Molecular Biotechnology最新文献

{"title":"Isolation and Characterization of Antimicrobial Peptides Isolated from Brevibacillus halotolerans 7WMA2 for the Activity Against Multidrug-Resistant Pathogens.","authors":"Ho Le Han, Phu Tran Vinh Pham, Song-Gun Kim, Sook Sin Chan, Kuan Shiong Khoo, Kit Wayne Chew, Pau Loke Show, Thi Ngoc Thu Tran, Hai Thi Viet Nguyen, Phuong Thi Dong Nguyen","doi":"10.1007/s12033-023-00963-0","DOIUrl":"10.1007/s12033-023-00963-0","url":null,"abstract":"<p><p>Multidrug resistance to pathogens has posed a severe threat to public health. The threat could be addressed by antimicrobial peptides (AMPs) with broad-spectrum suppression. In this study, Brevibacillus halotolerans 7WMA2, isolated from marine sediment, produced AMPs against Gram-positive and Gram-negative bacteria. The AMPs were precipitated by ammonium sulfate 30% (w/v) from culture broth and dialyzed by a 1 kDa membrane. Tryptone Soy Agar (TSA) was used for the cultivation and resulted in the largest bacteria-inhibiting zones under aerobic conditions at 25 °C, 48 h. An SDS-PAGE gel overlay test revealed that strain 7WMA2 could produce AMPs of 5-10 kDa and showed no degradation when held at 121 °C for 30 min at a wide pH 2-12 range. The AMPs did not cause toxicity to HeLa cells with concentrations up to 500 µg/mL while increasing the arbitrary unit up to eight times. The study showed that the AMPs produced were unique, with broad-spectrum antimicrobial ability.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3618-3627"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138478189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"O-Linked N-Acetylglucosamine Transferase Regulates Bone Homeostasis Through Alkaline Phosphatase Pathway in Diabetic Periodontitis.","authors":"Wei Luo, Lu Sun","doi":"10.1007/s12033-023-00947-0","DOIUrl":"10.1007/s12033-023-00947-0","url":null,"abstract":"<p><p>Periodontitis is one of the most common complications of diabetes, which seriously affects patients' life quality. It is important to find the key factors and mechanisms to improve the treatment of periodontitis. In our study, high glucose (HG) and lipopolysaccharide (LPS) treated human periodontal ligament cells (hPDLCs) and LPS treated diabetic mice was used to establish the diabetic periodontitis model in vitro and in vivo. O-linked beta-N-acetylglucosamine glycosylation (O-GlcNAcylation) and O-linked N-acetylglucosamine transferase (OGT) protein levels were detected by western blot assay. Cell counting kit-8, alkaline phosphatase (ALP), and alizarin red staining (ARS) assays were used to observe the O-GlcNAcylation and OGT effects on cell viability and osteoblast differentiation. Co-immunoprecipitation (Co-IP) assay was used to detect the relationship between OGT and ALP. The results showed that the levels of OGT and O-GlcNAcylation were significantly increased in both cell and mouse models. ALP and ARS staining results showed that silencing of OGT or inhibition of O-glycosylation notably improved osteogenic differentiation, increased the osteoprotegerin (OPG) protein levels and decreased the receptor activator for nuclear factor-κB Ligand (RANKL) protein levels of the HG and LPS treated hPDLCs. In diabetic periodontitis mice, knockdown of OGT relieved the injury of gingival tissue, increased the ALP and OPG levels and decreased the RANKL levels. Besides, ALP interacted with OGT protein, and OGT protein was found to act on ALP serine 513 glycosylation. In conclusion, our study demonstrated that excessive O-GlcNAcylation could restrain osteoblast differentiation by O-glycosylation in ALP.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3475-3484"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89718947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Influence of Extracellular Vesicles Secreted by Dural Cells on Osteoblasts.","authors":"Fangning Zhao, Jinglin Zhu, Xinhang Dong, Xiaoshuang Guo, Chenzhi Lai, Jingyi Zhao, Xianlei Zong, Guodong Song, Xiaolei Jin","doi":"10.1007/s12033-023-00974-x","DOIUrl":"10.1007/s12033-023-00974-x","url":null,"abstract":"<p><p>To explore the influence of extracellular vesicles secreted by dural cells (Dura-EVs) on osteoblasts. Our methodology involves assessing the effects of these EVs at concentrations of 50ug/ml, 100ug/ml, and 200ug/ml on osteoblasts proliferation, differentiation, migration, osteogenesis, and inhibition of apoptosis. We also treated a cranial defect model with injections of these Dura-EVs and monitored the healing rate of cranial defects. Tissue sections were analyzed using Hematoxylin and Eosin (H & E), Masson's trichrome, and immunofluorescence (IF) staining. Our results suggest that Dura-EVs can enhance osteoblasts proliferation, migration, differentiation, and osteogenesis in a dose-dependent manner in vitro. In vivo, Dura-EVs may promote the repair of skull defects. Dura-EVs have an important influence on osteoblasts, our findings shed light on a novel aspect of the dura mater's contribution to cranial osteogenesis.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3674-3687"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138470451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Crucial Genes and Signaling Pathways in Alectinib-Resistant Lung Adenocarcinoma Using Bioinformatic Analysis.","authors":"Zhilong Li, Yafeng Fan, Yong Ma, Nan Meng, Dongbing Li, Dongliang Wang, Jianhong Lian, Chengguang Hu","doi":"10.1007/s12033-023-00973-y","DOIUrl":"10.1007/s12033-023-00973-y","url":null,"abstract":"<p><p>Alectinib, a second-generation anaplastic lymphoma kinase (ALK) inhibitor, has been shown to be effective for patients with ALK-positive non-small cell lung cancer (NSCLC). However, alectinib resistance is a serious problem worldwide. To the best of our knowledge, little information is available on its molecular mechanisms using the Gene Expression Omnibus (GEO) database. In this study, the differentially expressed genes (DEGs) were selected from the gene expression profile GSE73167 between parental and alectinib-resistant human lung adenocarcinoma (LUAD) cell samples. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) annotation enrichment analyses were conducted using Database for Annotation, Visualization and Integrated Discovery (DAVID). The construction of protein-protein interaction (PPI) network was performed to visualize DEGs. The hub genes were extracted based on the analysis of the PPI network using plug-in cytoHubba of Cytoscape software. The functional roles of the key genes were investigated using Gene Expression Profiling Interactive Analysis (GEPIA), University of Alabama at Birmingham Cancer (UALCAN), Gene Set Enrichment Analysis (GSEA), and Tumor Immune Estimation Resource (TIMER) analysis. The networks of kinase, miRNA, and transcription-factor targets of SFTPD were explored using LinkedOmics. The drug sensitivity analysis of SFTPD was analyzed using the RNAactDrug database. Results showed a total of 144 DEGs were identified. Five hub genes were extracted, including mucin 5B (MUC5B), surfactant protein D (SFTPD), deleted in malignant brain tumors 1 (DMBT1), surfactant protein A2 (SFTPA2), and trefoil factor 3 (TFF3). The survival analysis using GEPIA displayed that low expression of SFTPD had a significantly negative effect on the prognosis of patients with LUAD. GSEA revealed that low expression of SFTPD was positively correlated with the pathways associated with drug resistance, such as DNA replication, cell cycle, drug metabolism, and DNA damage repair, including mismatch repair (MMR), base excision repair (BER), homologous recombination (HR), and nucleotide excision repair (NER). The SFTPD expression was negatively correlated with the drug sensitivity of alectinib according to RNAactDrug database. The expression of SFTPD was further validated in parental H3122 cells and alectinib-resistant H3122 cells by quantitative reverse transcription PCR (RT-qPCR). In conclusion, our study found that the five hub genes, especially low expression of SFTPD, are closely related to alectinib resistance in patients with LUAD.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3655-3673"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139032456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Superior Performance of Iron-Coated Silver Nanoparticles and Cefoxitin as an Antibiotic Composite Against Methicillin-Resistant  Staphylococcus aureus (MRSA): A Population Study.","authors":"Nahal Hadi, Sedigheh Nakhaeitazreji, Farshad Kakian, Zahra Hashemizadeh, Alireza Ebrahiminezhad, Jun Wei Roy Chong, Aydin Berenjian, Pau Loke Show","doi":"10.1007/s12033-023-00957-y","DOIUrl":"10.1007/s12033-023-00957-y","url":null,"abstract":"<p><p>The synergistic effects of antimicrobial nanostructures with antibiotics present a promising solution for overcoming resistance in methicillin-resistant Staphylococcus aureus (MRSA). Previous studies have introduced iron as a novel coating for silver nanoparticles (AgNPs) to enhance both economic efficiency and potency against S. aureus. However, there are currently no available data on the potential of these novel nanostructures to reverse MRSA resistance. To address this gap, a population study was conducted within the MRSA community, collecting a total of 48 S. aureus isolates from skin lesions. Among these, 21 isolates (43.75%) exhibited cefoxitin resistance as determined by agar disk diffusion assay. Subsequently, a PCR test confirmed the presence of the mecA gene in 20 isolates, verifying them as MRSA. These results highlight the cefoxitin disk diffusion susceptibility test as an accurate screening method for predicting mecA-mediated resistance in MRSA. Synergy tests were performed on cefoxitin, serving as a marker antibiotic, and iron-coated AgNPs (Fe@AgNPs) in a combination study using the checkerboard assay. The average minimal inhibitory concentration (MIC) and fractional inhibitory concentration (FIC) of cefoxitin were calculated as 11.55 mg/mL and 3.61 mg/mL, respectively. The findings indicated a synergistic effect (FIC index < 0.5) between Fe@AgNPs and cefoxitin against 90% of MRSA infections, while an additive effect (0.5 ≤ FIC index ≤ 1) could be expected in 10% of infections. These results suggest that Fe@AgNPs could serve as an economically viable candidate for co-administration with antibiotics to reverse resistance in MRSA infections within skin lesions. Such findings may pave the way for the development of future treatment strategies against MRSA infections.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3573-3582"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92155363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inhibition of PI3K/Akt/mTOR Signaling Pathway Suppresses 5-Fluorouracil Resistance in Gastric Cancer.","authors":"Zhiwei Xing, Yanan Gao, Yaxuan Shi, Ziyu Gao, Caixia Liu","doi":"10.1007/s12033-023-00966-x","DOIUrl":"10.1007/s12033-023-00966-x","url":null,"abstract":"<p><strong>Background: </strong>At present, 5-Fluorouracil (5-FU) is a crucial anti-cancer drug and is widely used for the treatment of various carcinomas, including gastric cancer (GC). The resistance of GC cells to 5-FU is still a matter of great concern.</p><p><strong>Objective: </strong>To illustrate the role of PI3K/Akt/mTOR signaling in regulating the cell cycle progression and migration of 5-FU-resistant GC cells.</p><p><strong>Material and methods: </strong>After the establishment of drug-resistant GC cell lines, the effects of 5-FU and/or BEZ235 (the dual inhibitor of PI3K and mTOR) on the activity of parental or drug-resistant GC cells were explored. The viability and localization of GC cells (MKN-45 and MKN-74) and their drug-resistant cells (MKN-45/R and MKN-74/R) were assessed using MTT assays and immunofluorescence staining. The impacts of 5-FU and/or BEZ235 on GC cell cycle progression and cell migration were assessed via flow cytometry analyses and wound healing assays, respectively. GC tissues were collected from patients with GC sensitive or refractory to 5-FU chemotherapy. RT-qPCR and western blot were conducted to measure PI3K, AKT, and mTOR levels in GC cells or tissues.</p><p><strong>Results: </strong>After 5-FU treatment, GC cells displayed 5-FU resistance and the viability of drug-resistant cells (MKN-45/R and MKN-74/R) was higher than that of parental cells (MKN-45 and MKN-74). The IC50 values for MKN-45 and MKN-45/R were 8.93 ug/ml and 140 ug/ml, and the values for MKN-74 and MKN-74/R were 3.93 ug/ml and 114.29 ug/ml. Additionally, the PI3K/Akt/mTOR signaling pathway was activated in drug-resistant GC cells and tumor tissues of patients refractory to 5-FU chemotherapy, as evidenced by high PI3K, Akt, and mTOR levels in MKN-45/R, MKN-74/R, and GC tissues resistant to 5-FU. BEZ235 promoted cell cycle arrest and suppressed the migration of GC cells. Moreover, the combination of BEZ235 and 5-FU led to more effective suppressive influence on cell cycle progression and cell migration relative to the single 5-FU or BEZ235 treatment.</p><p><strong>Conclusions: </strong>Silencing of the PI3K/Akt/mTOR signaling pathway suppressed the 5-FU resistance of GC cells.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3640-3654"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138299625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"METTL3 Mediated MALAT1 m6A Modification Promotes Proliferation and Metastasis in Osteosarcoma Cells.","authors":"Yuanzhuang Zhang, Yeqiu Xu, Guanzhen Qiu, Yinzhou Luo, Yuxin Bao, Jie Lu, Tao Wang, Yong Wang","doi":"10.1007/s12033-023-00953-2","DOIUrl":"10.1007/s12033-023-00953-2","url":null,"abstract":"<p><strong>Background: </strong>As one of the most ubiquitous types of posttranscriptional modification, N6-methyladenosine (m6A) is extensively implicated in almost all types of cancers, including osteosarcoma. Our previous research partially uncovered the role of Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) in osteosarcoma. However, the relationships between methyltransferase-like 3 (METTL3) and noncoding RNAs modified by METTL3, especially MALAT1, in osteosarcoma remain obscure.</p><p><strong>Methods: </strong>The expression of METTL3 in osteosarcoma was evaluated by online bioinformatics analysis, immunohistochemical (IHC) staining, western blotting (WB), and reverse transcription-quantitative PCR (RT‒qPCR). Cell Counting Kit 8 (CCK-8) and Transwell assays were used to evaluate the cell proliferation and invasion abilities. The expression of MALAT1 in osteosarcoma was evaluated by online bioinformatics analysis and RT‒qPCR analysis. m6A methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) was used to detect m6A modification changes in MALAT1. An actinomycin D assay was used to study changes in the stability of MALAT1.</p><p><strong>Results: </strong>METTL3 was upregulated in osteosarcoma tissues and cell lines. Functionally, METTL3 promoted the proliferation and migration of osteosarcoma cells. Moreover, a clear positive correlation was found between METTL3 and MALAT1 expression, and MALAT1 was upregulated in osteosarcoma tissues and cells. Mechanistically, the presence of m6A modification sites in MALAT1 and METTL3-mediated m6A modification increased the stability of MALAT1 in osteosarcoma cells and promoted their proliferation and migration.</p><p><strong>Conclusion: </strong>In this study, it was concluded that in osteosarcoma cells, METTL3, acting as an oncogene, promoted m6A modification of MALAT1, increased the stability of MALAT, and enhanced MALAT1-mediated oncogenic function.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3538-3548"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66784085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Green Synthesis and Characterization of Silver Nanoparticles from Eclipta alba and Its Activity Against Triple-Negative Breast Cancer Cell Line (MDA-MB-231).","authors":"Suresh Thanjavur Mani, P Jayakumar, Marimuthu E Pavithra, K Saranya, Thirumalaisamy Rathinavel, Subramanian Ammashi","doi":"10.1007/s12033-023-00959-w","DOIUrl":"10.1007/s12033-023-00959-w","url":null,"abstract":"<p><p>Triple-negative breast cancer (TNBC) doesn't have well-defined molecular targets making it unable to treat with chemotherapy also have faster metastatic rate and worse survival rate. In the current study we aim to target TNBC through eco-friendly green synthesized silver nanoparticles having anti-cancer phytoconstituents from the traditional anti-cancer medicinal plant Eclipta alba. Green synthesized silver nanoparticles (AgNPs) are agglomerates of spherical shaped 40-60 nm sized showing characteristic light absorption at 437 nm, banding pattern at 1479, 1285, 1036, and 471 showing and further X-ray diffraction pattern confirm face-centered cubic crystal silver structure exist in the green synthesized silver nanoparticle preparation. Further in vitro anti-oxidant analysis results revealed that green synthesized AgNPs showed 2.6-fold higher anti-oxidant potential (IC50 15.70 g/ml) than that of aqueous plant leaf extract (IC50 39.80 g/ml). In MTT cytotoxicity analysis Eclipta alba plant extract and AgNPs both display dose-dependent cytotoxicity against triple-negative breast cancer cells (MDA-MB-231), although their IC₅₀ values differ substantially, at 105.80 µg/ml and 77.20 g/ml, respectively. Finally, AgNPs from Eclipta alba tested for anti-leishmanial activity and it showed 91.36 ± 1.05 for promastigotes and 76.62 ± 0.95 for amastigotes at the highest dose of 400 g/ml. Altogether present data showed that Eclipta alba leaf extract actively bonded with silver nanoparticles suppresses the MDA-MB-231 cells growth through high antioxidant characters and anti-leishmanial activity. From together we confirm that Eclipta alba was recommended to a future therapeutic drug and agent to control breast cancer in the clinical level.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3597-3607"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138295493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circular RNA PIP5K1A Promotes Glucose and Lipid Metabolism Disorders and Inflammation in Type 2 Diabetes Mellitus.","authors":"Ge Song, YiQian Zhang, YiHua Jiang, Huan Zhang, Wen Gu, Xiu Xu, Jing Yao, ZhengFang Chen","doi":"10.1007/s12033-023-00954-1","DOIUrl":"10.1007/s12033-023-00954-1","url":null,"abstract":"<p><p>Disorders of glucose and lipid metabolism are an important cause of type 2 diabetes mellitus (T2DM). Identifying the molecular mechanism of metabolic disorders is key to the treatment of T2DM. The study was to investigate the effect of circRNA PIP5K1A (circPIP5K1A) on glucose and lipid metabolism and inflammation in T2DM rats. A T2DM rat model was established, and then the T2DM rats were injected with lentiviral vectors that interfere with circPIP5K1A, miR-552-3p, or ENO1 expression. Fasting blood glucose (FBG) and fasting insulin (FINS) levels of rats were detected by an automatic analyzer and insulin detection kit, and HOMA-IR was calculated. Lipid metabolism was assessed by measuring serum levels of TG, TC, LDL-C, leptin, and resistin. Serum levels of inflammatory factors (TNF-α and IL-6) were detected by ELISA. The pathological conditions of pancreatic tissue were observed by HE staining. circPIP5K1A, miR-552-3p and ENO1 levels were recorded. The experimental results showed that circPIP5K1A and ENO1 were up-regulated, and miR-552-3p was down-regulated in T2DM rats. Down-regulating circPIP5K1A or up-regulating miR-552-3p reduced blood glucose and lipid levels, inhibited inflammation, and improved pancreatic histopathological changes in T2DM rats. In addition, up-regulating ENO1 rescued the ameliorating effects of down-regulated circPIP5K1A on T2DM rats. In general, downregulating circPIP5K1A improves insulin resistance and lipid metabolism disorders and inhibits inflammation by targeting miR-552-3p to mediate ENO1 expression.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3549-3558"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"107591783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive Analysis of the Complete Chloroplast Genome of Cinnamomum daphnoides (Lauraceae), An Endangered Island Endemic Plant.","authors":"Hong Zhu, Hepeng Li","doi":"10.1007/s12033-023-00950-5","DOIUrl":"10.1007/s12033-023-00950-5","url":null,"abstract":"<p><p>Cinnamomum daphnoides (Siebold & Zucc 1846) is a rare and endangered island species with a unique Sino-Japanese distribution pattern. However, inormation regarding the species' chloroplast (cp) genome, structural features, and the phylogenetic relationship is still lacking. We utilized high-throughput sequencing technology to assemble and annotate the first cp genome of C. daphnoides (GenBank OR654104), followed by genomic characterization and phylogenetic analysis to fill the gaps in this species' cp genome. Our analysis showed that the cp genome has a quadripartite structure spanning 152,765 bp with a GC content of 39.15%. The genome encodes 126 genes, which include 36 tRNA genes, 8 rRNA genes, and 82 mRNA genes. Specifically, 44 genes are related to photosynthesis, 59 are associated with self-replication, six are other genes, and four have unknown functionality. The Codon usage bias in the genome exhibits a preference for A/U bases. We identified 29 interspaced repeat sequences that belonging to three types of repeat sequences. A total of 217 cpSSR loci were detected with single nucleotide repeats (59.91%) being the most frequent loci, mainly composed of A/T repeats. Our selection pressure analysis revealed that the ycf2 gene experienced strong positive selection (Ka/Ks = 1.81, P > 0.844). Further, we identified three highly variable fragments (psbM, psbT, and ycf1) that can be utilized as specific DNA barcoding markers for species definition and population genetic studies. We conducted boundary analysis, which showed that the structure and gene sequence of the two species were highly conserved. Finally, our phylogenetic analysis supports that C. daphnoides is close to C. cassia in the Cinnamomum genes, indicating that the two species share a common ancestry. Overall, providing genomic information on C. daphnoides will be beneficial for the conservation and utilization of endangered plant genetic resources. It will also serve as a reference for the identification of species and the phylogenetic analysis of Cinnamomum. This information will be useful in future research.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3514-3525"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71483837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}