scholarly journals Exploration of the effects of a degS mutant on the growth of Vibrio cholerae and the global regulatory function of degS by RNA sequencing

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7959
Author(s):  
Jian Huang ◽  
Yuxi Chen ◽  
Jie Chen ◽  
Changjin Liu ◽  
Tao Zhang ◽  
...  

Background DegS is a periplasmic serine protease that is considered to be the initiator of the σE stress response pathway, and this protein plays an important role in the regulation of the stress response in E. coli. However, knowledge of the biological function and global regulatory network of DegS in Vibrio cholerae remains limited. In this study, we aimed to characterize the molecular functions and further investigate the regulatory network of degS in V. cholerae. Methods A deletion mutant of degS was constructed in the V. cholerae HN375 strain. Bacterial colony morphology was observed by a plate-based growth experiment, and bacterial growth ability was observed by a growth curve experiment. High-throughput RNA sequencing (RNA-Seq) technology was used to analyze the differential transcriptomic profiles between the wild-type and degS mutant strains. Gene ontology (GO), pathway analysis and Gene-Act-network analysis were performed to explore the main functions of the differentially expressed genes. Quantitative real-time PCR (qRT-PCR) was performed to validate the reliability and accuracy of the RNA-Seq analysis. The complementation experiments were used to test the roles of degS and ropS in the small colony degS mutant phenotype. Results When degS was deleted, the degS mutant exhibited smaller colonies on various media and slower growth than the wild-type strain. A total of 423 differentially expressed genes were identified, including 187 genes that were upregulated in the degS mutant compared to the wild-type strain and 236 genes that were relatively downregulated. GO categories and pathway analysis showed that many differentially expressed genes were associated with various cellular metabolic pathways and the cell cycle. Furthermore, Gene-Act network analysis showed that many differentially expressed genes were involved in cellular metabolic pathways and bacterial chemotaxis. The cAMP-CRP-RpoS signaling pathway and the LuxPQ signal transduction system were also affected by the degS mutant. The expression patterns of nine randomly selected differentially expressed genes were consistent between the qRT-PCR and RNA-seq results. The complementation experiments showed that the small colony degS mutant phenotype could be partially restored by complementation with the pBAD24-degS or pBAD24-rpoS plasmid. Discussion These results suggest that the degS gene is important for normal growth of V. cholerae. Some of the differentially expressed genes were involved in various cellular metabolic processes and the cell cycle, which may be associated with bacterial growth. Several new degS-related regulatory networks were identified. In addition, our results suggested that the cAMP-CRP-RpoS signaling pathway may be involved in the small colony degS mutant phenotype. Overall, we believe that these transcriptomic data will serve as useful genetic resources for research on the functions of degS in V. cholerae.

Author(s):  
Yuanyuan Zhao ◽  
Guoqing Cao ◽  
Pengfei Gao ◽  
Guifang Jia ◽  
Fei Yang ◽  
...  

To explore the differentially expressed mRNAs between oxidative and glycolytic muscles, Qianbei black pigs were slaughtered and longissimus dorsi muscle (LDM) and psoas major muscle (PMM) were selected and sequenced using Illumina Hiseq TM 4000. Bioinformatics analysis and differentially expressed genes were analyzed by GO and KEGG. qRT-PCR was used to validate the RNA-seq result. As a result, 69 differentially expressed genes were identified, with 46 down regulated genes and 23 up regulated genes in LDM versus PMM, which were categorized into 44 functional groups under three GO classifications. KEGG pathway analysis revealed 20 pathways were enriched. qRT-PCR shows the expression trends of ND6, MYH7, TBX1, FOS and SLC7A5 are consist with the RNA-seq result. We speculated these five genes may involve in differentiation of muscle cells, metabolism of carbohydrate and lipid, deposits of intramuscular fat and transformation of different types of muscle fibers.


2019 ◽  
Author(s):  
Akanksha Rajput ◽  
Manoj Kumar

AbstractThe Nipah virus is responsible various outbreaks among countries of south east Asia, most recent is in Kerala, India. It is considered to be highly contagious and having a range of vectors for transmission. The condition worsens due to the lack of effective inhibitors. This study is first study, which focused to detect the differentially expressed genes among two different NiV studies from 2012 and 2017. The transcriptomic profiling data were retrieved from the sequence archives. The multivariate gene enrichment analyses were performed on the log transformed data from them using pathway, gene ontology, disease, reactome, etc. The comparison study suggests that the down regulated differentially expressed genes are common among them as compared to up regulated ones with statistical significance. However, among the diseased category the upregulated genes are mostly from metabolic pathways and diseased category like metabolic pathways, heart failure, cholesterol metabolism while the downregulated genes linked to various cancers, and viral diseases like hepatitis, dengue, influenza, etc. We found various small molecules mapped in the pathways which are differentially expressed among the studies, which could be targeted so as to control the Nipah infection. In order to design the inhibitors, our study would be useful to extract the effective and broad-spectrum drug targets.


Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2374
Author(s):  
Joanna Sajewicz-Krukowska ◽  
Jan Paweł Jastrzębski ◽  
Maciej Grzybek ◽  
Katarzyna Domańska-Blicharz ◽  
Karolina Tarasiuk ◽  
...  

Astrovirus infections pose a significant problem in the poultry industry, leading to multiple adverse effects such as a decreased egg production, breeding disorders, poor weight gain, and even increased mortality. The commonly observed chicken astrovirus (CAstV) was recently reported to be responsible for the “white chicks syndrome” associated with an increased embryo/chick mortality. CAstV-mediated pathogenesis in chickens occurs due to complex interactions between the infectious pathogen and the immune system. Many aspects of CAstV–chicken interactions remain unclear, and there is no information available regarding possible changes in gene expression in the chicken spleen in response to CAstV infection. We aim to investigate changes in gene expression triggered by CAstV infection. Ten 21-day-old SPF White Leghorn chickens were divided into two groups of five birds each. One group was inoculated with CAstV, and the other used as the negative control. At 4 days post infection, spleen samples were collected and immediately frozen at −70 °C for RNA isolation. We analyzed the isolated RNA, using RNA-seq to generate transcriptional profiles of the chickens’ spleens and identify differentially expressed genes (DEGs). The RNA-seq findings were verified by quantitative reverse-transcription PCR (qRT-PCR). A total of 31,959 genes was identified in response to CAstV infection. Eventually, 45 DEGs (p-value < 0.05; log2 fold change > 1) were recognized in the spleen after CAstV infection (26 upregulated DEGs and 19 downregulated DEGs). qRT-PCR performed on four genes (IFIT5, OASL, RASD1, and DDX60) confirmed the RNA-seq results. The most differentially expressed genes encode putative IFN-induced CAstV restriction factors. Most DEGs were associated with the RIG-I-like signaling pathway or more generally with an innate antiviral response (upregulated: BLEC3, CMPK2, IFIT5, OASL, DDX60, and IFI6; downregulated: SPIK5, SELENOP, HSPA2, TMEM158, RASD1, and YWHAB). The study provides a global analysis of host transcriptional changes that occur during CAstV infection in vivo and proves that, in the spleen, CAstV infection in chickens predominantly affects the cell cycle and immune signaling.


Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1011
Author(s):  
Junping Xu ◽  
Chang Ho Ahn ◽  
Ju Young Shin ◽  
Pil Man Park ◽  
Hye Ryun An ◽  
...  

Toluene is an industrial raw material and solvent that can be found abundantly in our daily life products. The amount of toluene vapor is one of the most important measurements for evaluating air quality. The evaluation of toluene scavenging ability of different plants has been reported, but the mechanism of plant response to toluene is only partially understood. In this study, we performed RNA sequencing (RNA-seq) analysis to detect differential gene expression in toluene-treated and untreated leaves of Ardisiapusilla. A total of 88,444 unigenes were identified by RNA-seq analysis, of which 49,623 were successfully annotated and 4101 were differentially expressed. Gene ontology analysis revealed several subcategories of genes related to toluene response, including cell part, cellular process, organelle, and metabolic processes. We mapped the main metabolic pathways of genes related to toluene response and found that the differentially expressed genes were mainly involved in glycolysis/gluconeogenesis, starch and sucrose metabolism, glycerophospholipid metabolism, carotenoid biosynthesis, phenylpropanoid biosynthesis, and flavonoid biosynthesis. In addition, 53 transcription factors belonging to 13 transcription factor families were identified. We verified 10 differentially expressed genes related to metabolic pathways using quantitative real-time PCR and found that the results of RNA-seq were positively correlated with them, indicating that the transcriptome data were reliable. This study provides insights into the metabolic pathways involved in toluene response in plants.


2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi189-vi189
Author(s):  
Yosuke Shimazu ◽  
Agila Somasundaram ◽  
Daniel Brat ◽  
Oren Becher

Abstract Diffuse intrinsic pontine glioma (DIPG) is an incurable brain tumor that arises in the pons of children. Recent studies using single cell RNA-seq and enhancer analysis of DIPG tumor cells, together with analysis of the developing human pons, strongly suggest that an oligodendrocyte progenitor cell is the most likely cell-of-origin for DIPG. Here we describe a novel mouse model by expressing PDGF-B, with H3.3K27M or H3.3 wild-type in Olig2-expressing progenitors via injection into the 4th ventricle using Olig2-tva-cre;p53fl/fl mice. H3.3K27M tumors have high rate of Ki-67, Sox2, and Olig2 positivity and show a higher rate of leptomeningeal dissemination than H3.3 wild-type tumors (95.2% vs 68.8%, p=0.0303) and mice harboring H3.3K27M tumors demonstrate a significantly shorter survival period than those harboring H3.3 wild-type tumors (31 days vs. 37 days, p=0.0473). While there is not any difference in survival between mice harboring PDGF-B; p53 wild-type; H3.3K27M tumors and those harboring PDGF-B; p53 wild-type; H3.3 wild-type tumors at the 6-month endpoint, we found that H3.3K27M tumors show a higher rate of high-grade glioma than H3.3 wild-type tumors (100% vs. 41.7%, p=0.0017). RNA-seq analysis identified 25 significantly differentially expressed genes with 23 upregulated and 2 downregulated genes in the PDGF-B; p53 null; H3.3K27M tumors compared with the H3.3 wild-type tumors. Phox2b, which is the most upregulated gene in the PDGF-B; p53 null; H3.3K27M tumors, was validated by qRT-PCR and expressed only in brainstem tumors and not expressed in tumors located in any other areas. IHC with Phox2b also revealed positivity in PDGF-B; p53 null; H3.3K27M tumors located only in the brainstem. Ongoing work includes validation of other significant differentially expressed genes as well as elucidation of their role in K27M-mediated gliomagenesis.


Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 467 ◽  
Author(s):  
Lilibeth Lanceta ◽  
Conor O'Neill ◽  
Nadiia Lypova ◽  
Xiahong Li ◽  
Eric Rouchka ◽  
...  

Acquired resistance to cyclin-dependent kinases 4 and 6 (CDK4/6) inhibition in estrogen receptor-positive (ER+) breast cancer remains a significant clinical challenge. Efforts to uncover the mechanisms underlying resistance are needed to establish clinically actionable targets effective against resistant tumors. In this study, we sought to identify differentially expressed genes (DEGs) associated with acquired resistance to palbociclib in ER+ breast cancer. We performed next-generation transcriptomic RNA sequencing (RNA-seq) and pathway analysis in ER+ MCF7 palbociclib-sensitive (MCF7/pS) and MCF7 palbociclib-resistant (MCF7/pR) cells. We identified 2183 up-regulated and 1548 down-regulated transcripts in MCF7/pR compared to MCF7/pS cells. Functional analysis of the DEGs using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database identified several pathways associated with breast cancer, including ‘cell cycle’, ‘DNA replication’, ‘DNA repair’ and ‘autophagy’. Additionally, Ingenuity Pathway Analysis (IPA) revealed that resistance to palbociclib is closely associated with deregulation of several key canonical and metabolic pathways. Further studies are needed to determine the utility of these DEGs and pathways as therapeutics targets against ER+ palbociclib-resistant breast cancer.


2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Lucia Seale ◽  
Vedbar Khadka ◽  
Mark Menor ◽  
Alexandru Sasuclark ◽  
Kyrillos Guirguis ◽  
...  

Abstract Objectives Selenium is a trace element critical for appropriate response to oxidative stress in cells. Once ingested, dietary selenium is mostly metabolized by the liver. Selenium is utilized to produce the amino acid selenocysteine, which can be incorporated into selenoproteins, most of them functioning in curbing reactive oxygen species. The enzyme selenocysteine lyase (Scly) decomposes selenocysteine into selenide, and its highest expression and activity occurs in the liver. Disrupting the Scly gene (Scly−/−) resulted in overweight mice with hyperlipidemia, hyperinsulinemia and glucose intolerance, phenotype traits that were aggravated by a selenium-deficient diet. In the liver, Scly−/−mice had lower hepatic selenium levels than their wild-type mice counterparts. Our objective was to identify differentially expressed genes and pathways in Scly−/- mice livers affected by dietary selenium levels. Methods Scly−/- and wild-type mice were fed diets containing 0.08 (mildly low) or 0.25 (adequate) ppm of sodium selenite. We extracted total RNA from livers with a commercial kit. High-quality RNA (RIN ≥ 7) as assessed by a BioAnalyzer was employed in RNA-sequencing. RNA-Seq data analysis was performed on Partek flow software followed by pathway analysis using Ingenuity Pathway Analysis software. Validation of results was pursued by real-time RT-qPCR using specific primer sets. Results Hepatic RNA-Seq analysis revealed 52 genes differentially regulated by Scly disruption and low dietary selenium levels, encompassing 41 pathways, including PXR/RXR activation, LPS/IL-1-mediated inhibition of RXR function, xenobiotic metabolism signaling, nicotine degradation, adipogenesis, and acyl-CoA hydrolysis. Ten differentially expressed genes were validated by real-time RT-qPCR, including Selenobp2, Eif4ebp3, Mt1, and Mt2. Conclusions We identified pathways and validated genes in the Scly−/- mouse liver that are implicated in the metabolic phenotype displayed by this model on a low selenium diet. Funding Sources This project was supported by the National Institutes of Health (NIH) grants U54MD007601 Ola Hawaii (subproject 5544), P30-CA071789–128, R01DK47320, and P20GM103466. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuanxiang Lu ◽  
Wensen Li ◽  
Ge Liu ◽  
Yongbo Yang ◽  
Erwei Xiao ◽  
...  

Abstract Background Duodenal papilla carcinoma (DPC) is a rare malignancy of the gastrointestinal tract with high recurrence rate, and the pathogenesis of this highly malignant neoplasm is yet to be fully elucidated. This study aims to identify key genes to further understand the biology and pathogenesis underlying the molecular alterations driving DPC, which could be potential diagnostic or therapeutic targets. Methods Tumor samples of three DPC patients were collected and integrating RNA-seq analysis of tumor tissues and matched normal tissues were performed to discover differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were carried out to understand the potential bio-functions of the DPC differentially expressed genes (DEGs). Protein–protein interaction (PPI) network was constructed for functional modules analysis and identification of hub genes. qRT-PCR of clinical samples was conducted to validate the expression level of the hub genes. Results A total of 110 DEGs were identified from our RNA-seq data, GO and KEGG analyses showed that the DEGs were mainly enriched in multiple cancer-related functions and pathways, such as cell proliferation, IL-17signaling pathway, Jak-STAT signaling pathway, PPAR signaling pathway. The PPI network screened out five hub genes including IL-6, LCN2, FABP4, LEP and MMP1, which were identified as core genes in the network and the expression value were validated by qRT-PCR. The hub genes identified in this work were suggested to be potential therapeutic targets of DPC. Discussion The current study may provide new insight into the exploration of DPC pathogenesis and the screened hub genes may serve as potential diagnostic indicator and novel therapeutic target.


2020 ◽  
Vol 16 (5) ◽  
pp. 635-642 ◽  
Author(s):  
Yuchi Zhang ◽  
Xinyu Wu ◽  
Cong Zhao ◽  
Kai Li ◽  
Yi Zheng ◽  
...  

Background: Molecular characterization of insulin resistance, a growing health issue worldwide, will help to develop novel strategies and accurate biomarkers for disease diagnosis and treatment. Objective: Integrative analysis of gene expression profiling and gene regulatory network was exploited to identify potential biomarkers early in the development of insulin resistance. Methods: RNA was isolated from livers of animals at three weeks of age, and whole-genome expression profiling was performed and analyzed with Agilent mouse 4×44K microarrays. Differentially expressed genes were subsequently validated by qRT-PCR. Functional characterizations of genes and their interactions were performed by Gene Ontology (GO) analysis and gene regulatory network (GRN) analysis. Results: A total of 197 genes were found to be differentially expressed by fold change ≥2 and P < 0.05 in BKS-db +/+ mice relative to sex and age-matched controls. Functional analysis suggested that these differentially expressed genes were enriched in the regulation of phosphorylation and generation of precursor metabolites which are closely associated with insulin resistance. Then a gene regulatory network associated with insulin resistance (IRGRN) was constructed by integration of these differentially expressed genes and known human protein-protein interaction network. The principal component analysis demonstrated that 67 genes in IRGRN could clearly distinguish insulin resistance from the non-disease state. Some of these candidate genes were further experimentally validated by qRT-PCR, highlighting the predictive role as biomarkers in insulin resistance. Conclusions: Our study provides new insight into the pathogenesis and treatment of insulin resistance and also reveals potential novel molecular targets and diagnostic biomarkers for insulin resistance.


2016 ◽  
Author(s):  
Shaoyin Fu ◽  
YunXia Qi ◽  
Xiaolong He ◽  
Lai Da ◽  
biao Wang ◽  
...  

AbstractWool is one of the most important animal fibers in the textile industry and the diameter directly affects its economic value. However, the molecular mechanisms underlying the wool diameter have not been fully elucidated. In the present study, high-throughput RNA-Seq technology was employed to explore the skin transcriptome using 3 sheep with fine wool (fiber diameter, FD<21.0μm) and 3 sheep with coarse wool (fiber diameter, FD>27.0μm). In total, 28,607,228 bp clean reads were obtained, and 78.88%+/-3.84% was uniquely aligned to the reference genome across the six samples. In total, 19,914 mRNA transcripts were expressed (FPKM>0) in the six skin samples, among which there were certain well-known genes affecting the skin hair cycle, such as KRTAP7-1, KRT14, Wnt10b, Wnt2b, β-catenin, and FGF5. Furthermore, 467 expressed genes were significantly differentially expressed between the two groups, including 21 genes up-regulated and 446 genes down-regulated in the sheep with the smaller fiber diameter. To verify the results, 13 differentially expressed genes were randomly selected to validate the expression patterns using qRT-PCR, and the correlation between the mRNA expression level from qRT-PCR and RNA-Seq data was 0.999 ( P<0.05). These differentially expressed genes were particularly enriched in GO processes related to lipid metabolism, skin development, differentiation, and immune function (P<0.05). The biological processes were involved in collagen catabolism, negative regulation of macromolecule metabolism, steroid hormone stimulation and lipid metabolism. A significant KEGG pathway involving the “metabolism of lipids and lipoproteins” was also enriched. This study revealed that the lipid metabolism might constitute one of the major factors related to wool diameter.


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