Dataset Information

Transcriptome analysis of S. maltophilia in the exponential and stationary phases and after a treatment with quorum sensing autoinducers.

ABSTRACT: Stenotrophomonas maltophilia is an emerging opportunistic multidrug-resistant pathogen frequently co-isolated with other relevant nosocomial pathogens in respiratory tract infections. S. maltophilia uses the endogenous DSF quorum sensing (QS) system to regulate virulence processes but can also respond to exogenous AHL signals produced by neighboring bacteria. A whole-transcriptome sequencing analysis was performed for S. maltophilia strain K279a in the exponential and stationary phases and in exponential cultures after a treatment with exogenous DSF or AHLs. Our first analysis reveals that during the beginning of the stationary phase 1673 genes are differentially expressed representing 37% of total genomic content. COG analysis showed that most of these genes were enriched for energetic metabolism processes and regulation of gene expression. In a second analysis, and after adding DSF or AHLs to cultures in exponential phase, 82 and 28 were found deregulated respectively, 22 of which were commonly upregulated by both autoinducers. Interestingly, among these genes affected by both DSFs and AHLs, 14 functional genes were also upregulated in the stationary phase. Gene functions regulated by all tested conditions include lipid and amino acid metabolism, stress response and signal transduction mechanisms, nitrogen and iron metabolism, and adaptation to microoxic conditions. Overall, our findings provide clues on the role that the QS could have in the transition from the exponential to the stationary phase in S. maltophilia and for the bacterial fitness for high-density growth.

ORGANISM(S): Stenotrophomonas maltophilia K279a

PROVIDER: GSE206442 | GEO | 2023/05/16

REPOSITORIES: GEO

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Project description:The M-NM-1-proteobacterium Sinorhizobium fredii NGR234 has an exceptionally wide host range as it forms nitrogen-fixing nodules with more legumes than any other known microsymbiont. Within its 6.9 Mbp genome it encodes two N-acyl-homoserine-lactone synthase genes (i.e. traI and ngrI) involved in the biosynthesis of two distinct autoinducer I-type molecules. Here we report on the construction of a NGR234-M-NM-^TtraI and a NGR234-M-NM-^TngrI mutant and the genome wide RNA-seq-based transcriptome analysis in the parent strain and in the two constructed mutants. A high-resolution RNA-seq analysis of early stationary phase cultures in the background of NGR234-M-NM-^TtraI suggested that up to 316 genes (4.9% of all predicted genes) were differentially expressed in the mutant vs. the parent strain. Similarly, in the background of NGR234-M-NM-^TngrI 466 differentially regulated genes (7.3% of all predicted genes) were identified. A considerable overlap in the gene expression pattern was uncovered between both mutants resulting in a common set of 186 genes which were almost identically regulated. Co-regulated genes that were linked to the ngrI- and the traI-dependent autoinducer regulatory circuits included 53 flagella biosynthesis genes and genes linked to EPS succinoglycan biosynthesis. Among the genes and ORFs that were differentially regulated in NGR234-M-NM-^TtraI were those linked to replication of the pNGR234a symbiotic plasmid and cytochrome c-related genes. In the NGR234-M-NM-^TngrI mutant biotin and pyrroloquinoline quinone (PQQ) biosynthesis genes were differentially expressed as well as the entire cluster of 21 genes linked to assembly of the NGR234 type three secretion system II (T3SS-II). We also discovered that genes responsible for octopine catabolism in NGR234 are strongly repressed in the presence of high levels of N-acyl-homoserine-lactones (AHLs). Surprisingly, only few truly symbiosis-related genes were identified that appeared to be quorum sensing regulated. Together with nodulation assays, the RNAseq-based findings suggested that QS-dependent gene regulation appears to be of higher relevance during non-symbiotic growth rather than for life within root nodules. In total 12 samples were analyzed (six different treatments with two independent samples), treatment A: NGR234 wild type strain in stationary phase, treatment B: NGR234 traI-mutant strain in stationary phase, treatment C: NGR234 ngrI-mutant strain in stationary phase, treatment D: NGR234 wild type strain in exponential phase, treatment E: NGR234 wild type supplemented with 0.05 M-BM-5M AHLs in exponential phase, treatment F: NGR234 wild type supplemented with 50 M-BM-5M AHLs in exponential phase

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Dataset Information

Transcriptome analysis of S. maltophilia in the exponential and stationary phases and after a treatment with quorum sensing autoinducers.

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