Comparative Transcriptomic Profiling of Yersinia enterocolitica O:3 and O:8 Reveals Major Expression Differences of Fitness- and Virulence-Relevant Genes Indicating Ecological Separation

Abstract

Yersinia enterocolitica is a zoonotic pathogen and an important cause of bacterial gastrointestinal infections in humans. Large-scale population genomic analyses revealed genetic and phenotypic diversity of this bacterial species, but little is known about the differences in the transcriptome organization, small RNA (sRNA) repertoire, and transcriptional output. Here, we present the first comparative high-resolution transcriptome analysis of Y. enterocolitica strains representing highly pathogenic phylogroup 2 (serotype O:8) and moderately pathogenic phylogroup 3 (serotype O:3) grown under four infection-relevant conditions. Our transcriptome sequencing (RNA-seq) approach revealed 1,299 and 1,076 transcriptional start sites and identified strain-specific sRNAs that could contribute to differential regulation among the phylogroups. Comparative transcriptomics further uncovered major gene expression differences, in particular, in the temperature-responsive regulon. Multiple virulence-relevant genes are differentially regulated between the two strains, supporting an ecological separation of phylogroups with certain niche-adapted properties. Strong upregulation of the ystA enterotoxin gene in combination with constitutive high expression of cell invasion factor InvA further showed that the toxicity of recent outbreak O:3 strains has increased. Overall, our report provides new insights into the specific transcriptome organization of phylogroups 2 and 3 and reveals gene expression differences contributing to the substantial phenotypic differences that exist between the lineages. IMPORTANCE Yersinia enterocolitica is a major diarrheal pathogen and is associated with a large range of gut-associated diseases. Members of this species have evolved into different phylogroups with genotypic variations. We performed the first characterization of the Y. enterocolitica transcriptional landscape and tracked the consequences of the genomic variations between two different pathogenic phylogroups by comparing their RNA repertoire, promoter usage, and expression profiles under four different virulence-relevant conditions. Our analysis revealed major differences in the transcriptional outputs of the closely related strains, pointing to an ecological separation in which one is more adapted to an environmental lifestyle and the other to a mostly mammal-associated lifestyle. Moreover, a variety of pathoadaptive alterations, including alterations in acid resistance genes, colonization factors, and toxins, were identified which affect virulence and host specificity. This illustrates that comparative transcriptomics is an excellent approach to discover differences in the functional output from closely related genomes affecting niche adaptation and virulence, which cannot be directly inferred from DNA sequences.

The Small Protein YmoA Controls the Csr System and Adjusts Expression of Virulence-Relevant Traits of Yersinia pseudotuberculosis

“…This reprogramming implicates control of the Csr system which (i) plays a central role coordinating virulence gene expression with adaptative responses functions for different nutritional demands and stress resistance during infections (Lucchetti-Miganeh et al, 2008;Timmermans and Van Melderen, 2010;Bücker et al, 2014;Kusmierek and Dersch, 2017) and (ii) promotes transition between different physiological stages of pathogens, e.g., the switch from an acute to a chronic infection or from a transmission into an intracellular replication state (Molofsky and Swanson, 2003;Goodman et al, 2004;Laskowski and Kazmierczak, 2006;Mulcahy et al, 2008;Brencic and Lory, 2009;Sahr et al, 2009). One important environmental parameter, which induce global alterations in the gene expression and reprogramming between the different virulence-related stages of Yersinia, is temperature (Nuss et al, 2015;Schmühl et al, 2019). As YmoA turnover by the ClpP and Lon proteases is modulated by temperature (Jackson et al, 2004) (Supplementary Figure 8), it is tempting to speculate that YmoA plays a crucial role adjusting the Csr regulon in response to temperature which is pivotal for the establishment of a successful infection.…”

“…One important environmental parameter, which induce global alterations in the gene expression and reprogramming between the different virulence-related stages of Yersinia , is temperature ( Nuss et al, 2015 ; Schmühl et al, 2019 ). As YmoA turnover by the ClpP and Lon proteases is modulated by temperature ( Jackson et al, 2004 ) ( Supplementary Figure 8 ), it is tempting to speculate that YmoA plays a crucial role adjusting the Csr regulon in response to temperature which is pivotal for the establishment of a successful infection.…”

Urease Expression in Pathogenic Yersinia enterocolitica Strains of Bio-Serotypes 2/O:9 and 1B/O:8 Is Differentially Regulated by the OmpR Regulator

“…Secondly, we demonstrated that OmpR acts as a positive regulator of the ureABC, ureEF and ureGD operons in strain Ye9N, both at 26 • C and 37 • C. The OmpR-dependent regulation of urease cluster transcription was not observed in strain Ye8N, even though the ure loci of both strains exhibit high nucleotide sequence identity (98%). It has been relatively well established that although Y. enterocolitica strains possess the same virulence factors, their expression profiles can differ significantly (Schmühl et al, 2019). This may be the consequence of the finding that even small alterations in the content and organization of the genetic information may alter the expression pattern of virulence genes and their regulators in response to environmental factors (Uliczka et al, 2011;Erhardt and Dersch, 2015).…”

φYeO3-12 phage tail fiber Gp17 as a promising high specific tool for recognition of Yersinia enterocolitica pathogenic serotype O:3

“…YeO:3 appears to be an example of a zoonotic pathogen perfectly adapted to infect humans. It can be seen in the genomic variations of YeO:3 that streamline the physiology and metabolism of the bacteria (Schmühl et al, 2019 ). It is commonly known that the composition and modification of mucin is a critical defense mechanism in the prevention of pathogenic bacteria in the intestine.…”

“…In contrast, N -acetyl- d -glucosamine (GlcNAc) is the major amino sugar in human mucin. One of the adaptive features of the YeO:3 bacteria in contrast to the nonpathogenic Ye bacteria, is the ability to uptake GlcNAc and GalNAc as a source of carbon (Schmühl et al, 2019 ).…”