Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Corrigendum to “Unveiling promising phytocompounds from Moringa oleifera as dual inhibitors of EGFR(T790M/C797S) and VEGFR-2 in non-small cell lung cancer through in silico screening, ADMET, dynamics simulation, and DFT analysis” [J. Genet. Eng. Biotechnol. 22(3) (2024) 100406]","authors":"Md. Masudur Rahman Munna , Md. Touki Tahamid Tusar , Saima Sajnin Shanta , Md. Hossain Ahmed , Md. Sarafat Ali","doi":"10.1016/j.jgeb.2025.100499","DOIUrl":"10.1016/j.jgeb.2025.100499","url":null,"abstract":"","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100499"},"PeriodicalIF":3.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multidrug resistance and virulence profile of the commensal Proteus mirabilis isolated from a native Iraqi frozen chicken carcass","authors":"Zaid A. Thabit ,&nbsp;Zahraa A. AlShaheeb ,&nbsp;May Ridha Jaafar ,&nbsp;Safaa A.S. Al-Qaysi ,&nbsp;Sana M.H. Al-Shimmary","doi":"10.1016/j.jgeb.2025.100490","DOIUrl":"10.1016/j.jgeb.2025.100490","url":null,"abstract":"<div><div>This study aimed to determine the prevalence of <em>Proteus mirabilis</em> in frozen chicken carcass from local slaughterhouse. It assesses the activities of nine antimicrobial agents and the presence of antimicrobial resistance genes and virulence genes. Thirty samples were collected from five local Iraqi companies. and then the antibiotic-resistance genes and virulence factor-related genes were detected via polymerase chain reaction (PCR). The results revealed that Nine <em>P. mirabilis</em> isolates were recovered, and the majority of the isolates were resistant to both nalidixic acid and azithromycin at a ratio of (100 %), followed by trimethoprim-sulfamethoxazole (<em>sul1</em>) (88.8 %), whereas the isolates were susceptible to imipenem and meropenem, and both ceftazidime and cefotaxime were efficient at a ratio of (88.8 %). All the isolates (100 %) were resistant to at least three classes of antibiotics and were classified as multidrug resistant. The PCR results indicated that the most common resistance genes were DNA Gyrase Subunit A Gene (<em>gyrA</em>) (100 %), Dihydropteroate Synthase Gene (<em>sul1</em>) (88.8 %), and Florenicol Resistance Gene (<em>floR</em>) (88.8 %), followed by Aminoglycoside N-Acetyltransferase Gene (<em>acc (6′)-lb</em>) (44.4 %) and Macrolide Phosphotransferase Gene (<em>mphA</em>) (33.3 %). In addition, the virulence genes Zinc Metalloprotease A Gene (<em>zapA</em>), Uridine Monophosphate Synthase Gene (<em>uraC</em>), Histone-Modifying Protein A Gene (<em>hpmA</em>), Flagellin A Gene (<em>flaA</em>), Anti-Sigma Factor <em>RsbA</em> Gene (<em>rsbA</em>), and Multidrug Resistance Protein A Gene (<em>mrpA</em>) were found in the same proportion (100 %) of all <em>P. mirabilis</em> isolates. Our study emphasized that <em>Proteus mirabilis</em> has a high frequency of antibiotic resistance as a multidrug resistance pattern and furthermore demonstrated a high level of virulence factor gene detection, which might be a threat to food safety and human health. The phylogenetic tree analysis of the <em>P. mirabilis</em> isolates from chicken meat revealed high similarity to the database strain.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100490"},"PeriodicalIF":3.5,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity and population structure analysis in Asparagus officinalis","authors":"Gurleen Sidhu ,&nbsp;Travis Banks ,&nbsp;David Wolyn","doi":"10.1016/j.jgeb.2025.100491","DOIUrl":"10.1016/j.jgeb.2025.100491","url":null,"abstract":"<div><div>Asparagus cultivars grown worldwide are thought to have originated from a limited genetic base, however, selection has resulted in variation for climatic adaptation and other traits. Understanding genetic diversity of the crop is important to guide breeding decisions. The objectives of this research were to identify SNPs among 64 cultivated lines from different geographic areas and assess genetic variation, population structure and linkage disequilibrium. More than 55,000 SNPs were identified by GBS and subjected to filtration for minor allele frequency and missing data, resulting in 12,886 markers for all subsequent analysis. Markers exhibited a wide range of Expected Heterozygosity (He), Polymorphic Information Content (PIC) and Observed Heterozygosity (Ho) with mean values of 0.370, 0.310, and 0.450 respectively. Population STRUCTURE analysis indicated that the 64 lines were grouped into two, four, seven, and nine subpopulations. For K = 4, four distinct groups were defined: (1) New Zealand, New Jersey, France, and California; (2) Canada; (3) China, The Netherlands, and Germany; and (4) England, Denmark, Spain, Turkey, and India. The results were further confirmed by PCA, and a phylogenetic tree. LD declined rapidly with an increase in physical distance. A considerable amount of genetic diversity was observed, despite previous suggestions that asparagus cultivars may have originated from one open-pollinated population.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100491"},"PeriodicalIF":3.5,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Virtual screening and identification of potent phytoconstituents from Acorus calamus L. as inhibitors of Monkeypox virus infection","authors":"Shivani Lakhani ,&nbsp;Janki V. Rojmala ,&nbsp;Nisarginee M. Chotai ,&nbsp;Bhargav N. Waghela ,&nbsp;Parth Thakor","doi":"10.1016/j.jgeb.2025.100487","DOIUrl":"10.1016/j.jgeb.2025.100487","url":null,"abstract":"<div><h3>Background</h3><div>The threat posed by the Monkeypox (Mpox) disease has re-emerged globally while the world strives to recover from the Corona Virus Disease −19 (COVID-19) pandemic. The World Health Organization has declared Mpox a global health emergency. Monkeypox virus (MPXV), the causative agent of Mpox disease, is a zoonotic, large, enveloped, double-stranded deoxyribonucleic acid (DNA) virus that belongs to the <em>Orthopoxviridae</em> genus. The Food and Drug Administration (FDA), USA has approved repurposed antiviral agents Cidofovir and Tecovirimat as the primary treatment options for Mpox, however, they project systemic toxicity and have underwhelming clinical data. A <!--> <!-->plethora of medicinal plant compounds including flavonoids, phenolics, terpenoids, and alkaloids have a<!--> <!-->wide range of biological activities such as antimicrobial, antioxidant, antiulcer, antineoplastic, anti-inflammatory, and immuno-stimulating potentials. Since many of them are being studied in modern research to discover an active drug candidate, we turned to medicinal plants to explore potent antiviral compounds.</div></div><div><h3>Methods</h3><div>In the present study, we aimed to screen phytoconstituents of<em> <!-->Acorus calamus<!--> </em>L. (AC) against four essential virulence enabling proteins D8L, A48R, D13L, and A42R of MPXV by<em> <!-->in silico</em> <!-->approach. Further, we have elucidated pharmaceutical-relevant parameters of hit compounds through their absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties as well as drug-likeness parameters.</div></div><div><h3>Results</h3><div>Our results revealed that AC phytoconstituents such as β-Sitosterol against A42R and D8L, Lucenin-2 against D13L and Zingiberene against A48R showed the strongest binding affinities, respectively. Moreover, Galangin could prominently interact with all four proteins with lower binding energy and higher affinity. All top phytoconstituents obeyed Lipinski’s RO5 and drug-likeness properties.</div></div><div><h3>Conclusions</h3><div>The phytoconstituents of AC can act as potent inhibitors of essential virulence enabling proteins of MPXV. Thus, we recommend further experimental investigations to validate the promising results of the<!--> <!-->present <em>in silico</em> study.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100487"},"PeriodicalIF":3.5,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143869767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencing","authors":"Malyaj R. Prajapati ,&nbsp;Nitika Gupta ,&nbsp;Mailem Yazing Shimray ,&nbsp;Jayesh Gehlot ,&nbsp;Abhinav Tiwari ,&nbsp;Pooja Thapa ,&nbsp;Damini Diksha ,&nbsp;Somnath Kadappa Holkar ,&nbsp;Pallavi Jagannath Mahajan ,&nbsp;Sujoy Saha ,&nbsp;Virendra Kumar Baranwal ,&nbsp;Susheel Kumar Sharma","doi":"10.1016/j.jgeb.2025.100494","DOIUrl":"10.1016/j.jgeb.2025.100494","url":null,"abstract":"<div><h3>Background</h3><div>Transcriptome data obtained from plant samples often contain significant numbers of reads originating from viral genomes, which are typically co-isolated during the RNA extraction process. This occurs through the simultaneous presence of viral RNA alongside host plant RNA, leading to the inclusion of viral sequences in the transcriptomic data.</div></div><div><h3>Methods and results</h3><div>Here, we identify a novel member of the genus <em>Ampelovirus</em>, grapevine leafroll-associated virus S (GLRaV-S) by employing the high-throughput sequencing (HTS) of RNA of grape leaves showing leafroll symptoms using a bioinformatic pipeline for plant virus detection. The genomic RNA of GLRaV-S, measured 13,102 nucleotides (nts) and encompasses five open reading frames (ORF). Homology analysis of GLRaV-S genome showed sequence identity of 23.0 – 53.3 % with the sequences of known ampeloviruses. Phylogenetic analysis based on genome sequences showed that GLRaV-S clustered in a same clade of ampeloviruses. However, the RdRp and HSP70h of GLRaV-S clustered with subgroup II while the CP sequences clustered with subgroup I of ampeloviruses.</div></div><div><h3>Conclusions</h3><div>Based on the species demarcation criteria, GLRaV-S represents a newly discovered species within the genus <em>Ampelovirus</em> of the <em>Closteroviridae</em> family. This study on identification of novel virus will be useful in developing a robust certification program for the production of healthy plants of grapevine.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100494"},"PeriodicalIF":3.5,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of the gold nanoparticles biosynthesized using Casuarina equisetifolia bark extract against the ethion induced Hepato- and neurotoxicity in rats","authors":"Wael Mahmoud Aboulthana ,&nbsp;Noha El-Sayed Ibrahim ,&nbsp;Amal Gouda Hussien ,&nbsp;Amgad Kamal Hassan ,&nbsp;Wagdy K.B. Khalil ,&nbsp;Hassan Abdel-Gawad ,&nbsp;Hamdy Ahmed Taha ,&nbsp;Ayda K. Kelany ,&nbsp;Kawkab A. Ahmed","doi":"10.1016/j.jgeb.2025.100495","DOIUrl":"10.1016/j.jgeb.2025.100495","url":null,"abstract":"<div><div>Ethion (Etn) is classified as an organophosphate pesticide (OP) that causes toxicity even at low concentrations and targets the liver, brain, kidney, and blood. Gold nanoparticles (Au-NPs) were biosynthesized from the whole methanolic extract of <em>Casuarina equisetifolia</em> bark, and their efficacy against Etn-induced hepato- and neurotoxicity in rats was assessed. In addition to determining conventional biochemical measurements, the target tissues (liver and brain) were examined for oxidative stress, inflammatory, and fibrotic markers. The protein and isoenzyme patterns were also assayed using an electrophoretic technique. Additionally, apoptotic gene expression was measured. The target tissues were also subjected to histopathological analysis. In all groups treated with <em>C. equisetifolia</em> bark gold nano-extract, it was observed that the levels of the hematological measurements that were impacted by the oral injection of Etn had recovered to normal. Regarding the biochemical measurements, the group that received nano-extract pretreatment showed greater improvement than the therapeutic group. The levels of inflammatory indicators significantly decreased (<em>p</em> ≤ 0.05), while the antioxidant system markers increased in both liver and brain tissues in the group that received the nano-extract beforehand. In both target tissues, especially in the pre-treated group, the nano-extract reduced the severity of the Etn-caused lesions. During electrophoretic assays, the nano-extract in the pre-treated group prevented the qualitative alterations indicated by the lowest similarity index (SI%) values of the Etn-injected group compared to the normal group. The molecular assay showed that the nano-extract reduced the expression of apoptotic genes that were markedly elevated in the Etn-injected rats, but it was unable to return their values to normalcy. The study concluded that in the group that received nano-extract pretreatment, the biochemical, histopathological, physiological, and molecular abnormalities caused by Etn were reduced by the <em>C. equisetifolia</em> bark gold nano-extract.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100495"},"PeriodicalIF":3.5,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143869772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of key biomarker genes in liver hepatocellular carcinoma and kidney renal clear cell carcinoma progression: A shared high-throughput screening and molecular docking method with potentials for targeted therapeutic interventions","authors":"Maisha Tasneem ,&nbsp;Shipan Das Gupta ,&nbsp;Md Jubair Ahmed Jony ,&nbsp;Maya Minkara ,&nbsp;Rajib Kumar Dey ,&nbsp;Jannatul Ferdoush","doi":"10.1016/j.jgeb.2025.100497","DOIUrl":"10.1016/j.jgeb.2025.100497","url":null,"abstract":"<div><h3>Background and objectives</h3><div>Liver Hepatocellular Carcinoma (LIHC) and Kidney Renal Clear Cell Carcinoma (KIRC) are leading causes of cancer death worldwide, but their early detections remain hindered by a lack of genetic markers. Our study aims to find prospective biomarkers that could serve as prognostic indicators for efficient drug candidates for KIRC and LIHC treatment.</div></div><div><h3>Methods</h3><div>To detect differentially expressed genes (DEGs), four datasets were used: GSE66271 and GSE213324 for KIRC, and GSE135631 and GSE202853 for LIHC. Visualization of DEGs was done using heatmaps, volcano plots, and Venn diagrams. Hub genes were identified via PPI analysis and the cytoHubba plugin in Cytoscape. Their expression was evaluated using box plots, stage plots, and survival plots for prognostic assessment via GEPIA2. Molecular docking with PyRx’s AutoDock Vina identified optimal binding interactions between compounds and proteins. Pharmacokinetic and toxicity analyses reinforced the drug-likeness and safety of these compounds.</div></div><div><h3>Results</h3><div>In this study, 47 DEGs were identified, with the top 10 hub genes being <em>TOP2A</em>, <em>BUB1</em>, <em>PTTG1</em>, <em>CCNB2</em>, <em>NUSAP1</em>, <em>KIF20A</em>, <em>BIRC5</em>, <em>RRM2, NDC80</em> and <em>CDC45</em>, chosen for their high MCC scores. Data mining revealed a correlation between TOP2A expression and clinical survival outcomes in KIRC and LIHC patients. Docking studies of the TOP2A structure identified a promising compound from <em>Andrographis paniculata</em> with high binding energy and interactions with TOP2A. Pharmacokinetic and toxicity assessments support its potential as a drug candidate.</div></div><div><h3>Conclusion</h3><div>Our study emphasizes <em>TOP2A</em>’s prognostic significance in KIRC and LIHC and recognizes <em>Andrographis paniculata</em> compound as potential therapeutics, offering prospective for enhanced treatment and patient outcomes in these cancers.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100497"},"PeriodicalIF":3.5,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cardioprotective function of mixed spices against myocardial infarction injury: In-vivo and in-silico study","authors":"Md. Abdullah-Al-Mamun ,&nbsp;Dipa Islam ,&nbsp;Dipankar Chandra Roy ,&nbsp;Ayesha Ashraf ,&nbsp;Saifullah ,&nbsp;Chadni Lyzu ,&nbsp;Md. Enamul Kabir Talukder ,&nbsp;Samina Akhter ,&nbsp;Evana Parvin Lipy ,&nbsp;Liton Chandra Mohanta","doi":"10.1016/j.jgeb.2025.100492","DOIUrl":"10.1016/j.jgeb.2025.100492","url":null,"abstract":"<div><div>Myocardial infarction is the permanent necrosis of heart tissue caused by an artery obstruction. It causes an inadequate delivery of oxygen and nutrients, resulting in muscle injury in the afflicted areas. Here, water extract of mixed spices—onion, garlic, ginger, red chili, turmeric, cumin seed, coriander, cardamom, black pepper, cloves, fenugreek, nigella, cinnamon, and carom seed—was prepared to evaluate cardioprotective function in albino rats. To systematically investigate cardioprotective efficacy, isoproterenol was injected into albino rats to induce myocardial injury. The prepared extract was administrated orally to rats daily for 28 days (200 mg/kg body weight) before infusion of isoproterenol (100 mg/kg body weight) on 29th and 30th days. The induced cardiac injury was significantly ameliorated in rats based on cardiac hypertrophy, histopathology, and <em>Caspase-3</em> mRNA expression analysis by qRT-PCR. The Indian Medicinal Plants, Phytochemistry And Therapeutics (IMPPAT) chemical database of 820 natural compounds from the mixed spices was then screened against CASP-3 protein using cheminformatics tools, where thymohydroquinone, 4-isopropylbenzoic acid, and 1-naphthylacetic acid were found to be the best interacting ligands, with binding energy scores of −6.112 kcal/mol, −6.206 kcal/mol, and −6.112 kcal/mol, respectively. Notably, thymohydroquinone exhibited the lowest predicted cytotoxicity. Furthermore, molecular dynamic simulation was used to validate the binding stability of the thymohydroquinone with CASP-3 protein compared to CID-6167 (control). Thus, this study explored that mixed spices have cardioprotective effects in rats and identified thymohydroquinone as a natural lead compound against CASP-3, which may pave the way for the development of pharmacotherapy for myocardial damage.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100492"},"PeriodicalIF":3.5,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143848147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative proteomics and structure-based approach to unravel the therapeutic drug target of Theileria species","authors":"Anusha Majumder ,&nbsp;Jyotisha ,&nbsp;Fouzia Nasim,&nbsp;Insaf Ahmed Qureshi","doi":"10.1016/j.jgeb.2025.100488","DOIUrl":"10.1016/j.jgeb.2025.100488","url":null,"abstract":"<div><div>Theileriosis, caused by protozoan parasites of genus <em>Theileria</em>, primarily affects both domestic and wild ruminants. It can lead to significant economic losses in livestock farming due to decreased productivity and high mortality rates in susceptible animals, while treatment measures are not cost-effective. Since most of mechanisms of this disease remain unknown, this study investigates the differences in the mode of pathogenesis between transforming and non-transforming groups through an <em>in silico</em> comparative proteomics approach to recognize the key players involved in host cell transformation. Although the major biological processes and molecular functions are almost conserved between the two groups, PEST-motif containing secretory proteins of <em>Sfi</em>I, SVSP, and Tash-AT gene families were identified as important candidates with the potential to transform infected host cells. Several members of PEST-motif containing proteins possess signal peptides, nuclear localization signals, and <em>trans</em>-membrane helices, further supporting their potential to transform host cells. Additionally, structural analysis helped in the identification of a parasitic protein (<em>Sfi</em>Ip) from <em>Sfi</em>I family as a plausible drug target. Virtual screening revealed FDA-approved drugs (i.e. atogepant and rimegepant) as promising compounds, showing the highest affinity for <em>Sfi</em>Ip during molecular docking. Further studies, including molecular dynamics simulation, principal component analysis, and free energy landscape, suggested that these drug molecules exhibit the stable interaction with protein. Therefore, our research could facilitate the identification and targeting of novel drug candidates that may be further implemented to recognize effective therapeutics against <em>Theileria</em> infections.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100488"},"PeriodicalIF":3.5,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome analysis of endophytic strain PM1 reveals promising plant Growth-Promoting mechanisms in pomegranate","authors":"Poonam Patel,&nbsp;Fenil Patel,&nbsp;Chaitanya Joshi,&nbsp;Madhvi Joshi","doi":"10.1016/j.jgeb.2025.100486","DOIUrl":"10.1016/j.jgeb.2025.100486","url":null,"abstract":"<div><div>The plant ecosystem harbours diverse symbiotic microorganisms with plant growth promoting and biocontrol activities. The gram- negative endophytic bacterium PM1 strain, isolated from the nodal region of pomegranate. The strain PM1 was studied through whole-genome sequencing, functional annotation, and plant growth-promoting trait (PGPT) gene analysis. Phylogenetic tree analysis and 16S rDNA sequencing confirmed its classification within the genus <em>Brucella</em>. The assembled genome size was 5,200,895 bp with a G + C content of 56.4 %. The average nucleotide identity (ANI) analysis revealed a 97.62 % similarity between PM1 and <em>B. anthropi</em> ATCC 49188 T, a type strain derived from human clinical samples, indicating a close relationship with <em>Brucella anthropi.</em> The functional annotation revealed 2,945 PGPT-related genes, including 32 % linked to direct effects (phytohormone signal production, biofertilization, and bioremediation processes) and 67 % to indirect effects (plant colonization, biocontrol, and competitive exclusion). KEGG analysis revealed genes involved in nitrogen metabolism, phosphate solubilization, siderophore production, hormone biosynthesis (gibberellin, cytokinin, and auxin), root colonization, and stress mitigation. Virulence factor database (VFDB) data revealed the absence of complete virulence gene assemblies, indicating limited pathogenic potential. Furthermore, secondary metabolite analysis predicted the potential production of ochrobactin compounds, which are potent siderophores that are important traits associated with PGPTs. The complete genome analysis of <em>Brucella</em> sp. PM1 provides new insights into plant-bacteria interactions, laying a foundation for advanced postgenomic studies and facilitating the development of bioeffective strategies such as biofertilizers or biocontrol agents for sustainable improvement in crop yields.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100486"},"PeriodicalIF":3.5,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143777095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}