scholarly journals New insights into virulence mechanisms of rice pathogen Acidovorax avenae subsp. avenae strain RS-1 following exposure to ß-lactam antibiotics

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Bin Li ◽  
Mengyu Ge ◽  
Yang Zhang ◽  
Li Wang ◽  
Muhammad Ibrahim ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Extracellular Polymeric Substances ◽  
Expression Data ◽  
Rna Seq ◽  
Quantitative Real Time Pcr ◽  
Type Vi Secretion System ◽  
Pathogen Virulence ◽  
Type Vi Secretion ◽  
Genome Wide ◽  
Knockout Mutants

Abstract Recent research has shown that pathogen virulence can be altered by exposure to antibiotics, even when the growth rate is unaffected. Investigating this phenomenon provides new insights into understanding the virulence mechanisms of bacterial pathogens. This study investigates the phenotypic and transcriptomic responses of the rice pathogenic bacterium Acidovorax avenae subsp. avenae (Aaa) strain RS-1 to ß-lactam antibiotics especially Ampicillin (Amp). Our results indicate that exposure to Amp does not influence bacterial growth and biofilm formation, but alters the virulence, colonization capacity, composition of extracellular polymeric substances and secretion of Type VI secretion system (T6SS) effector Hcp. This attenuation in virulence is linked to unique or differential expression of known virulence-associated genes based on genome-wide transcriptomic analysis. The reliability of expression data generated by RNA-Seq was verified with quantitative real-time PCR of 21 selected T6SS genes, where significant down-regulation in expression of hcp gene, corresponding to the reduction in secretion of Hcp, was observed under exposure to Amp. Hcp is highlighted as a potential target for Amp, with similar changes observed in virulence-associated phenotypes between exposure to Amp and mutation of hcp gene. In addition, Hcp secretion is reduced in knockout mutants of 4 differentially expressed T6SS genes.

scholarly journals Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch

Forests ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 120
Author(s):  
Yijie Li ◽  
Song Chen ◽  
Yuhang Liu ◽  
Haijiao Huang
Keyword(s):  
Cell Cycle ◽  
Growth And Development ◽  
Betula Pendula ◽  
Cell Cycle Gene ◽  
Expression Data ◽  
Rna Seq ◽  
Specific Expression ◽  
Cell Cycles ◽  
Cell Cycle Genes ◽  
Genome Wide

Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during the plant’s growth and development. This analysis provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula Roth. Background and Objectives: The cell cycle factors not only influence cell cycles progression together, but also regulate accretion, division, and differentiation of cells, and then regulate growth and development of the plant. In this study, we identified the putative cell cycle genes in the B. pendula genome, based on the annotated cell cycle genes in Arabidopsis thaliana (L.) Heynh. It can be used as a basis for further functional research. Materials and Methods: RNA-seq technology was used to determine the transcription abundance of all cell cycle genes in xylem, roots, leaves, and floral tissues. Results: We identified 59 cell cycle gene models in the genome of B. pendula, with 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1, and BpWEE1. Conclusions: By combining phylogenetic analysis and tissue-specific expression data, we identified 17 core cell cycle genes in the Betulapendula genome.

scholarly journals YbeY controls the type III and type VI secretion systems and biofilm formation through RetS in Pseudomonas aeruginosa

2020 ◽  
Author(s):  
Yushan Xia ◽  
Congjuan Xu ◽  
Dan Wang ◽  
Yuding Weng ◽  
Yongxin Jin ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Type Iii Secretion ◽  
Biofilm Formation ◽  
Small Rnas ◽  
Type Iii Secretion System ◽  
Secretion System ◽  
Type Vi Secretion System ◽  
Chronic Infections ◽  
Type Iii ◽  
Type Vi Secretion

YbeY is a highly conserved RNase in bacteria and plays essential roles in the maturation of 16S rRNA, regulation of small RNAs (sRNAs) and bacterial responses to environmental stresses. Previously, we verified the role of YbeY in rRNA processing and ribosome maturation in Pseudomonas aeruginosa and demonstrated YbeY-mediated regulation of rpoS through a sRNA ReaL. In this study, we demonstrate that mutation of the ybeY gene results in upregulation of the type III secretion system (T3SS) genes as well as downregulation of the type VI secretion system (T6SS) genes and reduction of biofilm formation. By examining the expression of the known sRNAs in P. aeruginosa, we found that mutation of the ybeY gene leads to downregulation of the small RNAs RsmY/Z that control the T3SS, the T6SS and biofilm formation. Further studies revealed that the reduced levels of RsmY/Z are due to upregulation of retS. Taken together, our results reveal the pleiotropic functions of YbeY and provide detailed mechanisms of YbeY-mediated regulation in P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa causes a variety of acute and chronic infections in humans. The type III secretion system (T3SS) plays an important role in acute infection and the type VI secretion system (T6SS) and biofilm formation are associated with chronic infections. Understanding of the mechanisms that control the virulence determinants involved in acute and chronic infections will provide clues for the development of effective treatment strategies. Our results reveal a novel RNase mediated regulation on the T3SS, T6SS and biofilm formation in P. aeruginosa.

scholarly journals Contribution of the Pseudomonas fluorescens MFE01 Type VI Secretion System to Biofilm Formation

PLoS ONE ◽  
2017 ◽  
Vol 12 (1) ◽  
pp. e0170770 ◽  
Author(s):  
Mathias Gallique ◽  
Victorien Decoin ◽  
Corinne Barbey ◽  
Thibaut Rosay ◽  
Marc G. J. Feuilloley ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Biofilm Formation ◽  
Secretion System ◽  
Type Vi Secretion System ◽  
Type Vi Secretion

scholarly journals Molecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates

2020 ◽  
Vol 8 (3) ◽  
pp. 314
Author(s):  
Qianqian Li ◽  
Rebecca E. Cooper ◽  
Carl-Eric Wegner ◽  
Kirsten Küsel
Keyword(s):  
Hot Spots ◽  
Biofilm Formation ◽  
Extracellular Polymeric Substances ◽  
Molecular Mechanisms ◽  
Core Genome ◽  
Gene Clusters ◽  
Microbial Interactions ◽  
Aggregate Formation ◽  
Rna Seq ◽  
Metabolic Potential

Iron-rich pelagic aggregates (iron snow) are hot spots for microbial interactions. Using iron snow isolates, we previously demonstrated that the iron-oxidizer Acidithrix sp. C25 triggers Acidiphilium sp. C61 aggregation by producing the infochemical 2-phenethylamine (PEA). Here, we showed slightly enhanced aggregate formation in the presence of PEA on different Acidiphilium spp. but not other iron-snow microorganisms, including Acidocella sp. C78 and Ferrovum sp. PN-J47. Next, we sequenced the Acidiphilium sp. C61 genome to reconstruct its metabolic potential. Pangenome analyses of Acidiphilium spp. genomes revealed the core genome contained 65 gene clusters associated with aggregation, including autoaggregation, motility, and biofilm formation. Screening the Acidiphilium sp. C61 genome revealed the presence of autotransporter, flagellar, and extracellular polymeric substances (EPS) production genes. RNA-seq analyses of Acidiphilium sp. C61 incubations (+/− 10 µM PEA) indicated genes involved in energy production, respiration, and genetic processing were the most upregulated differentially expressed genes in the presence of PEA. Additionally, genes involved in flagellar basal body synthesis were highly upregulated, whereas the expression pattern of biofilm formation-related genes was inconclusive. Our data shows aggregation is a common trait among Acidiphilium spp. and PEA stimulates the central cellular metabolism, potentially advantageous in aggregates rapidly falling through the water column.

scholarly journals The LonA Protease Regulates Biofilm Formation, Motility, Virulence, and the Type VI Secretion System in Vibrio cholerae

2016 ◽  
Vol 198 (6) ◽  
pp. 973-985 ◽  
Author(s):  
Andrew Rogers ◽  
Loni Townsley ◽  
Ana L. Gallego-Hernandez ◽  
Sinem Beyhan ◽  
Laura Kwuan ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Biofilm Formation ◽  
Secretion System ◽  
Lon Protease ◽  
Human Pathogen ◽  
Type Vi Secretion System ◽  
Cyclic Diguanylate ◽  
Content Type ◽  
Infant Mouse ◽  
Type Vi Secretion

ABSTRACTThe presence of the Lon protease in all three domains of life hints at its biological importance. The prokaryotic Lon protease is responsible not only for degrading abnormal proteins but also for carrying out the proteolytic regulation of specific protein targets. Posttranslational regulation by Lon is known to affect a variety of physiological traits in many bacteria, including biofilm formation, motility, and virulence. Here, we identify the regulatory roles of LonA in the human pathogenVibrio cholerae. We determined that the absence of LonA adversely affects biofilm formation, increases swimming motility, and influences intracellular levels of cyclic diguanylate. Whole-genome expression analysis revealed that the message abundance of genes involved in biofilm formation was decreased but that the message abundances of those involved in virulence and the type VI secretion system were increased in alonAmutant compared to the wild type. We further demonstrated that alonAmutant displays an increase in type VI secretion system activity and is markedly defective in colonization of the infant mouse. These findings suggest that LonA plays a critical role in the environmental survival and virulence ofV. cholerae.IMPORTANCEBacteria utilize intracellular proteases to degrade damaged proteins and adapt to changing environments. The Lon protease has been shown to be important for environmental adaptation and plays a crucial role in regulating the motility, biofilm formation, and virulence of numerous plant and animal pathogens. We find that LonA of the human pathogenV. choleraeis in line with this trend, as the deletion of LonA leads to hypermotility and defects in both biofilm formation and colonization of the infant mouse. In addition, we show that LonA regulates levels of cyclic diguanylate and the type VI secretion system. Our observations add to the known regulatory repertoire of the Lon protease and the current understanding ofV. choleraephysiology.

scholarly journals Viewing RNA-seq data on the entire human genome

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 596 ◽  
Author(s):  
Eric M. Weitz ◽  
Lorena Pantano ◽  
Jingzhi Zhu ◽  
Bennett Upton ◽  
Ben Busby
Keyword(s):  
Web Application ◽  
Source Code ◽  
Gene Expression Omnibus ◽  
Expression Data ◽  
Rna Seq ◽  
Sequence Read Archive ◽  
Data Pipeline ◽  
Genome Wide ◽  
Small Team ◽  
Genome Wide Expression

RNA-Seq Viewer is a web application that enables users to visualize genome-wide expression data from NCBI’s Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. The application prototype was created by a small team during a three-day hackathon facilitated by NCBI at Brandeis University. The backend data pipeline was developed and deployed on a shared AWS EC2 instance. Source code is available at https://github.com/NCBI-Hackathons/rnaseqview.

scholarly journals Role of the Type VI Secretion System in the Pathogenicity of Pseudomonas syringae pv. actinidiae, the Causative Agent of Kiwifruit Bacterial Canker

2021 ◽  
Vol 12 ◽  
Author(s):  
Nana Wang ◽  
Ning Han ◽  
Runze Tian ◽  
Jiliang Chen ◽  
Xiaoning Gao ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Pseudomonas Syringae ◽  
Biofilm Formation ◽  
Wild Type Strain ◽  
Deletion Mutants ◽  
Wild Type ◽  
Type Vi Secretion System ◽  
Bacterial Competition ◽  
Type Vi Secretion

The type VI secretion system (T6SS), a macromolecular machine, plays an important role in the pathogenicity of many Gram-negative bacteria. However, the role of T6SS in the pathogenicity of Pseudomonas syringae pv. actinidiae (Psa), the pathogen of kiwifruit bacterial canker, is yet to be studied. Here, we found a T6SS gene cluster consisting of 13 core genes (A-J) in the genome of Psa M228 based on a genome-wide analysis. To determine whether the T6SS gene cluster affects the pathogenicity of Psa M228, T6SS and its 13 core gene deletion mutants were constructed and their pathogenicity was determined. The deletion mutants showed different degrees of reduction in pathogenicity compared with the wild-type strain M228; in tssM and tssJ mutants, pathogenicity was significantly reduced by 78.7 and 71.3%, respectively. The pathogenicity results were also confirmed by electron microscopy. To further confirm that the reduction in pathogenicity is related to the function of T6SS, we selected the T6SS gene cluster, comprising tssM and tssJ, for further analyses. Western blot results revealed that tssM and tssJ were necessary for hemolytic co-regulatory protein secretion, indicating that they encode a functional T6SS. Further, we explored the mechanism by which T6SS affects the pathogenicity of Psa M228. The ability of bacterial competition, biofilm formation, hydrogen peroxide tolerance, and proteolytic activity were all weakened in the deletion mutants M228ΔT6SS, M228ΔtssM, and M228ΔtssJ. All these properties of the two gene complementation mutants were restored to the same levels as those of the wild-type strain, M228. Quantitative real-time results showed that during the interaction between the deletion mutant M228ΔT6SS and the host, expression levels of T3SS transcriptional regulatory gene hrpR, structural genes hrpZ, hrcC, hopP1, and effector genes hopH1 and hopM1 were down-regulated at different levels. Taken together, our data provide evidence for the first time that the T6SS plays an important role in the pathogenicity of Psa, probably via effects on bacterial competition, biofilm formation, and environmental adaptability. Moreover, a complicated relationship exists between T6SS and T3SS.

scholarly journals The marine bacteriaShewanella frigidimarina NCIMB400 upregulates the type VI secretion system during early biofilm formation

2016 ◽  
Vol 8 (1) ◽  
pp. 110-121 ◽  
Author(s):  
Denis Linares ◽  
Natacha Jean ◽  
Perrine Van Overtvelt ◽  
Tassadit Ouidir ◽  
Julie Hardouin ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Secretion System ◽  
Type Vi Secretion System ◽  
Type Vi Secretion

scholarly journals Integrated analysis of transcriptome-wide m6A methylome of osteosarcoma stem cells enriched by chemotherapy

Epigenomics ◽  
2019 ◽  
Vol 11 (15) ◽  
pp. 1693-1715 ◽  
Author(s):  
Yongjie Wang ◽  
Lin Zeng ◽  
Chao Liang ◽  
Rui Zan ◽  
Weiping Ji ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Poor Prognosis ◽  
Integrated Analysis ◽  
Expression Data ◽  
Rna Seq ◽  
Quantitative Real Time Pcr ◽  
Gene Expression Data Analysis ◽  
Doxorubicin Treatment ◽  
Differentially Methylated Genes

Aim: To analyze the m6A methylome of osteosarcoma stem cells (OSCs). Materials & methods: Chemoresistant OSCs were enriched by doxorubicin treatment. Expression of m6A-related enzymes was detected by quantitative real-time-PCR and western blot. MeRIP-seq and RNA-seq were performed to identify differences in m6A methylation and gene expression. Data analysis was conducted to explore the modified genes and their clinical significance. Results: Three m6A-related enzymes were altered in OSCs. Differentially methylated genes were enriched in some pathways regulating pluripotency of stem cells. The expression of several candidate genes were found consistent with that in GSE33458 dataset, and associated with poor prognosis in osteosarcoma patients. Conclusion: m6A may play a role in the emergence and maintaining of OSCs and affect the prognosis.

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