Phenotypic heterogeneity in Stenotrophomonas maltophilia K279a colony morphotypes WGS study
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ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1044130_1.fastq.gz | Fastqsanger.gz | |||
| ERR1044130_2.fastq.gz | Fastqsanger.gz | |||
| ERR1044140_1.fastq.gz | Fastqsanger.gz | |||
| ERR1044140_2.fastq.gz | Fastqsanger.gz | |||
| ERR1044150_1.fastq.gz | Fastqsanger.gz |
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Project description:Stenotrophomonas maltophilia K279a diverges into subpopulations with distinct but reversible phenotypes of small and big colonies when challenged with ampicillin. This observation is consistent with the formation of long cell chains during exponential growth phase and the occurrence of mainly coccoid– or rod-shaped cells in liquid media. Further, scanning electron micrographs of SMK279a revealed that cells formed gigantic outer membrane vesicles in response to β-lactam treatment. RNA-seq analysis of small vs. big colonies unveiled that cells regulate at least seven genes differentially among colony morphotypes. Among those were the blaL1 and blaL2 genes the most strongly regulated ones with an eleven- and six-fold increased transcription, respectively. Further studies with promoter fusions of blaL1 and blaL2 genes implied that expression of both genes is also subject to high levels of phenotypic heterogeneous expression on a single cell level. Additional RNA-seq analysis of this homogenously versus heterogeneously blaL2 expressing cells identified comE homologue as differentially expressed, in which by the expression of extra copies of comE in S. maltophilia K279a reduced the level of those cells that were in a blaL2-ON model to 1% or lower. Together with genome-wide sequence analysis of cells from the different colony morphotypes, the data presented here suggests that phenotypic heterogeneity in S. maltophilia K279a is a result of non-genetic variations within isogenic populations and also polymorphisms in this strain do not influence β-lactamase resistance phenotype.
2015-11-18 | GSE71735 | GEO
Project description:We sought to determine how a cystic fibrosis isolate of Stenotrophomonas maltophilia responds to relevant pH gradients (pH 5, 7, and 9) by growing the bacterium in phosphate buffered media and conducting RNAseq experiments. Our data suggests acidic conditions are stressful for strain FLR19, as it responded by increasing expression of stress-response and antibiotic-resistance genes.
2018-10-17 | GSE121347 | GEO
Project description:Phenotypic heterogeneity affects Stenotrophomonas maltophilia K279a colony morphotypes and β-lactamase expression
| PRJNA291965 | ENA
Project description:Phenotypic heterogeneity at the cellular level in response to various stresses, e.g., antibiotic treatment has been reported for a number of bacteria. In a clonal population, cell-to-cell variation may result in phenotypic heterogeneity that is a mechanism to survive changing environments including antibiotic therapy. Stenotrophomonas maltophilia has been frequently isolated from cystic fibrosis patients, can cause numerous infections in other organs and tissues, and is difficult to treat due to antibiotic resistances. S. maltophilia K279a produces the L1 and L2 ?-lactamases in response to ?-lactam treatment. Here we report that the patient isolate S. maltophilia K279a diverges into cellular subpopulations with distinct but reversible morphotypes of small and big colonies when challenged with ampicillin. This observation is consistent with the formation of elongated chains of bacteria during exponential growth phase and the occurrence of mainly rod-shaped cells in liquid media. RNA-seq analysis of small versus big colonies revealed differential regulation of at least seven genes among the colony morphotypes. Among those, bla L1 and bla L2 were transcriptionally the most strongly upregulated genes. Promoter fusions of bla L1 and bla L2 genes indicated that expression of both genes is also subject to high levels of phenotypic heterogeneous expression on a single cell level. Additionally, the comE homolog was found to be differentially expressed in homogenously versus heterogeneously bla L2 expressing cells as identified by RNA-seq analysis. Overexpression of comE in S. maltophilia K279a reduced the level of cells that were in a bla L2-ON mode to 1% or lower. Taken together, our data provide strong evidence that S. maltophilia K279a populations develop phenotypic heterogeneity in an ampicillin challenged model. This cellular variability is triggered by regulation networks including bla L1, bla L2, and comE.
| S-EPMC4667094 | biostudies-literature
Project description:Stenotrophomonas maltophilia is an important opportunistic pathogen affecting primarily hospitalized and immuno-compromised hosts. We constructed an hfq deletion mutant (Delta-hfq) of S. maltophilia, and compared the behaviour of wild-type and Delta-hfq S. maltophilia cells in a variety of assays. Differential RNA sequencing analysis (dRNA-seq) of RNA isolated from S. maltophilia wild-type and Delta-hfq strains showed that Hfq regulates expression of genes encoding flagellar and fimbrial components, transmembrane proteins, as well as enzymes involved in different metabolic pathways. Moreover, we analysed expression of several sRNAs identified by dRNA-seq in wild-type. The accumulation of two sRNAs was strongly reduced in the absence of Hfq. TEX (terminator exonuclease) treated and untreated libraries of the wild type and the Delta-hfq mutant were sequenced and compared
2012-10-02 | E-GEOD-39705 | biostudies-arrayexpress
Project description:The goal of this study was to elucidate genes that are employed by the bacterivorous nematode Caenorhabditis elegans to respond to the emerging nosocomial bacterial pathogen Stenotrophomonas maltophilia.
2018-02-01 | GSE107272 | GEO
Project description:Stenotrophomonas maltophilia is an important opportunistic pathogen affecting primarily hospitalized and immuno-compromised hosts. We constructed an hfq deletion mutant (Delta-hfq) of S. maltophilia, and compared the behaviour of wild-type and Delta-hfq S. maltophilia cells in a variety of assays. Differential RNA sequencing analysis (dRNA-seq) of RNA isolated from S. maltophilia wild-type and Delta-hfq strains showed that Hfq regulates expression of genes encoding flagellar and fimbrial components, transmembrane proteins, as well as enzymes involved in different metabolic pathways. Moreover, we analysed expression of several sRNAs identified by dRNA-seq in wild-type. The accumulation of two sRNAs was strongly reduced in the absence of Hfq.
2012-10-02 | GSE39705 | GEO
Project description:Stenotrophomonas maltophilia is an emerging multidrug resistance opportunistic pathogen affecting immunocompromised and hospitalized patients. S. maltophilia is an environmental bacterium which adapts to human body and causing infection. S. rhizophilia, a non-pathogenic and phylogenetic neighbour of S. maltophilia is unable to grow at human body temperature. Thus, to understand molecular mechanism underlying the adaptation of S. maltophilia at human body temperature, we performed the comparative transcriptome analysis of S.maltophilia at 28 °C (representative for the environmental niches) and 37 °C (representative for human body) by using RNA-Seq. The major temperature-induced genes include genes for Type IV secretion system, aerotaxis, and cation diffusion facilitator family transporter suggesting its potential role in the adaptation and virulence of S. maltophilia. The downregulated genes at 37 °C includes the genes for the cell motility, energy generation and metabolism, lipid metabolism, translation, amino acid metabolism and transport, replication and repair, inorganic ion and transport metabolism lipid metabolism, coenzyme metabolism.
2021-01-11 | GSE101926 | GEO
Project description:We calculated half-life values of mRNAs quantified by RNA-Seq by a suitable method of normalization. We determined the half-lives of more than 2200 mRNAs in the Stenotrophomonas maltophilia D457 wild-type strain and in an isogenic RNase G deficient mutant. Median half-lives were 2,74 and 3 min in the wild-type and the rng-deficient mutant respectively. We found an overall enhancement of half-life times of mRNAs when the gene encoding RNase G is lacking, showing that many RNAs are targets of RNase G in S. maltophilia. For achieving such goal, we propose a method for the normalization of RNA-Seq based studies on global bacterial mRNA decay.
2017-09-06 | GSE103467 | GEO
Project description:Biofilm formation by Escherichia coli was significantly inhibited when co-cultured with Stenotrophomonas maltophilia in static systems. Genes of E. coli involved in species interactions with S. maltophilia were identified in order to allow the study of the mechanisms of inhibited E. coli biofilm formation in co-culture. A total of 89 and 108 genes were identified as differentially expressed in mixed species cultures when growing as biofilm and as planktonic cultures, respectively, compared to the counterpart of pure cultured E. coli. Differential expression of certain identified genes was confirmed using E. coli reporter strains combined with single-cell based flow cytometry analysis. Co-culture with S. maltophilia affected genes involved in metabolism, signal transduction, cell wall composition, and biofilm formation of E. coli. Several selected genes were further confirmed as affecting E. coli biofilm formation in mixed species cultures with S. maltophilia. The data suggest that these genes were involved in species interactions between E. coli and S. maltophilia. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series.
2013-12-30 | E-GEOD-24915 | biostudies-arrayexpress