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1.
PLoS One ; 18(5): e0273592, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37163561

RESUMO

Apyrase (APY) is a nucleoside triphosphate (NTP) diphosphohydrolase (NTPDase) which is a member of the superfamily of guanosine diphosphatase 1 (GDA1)-cluster of differentiation 39 (CD39) nucleoside phosphatase. Under various circumstances like stress, cell growth, the extracellular adenosine triphosphate (eATP) level increases, causing a detrimental influence on cells such as cell growth retardation, ROS production, NO burst, and apoptosis. Apyrase hydrolyses eATP accumulated in the extracellular membrane during stress, wounds, into adenosine diphosphate (ADP) and adenosine monophosphate (AMP) and regulates the stress-responsive pathway in plants. This study was designed for the identification, characterization, and for analysis of APY gene expression in Oryza sativa. This investigation discovered nine APYs in rice, including both endo- and ecto-apyrase. According to duplication event analysis, in the evolution of OsAPYs, a significant role is performed by segmental duplication. Their role in stress control, hormonal responsiveness, and the development of cells is supported by the corresponding cis-elements present in their promoter regions. According to expression profiling by RNA-seq data, the genes were expressed in various tissues. Upon exposure to a variety of biotic as well as abiotic stimuli, including anoxia, drought, submergence, alkali, heat, dehydration, salt, and cold, they showed a differential expression pattern. The expression analysis from the RT-qPCR data also showed expression under various abiotic stress conditions, comprising cold, salinity, cadmium, drought, submergence, and especially heat stress. This finding will pave the way for future in-vivo analysis, unveil the molecular mechanisms of APY genes in stress response, and contribute to the development of stress-tolerant rice varieties.


Assuntos
Oryza , Oryza/metabolismo , Apirase/genética , Apirase/metabolismo , Nucleosídeos , Monofosfato de Adenosina , Trifosfato de Adenosina/metabolismo , Estresse Fisiológico/genética , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Perfilação da Expressão Gênica
2.
Biotechnol Rep (Amst) ; 35: e00740, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-35646621

RESUMO

It is essential to develop high salt-tolerant rice varieties in order to cultivate the salt-affected lands. In this study, Na+/H+ exchanger 1 (NHX1) gene isolated from Vigna radiata L. Wilczek was transferred in Bangladesh Rice Research Institute (BRRI) developed two indica rice genotypes BRRI Dhan28 and BRRI Dhan29 using in-planta approach for improvement of salinity tolerance. Embryonic axes of matured dehusked rice seeds were injured and co-cultivated with Agrobacterium strain harboring VrNHX1 gene and finally regenerated. GUS histochemical assay and PCR amplification of GUS-a and VrNHX1 were performed to confirm the transformation. Expression confirmation was done by semi-quantitative RT-PCR. Under salinity stress, transgenic lines showed higher chlorophyll, relative water content and decreased electrolyte leakage, proline content, lipid peroxidation level, and catalase enzyme activity which represent the better physiology than control plants. Moreover, under salinity stress (150 mM), transgenic lines exhibited superior growth and salt tolerant than non-transgenic plants.

3.
PLoS One ; 16(11): e0259691, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34735543

RESUMO

Cycline-dependent kinase 4 (CDK4), an enzyme of the cycline dependent or Ser/Thr protein kinase family, plays a role in cell cycle progression (G1 phase) by phosphorylating a tumor suppressor protein called pRB. Alteration of this enzyme due to missense mutation/ nonsynonymous single nucleotide polymorphisms (nsSNPs) are responsible for various types of cancer progression, e.g. melanoma, lung cancer, and breast cancer. Hence, this study is designed to identify the malignant missense mutation of CDK4 from the single nucleotide polymorphism database (dbSNP) by incorporating computational algorithms. Out of 239 nsSNPs; G15S, D140Y and D140H were predicted to be highly malignant variants which may have a devastating impact on protein structure or function. We also found defective binding motif of these three mutants with the CDK4 inhibitor ribociclib and ATP. However, by incorporating molecular dynamic simulation, our study concludes that the superiority of G15S than the other two mutants (D140Y and D140H) in destabilizing proteins nature.


Assuntos
Biologia Computacional/métodos , Quinases Ciclina-Dependentes/metabolismo , Polimorfismo de Nucleotídeo Único/genética , Trifosfato de Adenosina/farmacologia , Aminopiridinas/farmacologia , Quinases Ciclina-Dependentes/antagonistas & inibidores , Quinases Ciclina-Dependentes/genética , Simulação de Dinâmica Molecular , Mutação/genética , Purinas/farmacologia
4.
J Genet Eng Biotechnol ; 19(1): 167, 2021 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-34704216

RESUMO

BACKGROUND: Nitrogen and potassium are crucial supplements for plant development and growth. Plants can detect potassium and nitrate ions in soils and in like way, they modify root-to-shoot transport of these ions to adjust the conveyance among roots and shoots. Transcription factor MYB59 plays essential roles in numerous physiological processes inclusive of hormone response, abiotic stress tolerance, plant development, and metabolic regulation. In this study, we retrieved 56 MYB59 proteins from different plant species. Multiple sequence alignment, phylogenetic tree, conserved motif, chromosomal localization, and cis-regulatory elements of the retrieved sequences were analyzed. Gene structure, protein 3D structure, and DNA binding of OsMYB59 indica were also predicted. Finally, we characterized OsMYB59 and its function under low K+/NO3- conditions in Oryza sativa subsp. indica. RESULTS: Data analysis showed that MYB59s from various groups separated in terms of conserved functional domains and gene structure, where members of genus Oryza clustered together. Plants showed reduced height and yellowish appearance when grown on K+ and NO3- deficient medium. Quantitative real-time PCR uncovered that the OsMYB59 reacted to abiotic stresses where its expression was increased in BRRI dhan56 but decreased in other varieties on K+ deficient medium. In addition, OsMYB59 transcript level increased on NO3- deficient medium. CONCLUSIONS: Our results can help to explain the biological functions of indica rice MYB59 protein and gave a theoretical premise to additionally describe its biological roles in response to abiotic stresses particularly drought.

5.
Heliyon ; 7(3): e06396, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33732931

RESUMO

Being a Positive sense RNA virus the recent reemergence of Chikungunya and Mayaro virus has taken the concern of the leading scientific communities of the world. Though the outbreak of Mayaro virus is limited to Neotropical region only, Chikungunya is already identified in over 60 countries around the world. Besides, the lack of a strong protective treatment, misdiagnosis issue and co-circulation of both the viruses calls for a new strategy which could potentially prevent these infections from spreading. In this study, we therefore, identified the peptide based vaccine candidates e.g. epitopes for B cell and T cell from Chikungunya virus which also showed to be homologous to the Mayaro virus through immuno-informatics and computational approaches. Final epitopes identified from the most antigenic structural polyprotein of both the viruses were 5 for CD8+ T cell Epitopes (209KPGDSGRPI217, 219TGTMGHFIL227, 239ALSVVTWNK247, 98KPGRRERMC106 and 100GRRERMCMK108), 2 epitopes for CD4+ T cell (105MCMKIENDCIFEVKH119 and 502DRTLLSQQSGNVKIT516) and a single epitope for B cell (504GGRFTIPTGAGKPGDSGRPI518). Analysis of our predicted epitopes for population coverage showed prominent population coverage (92.43%) around the world. Finally, molecular docking simulation of the foreseen T cell epitopes with respondent HLA alleles secured good HLA-epitope interaction. This study was directed towards the discovery of potential antigenic epitopes which can open up a new skyline to design novel vaccines for combating both of the diseases at the same time.

6.
In Silico Pharmacol ; 5(1): 1, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28401513

RESUMO

Protein-protein interaction (PPI) and host-pathogen interactions (HPI) proteomic analysis has been successfully practiced for potential drug target identification in pathogenic infections. In this research, we attempted to identify new drug target based on PPI and HPI computation approaches and subsequently design new drug against devastating enterohemorrhagic Escherichia coli O104:H4 C277-11 (Broad), which causes life-threatening food borne disease outbreak in Germany and other countries in Europe in 2011. Our systematic in silico analysis on PPI and HPI of E. coli O104:H4 was able to identify bacterial D-galactose-binding periplasmic and UDP-N-acetylglucosamine 1-carboxyvinyltransferase as attractive candidates for new drug targets. Furthermore, computational three-dimensional structure modeling and subsequent molecular docking finally proposed [3-(5-Amino-7-Hydroxy-[1,2,3]Triazolo[4,5-D]Pyrimidin-2-Yl)-N-(3,5-Dichlorobenzyl)-Benzamide)] and (6-amino-2-[(1-naphthylmethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one) as promising candidate drugs for further evaluation and development for E. coli O104:H4 mediated diseases. Identification of new drug target would be of great utility for humanity as the demand for designing new drugs to fight infections is increasing due to the developing resistance and side effects of current treatments. This research provided the basis for computer aided drug design which might be useful for new drug target identification and subsequent drug design for other infectious organisms.

7.
Adv Appl Bioinform Chem ; 8: 49-63, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26677339

RESUMO

Bacterial enteric infections resulting in diarrhea, dysentery, or enteric fever constitute a huge public health problem, with more than a billion episodes of disease annually in developing and developed countries. In this study, the deadly agent of hemorrhagic diarrhea and hemolytic uremic syndrome, Escherichia coli O157:H7 was investigated with extensive computational approaches aimed at identifying novel and broad-spectrum antibiotic targets. A systematic in silico workflow consisting of comparative genomics, metabolic pathways analysis, and additional drug prioritizing parameters was used to identify novel drug targets that were essential for the pathogen's survival but absent in its human host. Comparative genomic analysis of Kyoto Encyclopedia of Genes and Genomes annotated metabolic pathways identified 350 putative target proteins in E. coli O157:H7 which showed no similarity to human proteins. Further bio-informatic approaches including prediction of subcellular localization, calculation of molecular weight, and web-based investigation of 3D structural characteristics greatly aided in filtering the potential drug targets from 350 to 120. Ultimately, 44 non-homologous essential proteins of E. coli O157:H7 were prioritized and proved to have the eligibility to become novel broad-spectrum antibiotic targets and DNA polymerase III alpha (dnaE) was the top-ranked among these targets. Moreover, druggability of each of the identified drug targets was evaluated by the DrugBank database. In addition, 3D structure of the dnaE was modeled and explored further for in silico docking with ligands having potential druggability. Finally, we confirmed that the compounds N-coeleneterazine and N-(1,4-dihydro-5H-tetrazol-5-ylidene)-9-oxo-9H-xanthene-2-sulfon-amide were the most suitable ligands of dnaE and hence proposed as the potential inhibitors of this target protein. The results of this study could facilitate the discovery and release of new and effective drugs against E. coli O157:H7 and other deadly human bacterial pathogens.

8.
Saudi J Biol Sci ; 21(1): 3-12, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24596494

RESUMO

MicroRNAs (miRNAs) are the group of ∼22 nucleotides long noncoding small endogenous and evolutionary conserved post-transcriptional regulatory RNAs, which show an enormous role in various biological and metabolic processes in both animals and plants. To date not a single miRNA has been identified in coffee (Coffea arabica), which is an economically important plant of Rubiaceae family. In this study a well-developed, powerful and comparative computational approach, EST-based homology search is applied to find potential miRNA of coffee. We blasted publicly available EST sequences obtained from NCBI GenBank against previously known plant miRNAs. For the first time, one potential miRNA from a large miRNA family with appropriate fold back structures was identified through a series of filtration criteria. A total of six potential target genes in Arabidopsis were identified based on their sequence complementarities. The target genes mainly encode transport inhibitor like protein, transcription factor, DNA-binding protein, and GRR1-like protein, and these genes play an important role in various biological processes like response to chitin, cold, salt stress, water deprivation etc. Overall, findings from this study will accelerate the way for further researches of miRNAs and their functions in coffee.

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