Gene最新文献

{"title":"Mathematical model for understanding the relationship between diabetes and novel coronavirus","authors":"Preety Kumari ,&nbsp;Harendra Pal Singh ,&nbsp;Swarn Singh","doi":"10.1016/j.gene.2024.148970","DOIUrl":"10.1016/j.gene.2024.148970","url":null,"abstract":"<div><div>A new model is proposed to explore interactions between diabetes and novel coronavirus. The model accounted for both the omicron variant and variants varying from omicron. The model investigated compartments such as hospitalization, diabetes, co-infection, omicron variant, and quarantine. Additionally, the impact of different vaccination doses is assessed. Sensitivity analysis is carried out to determine disease prevalence and control options, emphasizing the significance of knowing epidemics and their characteristics. The model is validated using actual data from Japan. The parameters are fitted with the help of ”Least Square Curve Fitting” method to describe the dynamic behavior of the proposed model. Simulation results and theoretical findings demonstrate the dynamic behavior of novel coronavirus and diabetes mellitus (DM). Biological illustrations that illustrate impact of model parameters are evaluated. Furthermore, effect of vaccine efficacy and vaccination rates for the vaccine’s first, second, and booster doses is conducted. The impact of various preventive measures, such as hospitalization rate, quarantine or self-isolation rate, vaccine dose-1, dose-2, and booster dose, is considered for diabetic individuals in contact with symptomatic or asymptomatic COVID-19 infectious people in the proposed model. The findings demonstrate the significance of vaccine doses on people with diabetes and individuals infectious with omicron variant. The proposed work helps with subsequent prevention efforts and the design of a vaccination policy to mitigate the effect of the novel coronavirus.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An overview of lncRNA NEAT1 contribution in the pathogenesis of female cancers; from diagnosis to therapy resistance","authors":"Sulieman Ibraheem Shelash Al-Hawari ,&nbsp;Saade Abdalkareem Jasim ,&nbsp;Farag M. A. Altalbawy ,&nbsp;Pooja Bansal ,&nbsp;Harpreet Kaur ,&nbsp;Ahmed Hjazi ,&nbsp;Jaafaru Sani Mohammed ,&nbsp;Mahamedha Deorari ,&nbsp;Salim B. Alsaadi ,&nbsp;Ahmed Hussein Zwamel","doi":"10.1016/j.gene.2024.148975","DOIUrl":"10.1016/j.gene.2024.148975","url":null,"abstract":"<div><div>Despite the ongoing progress in detecting and treating cancer, there is still a need for extensive research into the molecular mechanisms involved in the emergence, progression, and resistance to recurrence of female reproductive tissue-specific cancers such as ovarian, breast, cervical, and endometrial cancers. The nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) that exhibits increased expression in female tumors. Moreover, elevated levels of NEAT1 have been associated with poorer survival outcomes in cancer patients. NEAT1 plays a pivotal role in driving tumor initiation through modulating the expression of genes involved in various aspects of tumor cell proliferation, epithelial-to-mesenchymal transition (EMT), metastasis, chemoresistance, and radio-resistance. Mechanistically, NEAT1 acts as a scaffold RNA molecule via interacting with EZH2 (Enhancer of Zeste 2 Polycomb Repressive Complex 2 Subunit), thereby influencing the expression of downstream effectors of EZH2. Additionally, NEAT1 functions as a competing endogenous RNA (ceRNA) by microRNAs (miRNAs) sponging, consequently altering the expression levels of their target genes during the development of female cancers. This comprehensive review aims to shed light on the latest insights regarding the expression pattern, biological functions, and underlying mechanisms governing the function and regulation of NEAT1 in tumors. Furthermore, particular emphasis is placed on its clinical significance as a novel diagnostic biomarker and a promising therapeutic target for female cancers.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RFWD2 increases proliferation and CDDP resistance of osteosarcoma cells","authors":"Pingting Liu ,&nbsp;Na Xie","doi":"10.1016/j.gene.2024.148973","DOIUrl":"10.1016/j.gene.2024.148973","url":null,"abstract":"<div><div>P53, a key tumor suppressor gene, usually produces mtp53 proteins with oncogenic functions due to missense mutations in the DNA-binding domain. P53 is the most commonly mutated gene in osteosarcoma and plays an important role in the development and metastasis of osteosarcoma. The ubiquitin proteasome system is an evolutionarily conserved post-translational modification that regulates a variety of disease processes, including tumors. Researches have shown that RFWD2, as a function of an E3 ubiquitin ligase, plays an important role in regulating tumor progression. However, the biological function of RFWD2 in osteosarcoma cells with different p53 status remains to be clarified. Initially, we found that sarcoma patients with high levels of RFWD2 expression tended to have shorter overall survival time by analyzing UALCAN-TCGA data. Subsequently, we used CCK-8, colony formation, Transwell, and xenograft methods to confirm that RFWD2 acts as an oncogene, regulating the proliferation and invasion of osteosarcoma cells (HOS^(p53mut/-), U2OS^(p53wt/wt) and Saos-2^(p53-/-) cells) with different p53 status. Further co-IP experiments showed that in HOS^(p53mut/-) and U2OS^(p53wt/wt) cells, RFWD2 binds to p53 and participate in tumor progression. In addition, we demonstrated through both <em>in vitro</em> and <em>in vivo</em> experiments that RFWD2 regulates the sensitivity of osteosarcoma cells to CDDP. In conclusion, our study demonstrates that RFWD2 acts as an oncogene regulating osteosarcoma cell proliferation and sensitivity to CDDP. Our findings provide a new perspective and potential therapeutic target for the treatment of osteosarcoma.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration of bioinformatics and multi-layered experimental validation reveals novel functions of acetylation-related genes in intervertebral disc degeneration","authors":"Jun Zhu ,&nbsp;Tongqu Song ,&nbsp;Zheng Li ,&nbsp;Wei Zheng ,&nbsp;Yong Liu ,&nbsp;Hao Li ,&nbsp;Song Wang ,&nbsp;Jinlong Tang ,&nbsp;Shuo Feng ,&nbsp;Lei Wang ,&nbsp;Xiaoqing Lu ,&nbsp;Feng Yuan ,&nbsp;Zhengya Zhu","doi":"10.1016/j.gene.2024.148974","DOIUrl":"10.1016/j.gene.2024.148974","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;div&gt;The molecular mechanisms underlying intervertebral disc degeneration (IDD) remain poorly understood. The purpose of this work is to elucidate key molecules and investigate the roles of acetylation-related RNAs and their associated pathways in IDD.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Method&lt;/h3&gt;&lt;div&gt;Datasets GSE70362 and GSE124272 were obtained from the Gene Expression Omnibus (GEO) and combined to investigate differentially expressed genes (DEGs) associated with acetylation in IDD patients compared to healthy controls. Critical genes were pinpointed by integrating GO, KEGG and PPI networks. Furthermore, CIBERSORTx analysis was used to investigate the differences in immune cell infiltration between different groups and the biological processes (BP), cellular components (CC) and molecular functions (MF) were calculated by GSEA and GSVA. In addition, The single-cell database GSE165722 was incorporated to validate the specific expression patterns of hub genes in cells and identify distinct cell subtypes. This provides a theoretical basis for a more in-depth understanding of the roles played by critical cell subtypes in the process of IDD. Subsequently, tissues from IVD with varying degrees of degeneration were collected to corroborate the key DEGs using western blot, RT-qPCR, and immunofluorescence staining.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Results&lt;/h3&gt;&lt;div&gt;By integrating various datasets and references, we identified a total of 1620 acetylation-related genes. These genes were subjected to a combined analysis with the DEGs from the databases included in this study, resulting in the discovery of 358 acetylation-related differentially expressed genes (ARDEGs). A comparative analysis with differentially expressed genes obtained from three databases yielded 19 ARDEGs. The PPI network highlighted the top 10 genes (&lt;em&gt;IL1B, LAMP1, PPIA, SOD2, LAMP2, FBL, MBP, SELL, IRF1&lt;/em&gt; and &lt;em&gt;KHDRBS1&lt;/em&gt;) based on their protein interaction relationships. CIBERSORTx immune infiltration analysis revealed a moderate positive correlation between the gene &lt;em&gt;IL1β&lt;/em&gt; and Mast.cells.activated, as well as a similar correlation between the gene &lt;em&gt;IRF1&lt;/em&gt; and Mast.cells.activated. Single-cell dataset was used to identify cell types and illustrate the distribution of hub genes in different cell types. The two cell types with the highest AUCell scores (Neutrophils and Monocytes) were further explored, leading to the subdivision of Neutrophils into two new cell subtypes: S100A9-type Neutrophils and MARCKS-type Neutrophils. Monocytes were labeled as HLA-DRA9-type Monocytes and IGHG3-type Monocytes. Finally, molecular biology techniques were employed to validate the expression of the top 10 hub genes. Among them, four genes (&lt;em&gt;IL1β, SOD2, LAMP2, and IRF1&lt;/em&gt;) were confirmed at the gene level, while two (&lt;em&gt;IL1β and SOD2&lt;/em&gt;) were validated at the protein level.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Conclusion&lt;/h3&gt;&lt;div&gt;In this study, we carried out a thorough analysis across three data","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination","authors":"Yu-Chen Liu ,&nbsp;Masakazu Ishikawa ,&nbsp;Shuhei Sakakibara ,&nbsp;Mohamad Al Kadi ,&nbsp;Daisuke Motooka ,&nbsp;Yoko Naito ,&nbsp;Shingo Ito ,&nbsp;Yuko Imamura ,&nbsp;Hisatake Matsumoto ,&nbsp;Fuminori Sugihara ,&nbsp;Haruhiko Hirata ,&nbsp;Hiroshi Ogura ,&nbsp;Daisuke Okuzaki","doi":"10.1016/j.gene.2024.148971","DOIUrl":"10.1016/j.gene.2024.148971","url":null,"abstract":"<div><div>Circular RNAs (circRNA) lack 5′ or 3′ ends; their unique covalently closed structures prevent RNA degradation by exonucleases. These characteristics provide circRNAs with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNAs. CircRNA levels are reportedly associated with certain human diseases, making them novel disease biomarkers and a noncanonical class of therapeutic targets. In this study, the endogenous circRNAs underlying the response to BNT162b2 mRNA vaccination were evaluated. To this end, peripheral blood samples were subjected to full-length sequencing of circRNAs via nanopore sequencing and transcriptome sequencing. Fifteen samples, comprising pre-, first, and second vaccination cohorts, were obtained from five healthcare workers with no history of SARS-CoV-2 infection or previous vaccination. A total of 4706 circRNAs were detected; following full-length sequencing, 4217 novel circRNAs were identified as being specifically expressed during vaccination. These circRNAs were enriched in the binding motifs of stress granule assemblies and SARS-CoV-2 RNA binding proteins, namely poly(A) binding protein cytoplasmic 1 (PABPC1), pumilio RNA binding family member 1 (PUM1), and Y box binding protein 1 (YBX1). Moreover, 489 circRNAs were identified as previously reported miRNA sponges. The differentially expressed circRNAs putatively originated from plasma B cells compared to circRNAs reported in human blood single-cell RNA sequencing datasets. The pre- and post-vaccination differences observed in the circRNA expression landscape in response to the SARS-CoV-2 BNT162b2 mRNA vaccine.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of chicken LGALSL (galectin-related protein) gene’s proximal promoter and its control by Krüppel-like factors 3 and 7","authors":"Herbert Kaltner,&nbsp;Gabriel García Caballero,&nbsp;Sebastian Schmidt","doi":"10.1016/j.gene.2024.148972","DOIUrl":"10.1016/j.gene.2024.148972","url":null,"abstract":"<div><div>The <em>G</em>alectin-<em>R</em>elated <em>P</em>rotein (GRP), encoded by the <em>LGALSL</em> gene, assigned to the protein family of β-galactoside-binding Galectins, has lost carbohydrate-binding abilities. Its chicken homolog (C-GRP) occurs in the bursa of Fabricius’ epithelial and B cells. Our study investigates the unknown regulatory mechanisms controlling its expression by analyzing the promoter region of the chicken <em>(C-)LGALSL</em> gene in chicken cells. We aimed to identify the sequence elements of the <em>C-LGALSL</em> gene promoter responsible for maximum activity and transcription factors (TFs) that can modulate this activity. Using luciferase reporter assays, we investigated deletion variants of the 5′ region (−2480 bp to +26 bp). Through <em>in silico</em> analyses and site-directed mutagenesis, we explored potential transcription factor binding sites, identified crucial transcription factors through transient overexpression and tested its direct binding by ChIP. Our findings highlight that the region from −274 to −75 bp, conserved among bird species, is crucial for promoter regulation. Among other tested factors, only the chicken (ch) Krüppel-like factors, chKLF3 and chKLF7, modulate the promoter’s activity. The TFs chKLF3 acts as a repressor, and chKLF7 as an activator, although direct binding could not be confirmed. In conclusion, chKLF3 and chKLF7 contribute, in contrast to other factors with binding sites in the region from −274 to −75 bp, to <em>C-LGALSL</em> gene promoter regulation with a balanced impact on activity.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Peripherally-restricted recurrent infection by engineered E. coli strain modulates hippocampal proteome promoting memory impairments in a rat model","authors":"Anam Abdullah ,&nbsp;Anuranjani Kumar ,&nbsp;Ayesha Zainab Beg ,&nbsp;Anupam Chawla ,&nbsp;Sudeshna Kar ,&nbsp;Surajit Ganguly ,&nbsp;Asad U Khan","doi":"10.1016/j.gene.2024.148969","DOIUrl":"10.1016/j.gene.2024.148969","url":null,"abstract":"<div><div>Commensal bacteria that breach endothelial barrier has been reported to induce low grade chronic inflammation producing disease symptoms in major peripheral tissues. In this study, we investigated the role of genetically modified cellular invasive form of commensal <em>E. coli</em> K12 (SK3842) in cognitive impairment. Low-grade systemic infection model was developed using recurring peripheral inoculation of live bacteria in Wistar rats. To examine memory parameters, Novel object recognition test and Radial arm maze test were performed. Differential protein expression profiling of rat hippocampus was carried out using LC-MS/MS and subsequently quantified using SWATH. HBA1/2, NEFH, PFN1 and ATP5d were chosen for validation using quantitative RT-PCR. Results showed drastic decline in Recognition memory of the SK3842 infected rats. Reference and Working Memory of the infected group were also significantly reduced in comparison to control group. Proteome analysis using LC-MS/MS coupled with SWATH revealed differential expression of key proteins that are crucial for the maintenance of various neurological functions. Moreover, expression of NEFH and PFN1transcripts were found to be in line with the proteomics data. Protein interaction network of these validated proteins generated by STRING database converged to RhoA protein. Thus, the present study establishes an association between peripheral infection of a hippocampal protein network dysregulation and overall memory decline.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From sequence to significance: A thorough investigation of the distinctive genome features uncovered in C. Werkmanii strain NIB003","authors":"Mohammad Uzzal Hossain ,&nbsp;Neyamat Khan Tanvir ,&nbsp;A.B.Z. Naimur Rahman ,&nbsp;Zeshan Mahmud Chowdhury ,&nbsp;Md. Shahadat Hossain ,&nbsp;Shajib Dey ,&nbsp;Arittra Bhattacharjee ,&nbsp;Ishtiaque Ahammad ,&nbsp;Umme Salma Zohora ,&nbsp;Abu Hashem ,&nbsp;Keshob Chandra Das ,&nbsp;Chaman Ara Keya ,&nbsp;Md. Salimullah","doi":"10.1016/j.gene.2024.148965","DOIUrl":"10.1016/j.gene.2024.148965","url":null,"abstract":"<div><div><em>Citrobacter werkmanii</em> (<em>C. werkmanii</em>), an opportunistic urinary bacterium that causes diarrhea, is poorly understood. Our research focuses on genetic features that are crucial to disease development, such as pathogenic interactions, antibiotic resistance, virulence genes and genetic variation. Following its morphological, biochemical, and molecular identification, the whole genome of <em>C. werkmanii</em> strain NIB003 was sequenced in Bangladesh for the first time. Despite having around 80% whole genome conservation, the research shows that the Bangladeshi strain forms a separate phylogenetic cluster. This emphasises the genetic variability within <em>C. werkmanii</em>, resulting in particular modifications at the strain level and changes in its ability to cause disease. The results of the genetic diversity analysis indicate that the Bangladeshi sequenced genome is more diverse than the other strains due to the existence of unique features, such as the presence of t-RNA binding domain and N-6 adenine-specific DNA methylases.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome sequencing and identification of full-length genes involved in the biosynthesis of anticancer compounds Oleanolic acid and Ursolic acid in Achyranthes aspera L.","authors":"C.M. Jeevitha,&nbsp;Kumar Ravichandiran,&nbsp;Tanuja Tanuja,&nbsp;Madasamy Parani","doi":"10.1016/j.gene.2024.148964","DOIUrl":"10.1016/j.gene.2024.148964","url":null,"abstract":"<div><div>Achyranthes aspera is renowned for its rich medicinal properties since the Ayurvedic era. This plant is known for the presence of experimentally validated anticancer compounds like oleanolic acid (OA) and ursolic acid (UA). Our study involved sequencing the RNA from the root tissue of A. aspera to elucidate the genes responsible for synthesizing these two critical secondary metabolites. Through RNA-Seq analysis, we assembled approximately 167,698 transcripts, averaging 847 base pairs in length, with an N50 value of 1509 bp. From this data, we mapped 604 sequences involved in the metabolism of terpenoids and polyketide pathways. Among them, 241 transcripts were mapped to the triterpenoid biosynthesis pathway, which included 127 transcripts involved in OA and UA biosynthesis. From these transcripts, we identified 22 full-length genes coding for all the 21 enzymes required for OA and UA biosynthesis. Identifying these full-length genes will lead to a better understanding of the pathway and adopting genetic engineering approaches.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GefB, a GGDEF domain-containing protein, affects motility and biofilm formation of Vibrio parahaemolyticus and is regulated by quorum sensing regulators","authors":"Yining Zhou ,&nbsp;Jingyang Chang ,&nbsp;Miaomiao Zhang ,&nbsp;Xue Li ,&nbsp;Xi Luo ,&nbsp;Wanpeng Li ,&nbsp;Zhukang Tian ,&nbsp;Nan Zhang ,&nbsp;Bin Ni ,&nbsp;Yiquan Zhang ,&nbsp;Renfei Lu","doi":"10.1016/j.gene.2024.148968","DOIUrl":"10.1016/j.gene.2024.148968","url":null,"abstract":"<div><div><em>Vibrio parahaemolyticus</em> (<em>V. parahaemolyticus</em>) stands as the predominant etiological agent responsible for gastroenteritis associated with the consumption of seafood. Cyclic di-guanosine monophosphate (c-di-GMP), a secondary messenger in bacteria, controls multiple bacterial behaviors including pathogenesis, the development of biofilms, and motility. The protein GefB (VPA1478), characterized by the presence of a GGDEF domain, inhibits the swarming motility of <em>V. parahaemolyticus</em>. In this study, we showed that deletion of <em>gefB</em> remarkably reduced cellular c-di-GMP level and biofilm formation by <em>V. parahaemolyticus</em>, but significantly enhanced the swimming and swarming motility. In addition, GefB inhibited the polar and lateral flagellar genes but activated genes associated with exopolysaccharide production of <em>V. parahaemolyticus</em>. The data also demonstrated that <em>vpa1477</em> and <em>gefB</em> are co-transcribed as a single transcriptional unit, designated as <em>vpa1477</em>-<em>gefB</em>. Transcription of <em>vpa1477</em>-<em>gefB</em> was under the collective regulation of the master quorum sensing (QS) regulators AphA and OpaR, which function at low (LCD) and high cell density (HCD), respectively. AphA positively regulated <em>vpa1477</em>-<em>gefB</em> transcription at LCD, whereas OpaR negatively regulated its transcription at HCD. The findings significantly enhance our comprehension of the metabolism and regulatory mechanisms of c-di-GMP in <em>V. parahaemolyticus</em>.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}