was possible using a single virus-induced silencing vector. Co-suppression of NbClpC1/C2 resulted in a pleiotropic phenotype including disappearance of apical dominance and formation of chlorotic leaves. NbClpC1/C2 co-suppressed leaves accumulated 11.9-fold more free amino acids than the GFP-silenced leaves. The co-suppression of NbClpC1/C2 did not change the expression levels of some selected genes in the biosynthetic pathways for the free amino acids, but reduced the total protein amounts ...

We report the significant increase of the content of free amino acids in Nicotiana benthamiana by the co-suppression of the ClpC1 and ClpC2 genes, which are translated to be the chaperonic part in the Clp protease at plastids. Clp protease with ClpC1 and ClpC2 proteins as the chaperonic part degrades denatured or improperly folded protein in plastids. Nicotiana benthamiana ClpC1 and ClpC2 genes (NbClpC1 and NbClpC2: NbClpC1/C2) share 93 % similarities; therefore, co-suppression of the NbClpC1/C2 was possible using a single virus-induced silencing vector. Co-suppression of NbClpC1/C2 resulted in a pleiotropic phenotype including disappearance of apical dominance and formation of chlorotic leaves. NbClpC1/C2 co-suppressed leaves accumulated 11.9-fold more free amino acids than the GFP-silenced leaves. The co-suppression of NbClpC1/C2 did not change the expression levels of some selected genes in the biosynthetic pathways for the free amino acids, but reduced the total protein amounts to 32.5 %, indicating that co-suppression affected the incorporation of free amino acids in proteins during translation. The loosely packed mesophyll cells and abnormal vascular bundles in the leaves suggested structural problems associated with translocation of free amino acids to sink tissues. NbClpC1/C2 co-suppression can offer a novel strategy for accumulation of free amino acids though it results in stunted growth.