Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Marine microalgae and their industrial biotechnological applications: A review","authors":"Reham Gamal,&nbsp;Mohamed Attia Shreadah","doi":"10.1016/j.jgeb.2024.100407","DOIUrl":"10.1016/j.jgeb.2024.100407","url":null,"abstract":"<div><h3>Background</h3><p>For use in specialized programs in the food, pharmaceutical, nutraceutical, cosmetic, and animal feed sectors, micro-algal biomass has been generated industrially. They can be grown in closed buildings, such as photobioreactors, or open structures. The utilization of biomass from microalgae for energy production is another crucial topic. Because of the world’s diminishing petroleum sources and the greenhouse gas emissions from gasoline lines, it is now obvious that fuels generated from petroleum are not sustainable.</p></div><div><h3>Results</h3><p>Microalgae can produce a variety of unique, sustainable biofuels. These include biodiesel made from <em>trans</em>-esterification of microalgal lipids, bioethanol from fermentation of carbohydrates, methane created by anaerobic digestion of algal biomass, and biohydrogen produced by photobiological processes. The idea of using microalgae as a fuel source is not entirely novel.</p></div><div><h3>Conclusion</h3><p>This analysis emphasizes the significance of recent and noteworthy advancements in the industrial usage of microalgae, with an emphasis on their biotechnological applications.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001100/pdfft?md5=d000e2d2a6bd74aaaa255810987615ce&pid=1-s2.0-S1687157X24001100-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142050336","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}

{"title":"Genetic diversity assessment of clonal plant Rosa persica in China","authors":"Na Li,&nbsp;Xuesen Liu,&nbsp;Xiaolong Zhang,&nbsp;Chenjie Zhang,&nbsp;Xinyu Lu,&nbsp;Chenyang Sun,&nbsp;Chao Yu,&nbsp;Le Luo","doi":"10.1016/j.jgeb.2024.100405","DOIUrl":"10.1016/j.jgeb.2024.100405","url":null,"abstract":"<div><p><em>Rosa persica</em> is considered a clonal plant because it is mainly propagated by clonal growth. Due to environmental degradation and habitat devastation, <em>R. persica</em> has been listed as a national second-class protected plant in China. However, the absence of research on wild populations of <em>R. persica</em> has impeded progress in formulating efficient conservation strategies. In this study, we investigated the clonal dispersal distance of <em>R. persica</em> to accurately determine the genetic diversity and population structure of the wild population in Xinjiang. We suggested that 20 m was the threshold distance with which to distinguish between different genets of plants. Based on this, we collated sequencing data from a total of 70 different genets of plants from 117 test samples. Eight populations of <em>R. persica</em> were primarily categorized into three subgroups: BL (Bole), TC (Tacheng) and CG (Changji). Of these, the CG subgroup exhibited the most genetic diversity. This research is the first to illustrates the clonal dispersal distance of <em>R. persica</em>, thus providing valuable reference guidelines for understanding the reproductive characteristics of clonal plants. In addition, the genetic diversity of <em>R. persica</em> provides a theoretical foundation for the formulation of conservation policies.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001082/pdfft?md5=a541940c538d161e61279c6ab29318ad&pid=1-s2.0-S1687157X24001082-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142050311","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}

{"title":"Evaluating the anti-cancer potential and pharmacological in-sights of Physalis angulata Root Extract as a strong candidate for future research","authors":"Jayachithra Ramakrishna Pillai ,&nbsp;Adil Farooq Wali ,&nbsp;Pooja Shivappa ,&nbsp;Sirajunisa Talath ,&nbsp;Sabry M. Attia ,&nbsp;Ahmed Nadeem ,&nbsp;Muneeb U. Rehman","doi":"10.1016/j.jgeb.2024.100410","DOIUrl":"10.1016/j.jgeb.2024.100410","url":null,"abstract":"<div><p>The research targeting the prevention of complications through natural constituents, instigated by the cancer has recently drawn much more attention over the globe. The research in this direction also revealed that the use of natural constituents would considered a promising strategy for diminishing the aforementioned disease and its consequences. Because of the easy availability and safe nature, the recent years, natural resources as strong anticancer agents. In this regard, here we introduced the possibility of using the methanolic extract of <em>Physalis angulata</em> root as a strong candidate and implemented the applicability of LC-MS to unveil the presence of various phytocompounds. The anticancer potential exhibited by <em>Physalis angulata</em> root followed by its ability to induce toxicity against the microbial population enhanced the interest in unveiling the phytochemical compounds including Absintholide, Curcumin dimer 1, Mytilin A, Ginsenoside F1, Encecalin , Ganoderic acid TQ, Alnustone, Rhamnetin 3-sophoroside, Gibberellin A14 aldehyde, Thiolutin, Euglobal III and Epomusenin B. The presence of various macro and micronutrients suggested that <em>Physalis angulata</em> is a prominent resource for future research targeting pharmacological research, especially anticancer research.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001136/pdfft?md5=b685f42a3972a9fa6dc417e79c817446&pid=1-s2.0-S1687157X24001136-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142040400","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}

{"title":"Bioinformatics deciphers the thebaine biosynthesis pathway in opium poppy: Hub genes, network analysis, and miRNA regulation","authors":"Zahra Shirazi ,&nbsp;Mahsa Rostami ,&nbsp;Abozar Ghorbani ,&nbsp;Pietro Hiram Guzzi","doi":"10.1016/j.jgeb.2024.100422","DOIUrl":"10.1016/j.jgeb.2024.100422","url":null,"abstract":"<div><p>Thebaine, a vital precursor in the codeine and morphine pathway, shows promise in addiction treatment. We conducted a comprehensive study on the thebaine biosynthesis pathway in opium poppy, utilizing bioinformatics tools. The dataset comprising the thirteen genes associated with the thebaine biosynthesis pathway was compiled from an extensive review of published literature and validated using the NCBI BLAST tool. Utilizing STRING and Cytoscape, we analyzed gene interactions and visualized the molecular interaction network, respectively. To identify hub proteins, CytoHubba was administered. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) at STRING were used for the enrichment analysis of the hub genes. CytoCluster was used to analyze the network in clusters. Promoter regions of hub genes and potential miRNAs were explored using MEME and the psRNATarget database. Hub genes crucial to thebaine biosynthesis were identified, contributing to essential cellular functions like growth, development, stress response, and signal transduction. Metabolic processes emerged as pivotal for thebaine production, indicating a broader role for the thebaine pathway gene network beyond primary metabolite production. Cell component subnetwork genes demonstrated associations with anatomical units, indicating involvement in plant defense responses. Dominant molecular functions drove plant defense responses. KEGG pathway analysis highlighted the significance of metabolic pathways and biosynthesis of secondary metabolites. Cluster analysis emphasized the relevance of the biosynthesis of amino acids, confirming the link between primary and secondary metabolites. Promoter analysis suggested the potential involvement of signal transduction in thebaine production. Hub genes were targeted by 40 miRNAs, suggesting potential novel biomarkers or target genes within the thebaine biosynthesis pathway. Based on the role of miRNAs identified in connection with the hub genes of the thebaine production process, the secondary metabolite pathway of thebaine appears to be associated with several key plant pathways, e.g. growth, development and stress response. However, these findings, based on bioinformatics analysis, warrant further experimental validation and promise to advance our understanding of the biosynthesis of thebaine and its interactions with other genes and metabolic pathways that influence the production of metabolites.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001252/pdfft?md5=aea3ec5547ca0ed687a7bd402aa62071&pid=1-s2.0-S1687157X24001252-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142040401","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}

{"title":"Integrated analysis of hub genes and intrinsically disordered regions in triple-negative breast cancer","authors":"Azhar Iqbal ,&nbsp;Faisal Ali ,&nbsp;Sulaiman Ali Alharbi ,&nbsp;Muhammad Sajid ,&nbsp;Saleh Alfarraj ,&nbsp;Momina Hussain ,&nbsp;Tehmina Siddique ,&nbsp;Rakhshanda Mustaq ,&nbsp;Fakhra Shafique ,&nbsp;Muhammad Sarfaraz Iqbal","doi":"10.1016/j.jgeb.2024.100408","DOIUrl":"10.1016/j.jgeb.2024.100408","url":null,"abstract":"<div><p>Triple-negative breast cancer (TNBC) is the most prevalent breast cancer subtype. Its prognosis is poor because there are no effective treatment targets. Despite several attempts, the molecular pathways of TNBC remain unknown, posing a significant clinical barrier in the search for viable targets. Two microarray datasets were used to identify possible targets for TNBC, GSE38959 and GSE45827, retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in TNBC samples compared with normal samples were identified using the GEO2R program. KEGG pathway enrichment and Gene Ontology functions were assessed for DEG pathways and functional annotation using ShinyGO 0.77. The STRING database and Cytoscape program were used for protein-protein interaction (PPI) analysis. Furthermore, we evaluated the predictive significance of hub gene expression in TNBC patients using the GEPIA2 online tool. We developed a comprehensive technique to assess whether intrinsically disordered regions (IDRs) are present in the TNBC hub genes. There were 48 DEGs were identified, all of which were upregulated. A putative protein complex containing these four core genes was selected for further analysis. Breast cancer patients with TTK, TOP2A, CENPF, and CCNA2 upregulation had a poor prognosis; TTK and CCNA2 were partially disordered, whereas TOP2A and CENPF were primarily disordered, according to IDR analysis. According to our study, TOP2A and CENPF may be useful therapeutic targets for disruption of the TNBC PPI network.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001112/pdfft?md5=ad04e53bf476dff625423ed5e7bb0542&pid=1-s2.0-S1687157X24001112-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141992913","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}

{"title":"Potentials of cytokinesis blocked micronucleus assay in radiation triage and biological dosimetry","authors":"G. Tamizh Selvan ,&nbsp;P. Venkatachalam","doi":"10.1016/j.jgeb.2024.100409","DOIUrl":"10.1016/j.jgeb.2024.100409","url":null,"abstract":"<div><p>The measurement of micronucleus (MN) in the cytokinesis-block arrested binucleated cells has been extensively used as a biomarker in many radiation biology applications in specific biodosimetry. Following radiation casualties, medical management of exposed individuals begins with triage and biological dosimetry. The cytokinesis blocked micronucleus (CBMN) assay is the alternate for the gold standard dicentric chromosome assay in radiation dose assessment. In recent years, the CBMN assay has become well-validated and emerged as a method of choice for evaluating occupational and accidental exposures scenario. It is feasible due to its cost-effective, simple, and rapid dose assessment rather than a conventional chromosome aberration assay. PubMed search tool was used with keywords of MN, biodosimetry, radiotherapy and restricted to human samples. Since Fenech and Morely developed the assay, it has undergone many technical and technological reforms as a biomarker of various applications. In this review, we have abridged recent developments of the CBMN assay in radiation triage and biodosimetry, focusing on (a) the influence of variables on dose estimation, (b) the importance of baseline frequency and reported dose–response coefficient values among different laboratories, (c) inter-laboratory comparison and (d) its limitations and means to overcome them.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001124/pdfft?md5=8951d6d0237bb33ce10af29ffbbb0ad9&pid=1-s2.0-S1687157X24001124-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141992912","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}

{"title":"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","authors":"Md. Masudur Rahman Munna ,&nbsp;Md. Touki Tahamid Tusar ,&nbsp;Saima Sajnin Shanta ,&nbsp;Md. Hossain Ahmed ,&nbsp;Md. Sarafat Ali","doi":"10.1016/j.jgeb.2024.100406","DOIUrl":"10.1016/j.jgeb.2024.100406","url":null,"abstract":"<div><p>Non-small cell lung cancer (NSCLC) is among the main causes of mortality from cancer around the globe, affecting all genders. Current treatments mainly focus on tyrosine kinase inhibitors (TKIs) targeting the epidermal growth factor receptor (EGFR). However, resistance mechanisms, such as the emergence of T790M and C797S EGFR mutations and upregulation of VEGFR-2, often hinder the effectiveness of TKIs. Thereby, EGFR and VEGFR-2 present an intriguing opportunity for the treatment of NSCLC by developing dual-acting drugs. This research aims to evaluate prospective <em>Moringa oleifera</em> L. (MO)-originated compounds to efficiently block both of these receptors. In our research, we screened a library of 200 compounds sourced from MO, a plant known for its remarkable therapeutic potential. We identified five intriguing phytocompounds: hesperetin, gossypetin, quercetin, gallocatechin, and epigallocatechin, as potential anti-cancer agents. The compounds have demonstrated notable binding affinity in virtual screening and multi-stage molecular docking analysis, surpassing the controls, Erlotinib and Bevacizumab + Rituximab. In addition, these compounds demonstrate top-notch drug-likeness and ADMET properties. The five promising drug candidates also had a strong ability to bind to receptors and stayed stable with them during the 200 ns molecular dynamics (MD) simulation and MM-GBSA calculation. Furthermore, DFT analysis indicates that hesperetin, gossypetin, and quercetagetin stand out as the most promising drug candidates among all others. The findings of our study suggest that these three therapeutic candidates can precisely target both EGFR and VEGFR-2 and can potentially act on both of these pathways as a single agent.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001094/pdfft?md5=3766a05d978308b18458c5c524136bea&pid=1-s2.0-S1687157X24001094-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141964444","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}

{"title":"Can human IgG subclasses distinguish between confirmed and unconfirmed SARS-CoV-2 infections?","authors":"Mahmoud Mohamed Bahgat ,&nbsp;Mohamed Hassan Nasraa ,&nbsp;Rola Nadeem ,&nbsp;Khaled Amer ,&nbsp;Wael A. Hassan ,&nbsp;Ahmed Abd EL-Raouf ,&nbsp;Dina Nadeem Abd-Elshafy","doi":"10.1016/j.jgeb.2024.100399","DOIUrl":"10.1016/j.jgeb.2024.100399","url":null,"abstract":"<div><h3>Background</h3><p>Immunoglobulin G (IgG) subclasses play a crucial role in the immune response to viral infections. While total IgG levels can generally provide an indication on the immune response, specific IgG subclasses can offer more detailed information about nature of the immune response and stage of the infection. Herein, we addressed the value of both total (t) and SARS-CoV-2-specific (s) IgG-subclasses in distinguishing between infection-confirmed virus-qRT-PCR-positive (IC; V-qRT-PCR-P) and infection-unconfirmed virus-qRT-PCR-unchecked (IU; V-qRT-PCR-UC) Egyptians.</p></div><div><h3>Results</h3><p>Both the t-IgG2 and 4 means were significantly higher (SH) among the IU subjects, whereas, the s-IgG1 and 3 means were SH among the IC ones. On the gender levels, both the t-IgG2 and 4 means were SH among the IU females, whereas, the mean of the s-IgG1 was SH among the IC females. The t-IgG4 mean was SH among the IU males, whereas, both means of the s-IgG1 and 3 were SH among the IC males. Significant positive correlations (SPC) were recorded between both the t-IgG1 and 3 with the symptom grades (SG) among the IU humans (r² = 0.200 and 0.253, respectively). Also, SPC was noticed between the s-IgG2 and the SG among the IU females (r² = 0.6782). SPC was recorded between both the t-IgG1 and the s-IgG2 with the SG among the IU males (r² = 0.794 and 0.373, respectively). SPC was noticed between the t-IgG3 and the age among the IC males (r² = 0.779).</p></div><div><h3>Conclusion</h3><p>Although the limitation of the small studied sample size, our results suggest some total and SARS-CoV-2-specific IgG-subclasses as both supplemental and gender-specific immune markers to distinguish between confirmed and unconfirmed SARS-CoV-2 infections.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001021/pdfft?md5=5306b0c0d9b04f02e59420c85290fba4&pid=1-s2.0-S1687157X24001021-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141961787","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}

{"title":"Genome-wide characterization and expression profiling of FARL (FHY3/FAR1) family genes in Zea mays","authors":"Sharah Jabeen Mou ,&nbsp;Prodipto Bishnu Angon","doi":"10.1016/j.jgeb.2024.100401","DOIUrl":"10.1016/j.jgeb.2024.100401","url":null,"abstract":"<div><p>A significant role of the plant is played by the transcription factor FARL, which is light signal transduction as well as plant growth and development. Despite being transposases, FARL has developed a variety of dominant biological actions in evolution and speciation. On the other hand, little is known about the <em>Zea mays</em> FARL protein family. This study identifies and characterizes fifteen <em>ZmFARL</em> genes genome-wide, and RNA sequencing data was used to profile their expression. 105 FARL proteins from five plant species were classified into five groups based on sequence alignment and phylogeny. The <em>ZmFARL</em> genes’ exon–intron and motif distribution were conserved based on their evolutionary group. The fifteen <em>ZmFARL</em> genes were distributed over seven of the ten <em>Z. mays</em> chromosomes, although no duplication was discovered. <em>Cis</em>-element analysis reveals that <em>ZmFARL</em> genes play a variety of activities, including tissue-specific, stress- and hormone-responsive expressions. Furthermore, the results of the RNA sequencing used to profile expression showed that the genes <em>ZmFARL2</em> and <em>ZmFARL5</em> were much more expressed than other genes in various tissues, particularly in leaf characteristics. The identification of likely genes involved in cellular activity in <em>Z. mays</em> and related species will be aided by the characterization of the <em>FARL</em> genes.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001045/pdfft?md5=0994da1f5ea3024c87eb9a77ba33d9ab&pid=1-s2.0-S1687157X24001045-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141961786","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}

{"title":"Bioinformatic and functional analysis of a PHB polymerase (PhbC) from Azospirillum baldaniorum","authors":"Doris del Carmen Fuentes ,&nbsp;Lucía Soto-Urzua ,&nbsp;Lino Javier Martínez-Soto ,&nbsp;Luis Javier Martínez-Morales","doi":"10.1016/j.jgeb.2024.100403","DOIUrl":"10.1016/j.jgeb.2024.100403","url":null,"abstract":"<div><h3>Background</h3><p><em>Azospirillum baldaniorum</em> Sp245 produces poly-β-hydroxybutyrate, a biodegradable polymer with characteristics similar to synthetic thermoplastics, including polypropylene. In the synthesis pathway, the poly-β-hydroxybutyrate synthase enzyme uses thioesters of 3-hydroxy butyryl-CoA as a substrate and catalyzes their polymerization with HS-CoA release.</p></div><div><h3>Methods</h3><p>A study was conducted using <em>in silico</em> analysis of the two <em>phb</em>C genes of <em>A. baldaniorum</em> Sp245. One was selected for amplification and cloning into the pEXP5- CT/TOPO® vector, which was analysed by restriction pattern, polymerase chain reaction, and sequencing. SDS-PAGE analysis determined the molecular weight of the PhbC1 protein from <em>Azospirillum baldaniorum</em> (AbPhbC1). The presence of the protein was confirmed by Western blotting using anti-polyhistidine monoclonal antibodies. The enzymatic activity in the crude extract of AbPhbC1 was determined by measuring the concentration of sulfhydryl groups using the Ellman method. A UV–Vis assay was performed. To confirm the presence of the poly-β-hydroxybutyrate product, an NMR assay was performed.</p></div><div><h3>Results</h3><p><em>In silico</em> analyses, it is revealed that AbPhbC1 and the PhbC2 protein from <em>Azospirillum baldaniorum</em> (AbPhbC2) retain the poly-β-hydroxybutyrate polymerase and α/β hydrolase domain. The Cys-His-Asp catalytic triad is highly conserved in all four polyβ-hydroxyalkanoate synthases in the central subdomain, structurally similar to the reported crystallized proteins. The dimerization subdomain is different; in AbPhbC1, it is in the closed form; in AbPhbC2, it is in the open form; and in AbPhbC2, it lacks the EC region as class III and IV poly-β-hydroxyalcanoate synthases. In vitro, the molecular weight of AbPhbC1 was 68 kDa. The polymerization of PHB by AbPhbC1 was detected by the release of HS-CoA from the quantification of SH. The UV–Vis scan showed a characteristic peak at 264 nm. A comparison of the NMR spectra of the bacterial and commercial poly-β-hydroxybutyrate samples suggested their presence.</p></div><div><h3>Conclusion</h3><p><em>In silico</em> analyses suggested that AbPhbC1 and AbPhbC2 are structurally functional, except that AbPhbC2 might require the PhaR subunit for its activity; this strongly suggests that it could be a class IV poly-β-hydroxyalcanoate synthase. UV–Vis scanning and NMR spectroscopy revealed the synthesis of poly-β-hydroxybutyrate by the <em>A. baldaniorum</em> enzyme AbPhbC1, indicating that the enzyme is functional.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001069/pdfft?md5=afe7ad1f4b87cee05942aeb268459c3e&pid=1-s2.0-S1687157X24001069-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141954433","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}