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Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions

ABSTRACT: Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with downstream target mRNAs to attenuate translation of mRNA into protein at the post-transcriptional level. In response to specific environmental changes, sRNAs can modulate the expression levels of target genes, thus enabling adaptation of cellular physiology. We profiled sRNA expression in the Gram-negative bacteria Burkholderia thailandensis cultured under 54 distinct growth conditions using a Burkholderia-specific microarray that contains probe sets to all intergenic regions (IGRs) greater than 90 bases. We identified 38 novel sRNAs and performed experimental validation on five sRNAs that play a role in adaptation of Burkholderia to cell stressors.

ORGANISM(S): Burkholderia thailandensis E264

PROVIDER: GSE56502 | GEO | 2014/04/05

SECONDARY ACCESSION(S): PRJNA243618

REPOSITORIES: GEO

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Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions

Project description:Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with downstream target mRNAs to attenuate translation of mRNA into protein at the post-transcriptional level. In response to specific environmental changes, sRNAs can modulate the expression levels of target genes, thus enabling adaptation of cellular physiology. We profiled sRNA expression in the Gram-negative bacteria Burkholderia thailandensis cultured under 54 distinct growth conditions using a Burkholderia-specific microarray that contains probe sets to all intergenic regions (IGRs) greater than 90 bases. We identified 38 novel sRNAs and performed experimental validation on five sRNAs that play a role in adaptation of Burkholderia to cell stressors. A custom Affymetrix microarray was designed using Burkholderia thailandensis E264 gene annotations from Pathema and included 8711 probe sets targeting 5557 protein-coding genes and 2908 IGRs longer than 90 bases on the plus strand. Experiments were performed in four classes of media: nutrient broth, M9-minimal media, Luria broth, and various host conditions such as brain-heart infusion, calf serum, or tryptic soy broth. There were 101 samples in four time course arrays measuring temperature increase, pH drop, salt stress, and phosphate starvation (21 distinct conditions). Each condition was grown at 37° C, except the initial temperature experiment at 25°C, and replicated five times. In order to survey a diverse range of environmental and stress conditions, another 10 replicated and 23 unreplicated treatments were also tested.

2014-04-05 | E-GEOD-56502 | biostudies-arrayexpress

Regulation of Choline Catabolism in Burkholderia thailandensis

Project description:Burkholderia thailandensis is a soil-dwelling bacterium that shares many metabolic pathways with the ecologically similar, but evolutionarily distant, Pseudomonas aeruginosa. Among the diverse nutrients it can utilize is choline, which can be converted into the osmoprotectant glycine betaine and further catabolized as a source of carbon and nitrogen, similar to P. aeruginosa. Orthologs of genes in the choline catabolic pathway in these two bacteria showed distinct differences in gene arrangement as well as an additional orthologous transcriptional regulator in B. thailandensis. In this study, we showed that multiple glutamine amidotransferase1 (GATase1)-containing AraC-family transcription regulators (GATRs) are involved in regulation of the B. thailandensis choline catabolic pathway (gbdR1, gbdR2, souR). Using genetic analyses and sequencing the transcriptome in the presence and absence of choline, we identified the likely regulons of gbdR1 (BTH_II1869) and gbdR2 (BTH_II0968). We also identified a functional ortholog for P. aeruginosa souR, a GATR that regulates the metabolism of sarcosine to glycine. GbdR1 is absolutely required for expression of the choline catabolic locus, similar to P. aeruginosa GbdR, while GbdR2 is important to increase expression of the catabolic locus. Additionally, the B. thailandensis SouR ortholog (BTH_II0994) is required for catabolism of choline and its metabolites as carbon sources, whereas in P. aeruginosa, SouR function can by bypassed by GbdR. The strategy employed by B. thailandensis represents a distinct regulatory solution to control choline catabolism and thus provides both an evolutionary counterpoint and an experimental system to compare the acquisition and regulation of this pathway during environmental growth and infection.

2016-07-12 | GSE81652 | GEO

Interferon inducible GBPs restrict Burkholderia thailandensis motility induced cell-cell fusion

Project description:Innate immunity responds to pathogens by producing alarm signals and activating pathways that make host cells inhospitable for pathogen replication. The intracellular bacterium Burkholderia thailandensis invades the cytosol, hijacks host actin, and induces cell fusion to spread to adjacent cells, forming multinucleated giant cells (MNGCs) which promotes bacterial replication. We show that type I interferon (IFN) restricts macrophage MNGC formation during B. thailandensis infection. Guanylate-binding proteins (GBPs) expressed downstream of type I IFN were required to restrict MNGC formation through inhibition of Arp2/3-dependent actin motility during infection. GTPase activity and the CAAX prenylation domain were required for GBP2 recruitment to B. thailandensis, which restricted bacterial actin polymerization required for MNGC formation. Consistent with in vitro macrophages, Gbp2-/- Gbp5-/-, GbpChr3-KO mice were more susceptible to intranasal infection with B. thailandensis than wildtype mice. Our findings reveal that IFN and GBPs play a critical role in restricting cell-cell fusion during infection

2021-08-23 | GSE143936 | GEO

Proteomic profiling of Burkholderia thailandensis during host infection

Project description:Burkholderia pseudomallei and B. mallei are the causative agents of melioidosis and glanders, respectively, and are often fatal to humans and animals. Owing to the high fatality rate, potential for spread by aerosolization, and the lack of efficacious therapeutics, B. pseudomallei and B. mallei are considered biothreat agents of concern. In this study, we investigate the proteome of Burkholderia thailandensis, a closely related surrogate for the two more virulent Burkholderia species, during infection of host cells, and compare to that of B. thailandensis in culture. Studying the proteome of intracellular Burkholderia spp. is expected to reveal molecular mechanisms of intracellular survival and host immune evasion; but proteomic profiling of intracellular Burkholderia is challenging. Proteomic analyses of intracellular bacteria are typically hindered by the overwhelming host protein content recovered from infected cultures. To address this problem, we have applied bio-orthogonal noncanonical amino acid tagging (BONCAT) to B. thailandensis, enabling the enrichment of newly expressed bacterial proteins from virtually any growth condition, most importantly intracellular contexts. In this study, we show that B. thailandensis proteins were selectively labeled and efficiently enriched from infected host cells using BONCAT. We also demonstrate that this method can be used to label bacteria in situ by fluorescent tagging. Finally, we present a global proteomic profile of B. thailandensis as it infects host cells and a list of proteins that are differentially regulated in infection conditions as compared to bacterial monoculture. Among the identified proteins are quorum sensing regulated genes as well as homologs to previously identified virulence factors. This method provides a powerful tool to study the molecular processes during Burkholderia infection, a much-needed addition to the Burkholderia molecular toolbox.

2018-11-12 | PXD011042 | Pride

Burkholderia thailandensis stress response to 12-bis-THA

Project description:Examination of the 12-bis-THA stress response in Burkholderia thailandensis strain E555 to investigate its antimicrobial mechanism of action

2023-07-20 | PXD041456 | Pride

Burkholderia thailandensis

Project description:Burkholderia thailandensis Genome sequencing

| PRJNA611888 | ENA

Burkholderia thailandensis E264 proteome and its changes upon quorum sensing disruption

Project description:The proteome of Burkholderia thailandensis E264 was assessed by shotgun proteomics as well as the proteome of the strain after quorum sensing disruption.

2023-06-09 | PXD040565 | Pride

Validating the use of CRISPR interference for the modulation of glycosylation in Burkholderia thailandensis

Project description:To determine whether CRISPR interference can be used to modulate glycosylation in Burkholderia thailandensis

2023-03-20 | PXD036623 | Pride

Burkholderia thailandensis

Project description:Burkholderia thailandensis from Puerto Rico

| PRJNA575701 | ENA

Analysing the effects of glycosylation knockdown via CRISPR interference in Burkholderia thailandensis

Project description:To determine the effect of CRISPR interference-mediated silencing of glycosylation in Burkholderia thailandensis harbouring a pglL-targeted guide, and a nontarget guide using Data Independent Acquisition

2023-03-20 | PXD037595 | Pride

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