Dual-seq transcriptomics reveals the battle for iron during Pseudomonas aeruginosa acute murine pneumonia

Damron, F. Heath; Oglesby-Sherrouse, Amanda G.; Wilks, Angela; Barbier, Mariette

doi:10.1038/srep39172

Cited by 130 publications

(140 citation statements)

References 90 publications

Supporting

Mentioning

135

Contrasting

Order By: Relevance

“…Remarkably, the proteins and genomic organization of the Has and Hxu CSS systems are highly conserved among P. aeruginosa clinical isolates (Supporting Information Dataset S2), which highlights the importance that sensing haem during infection may have for this pathogen. In accordance, expression of most P. aeruginosa haem genes is considerably induced in murine models of acute and chronic infections (Turner et al ., ; Damron et al ., ). Because a mutant lacking the HasR haem receptor has attenuated virulence (Damron et al ., ), blocking haem sensing and acquisition may be a promising strategy to combat P. aeruginosa infections, and our work has revealed important new information that could be used to achieve this aim.…”

Section: Discussionmentioning

confidence: 97%

Pseudomonas aeruginosa possesses three distinct systems for sensing and using the host molecule haem

Otero-Asman

García‐García

Civantos

et al. 2019

Environmental Microbiology

View full text Add to dashboard Cite

Summary Pathogens have developed several strategies to obtain iron during infection, including the use of iron‐containing molecules from the host. Haem accounts for the vast majority of the iron pool in vertebrates and thus represents an important source of iron for pathogens. Using a proteomic approach, we have identified in this work a previously uncharacterized system, which we name Hxu, that together with the known Has and Phu systems, is used by the human pathogen Pseudomonas aeruginosa to respond to haem. We show that the Has and Hxu systems are functional signal transduction pathways of the cell‐surface signalling class and report the mechanism triggering the activation of these signalling systems. Both signalling cascades involve an outer membrane receptor (HasR and HxuA respectively) that upon sensing haem in the extracellular medium produces the activation of an σECF factor in the cytosol. HxuA has a major role in signalling and a minor role in haem acquisition in conditions in which the HasR and PhuR receptors or other sources of iron are present. Remarkably, P. aeruginosa compensates the lack of the HasR receptor by increasing the production of HxuA, which underscores the importance of haem signalling for this pathogen.

show abstract

Section: Discussionmentioning

confidence: 97%

Pseudomonas aeruginosa possesses three distinct systems for sensing and using the host molecule haem

Otero-Asman

García‐García

Civantos

et al. 2019

Environmental Microbiology

View full text Add to dashboard Cite

show abstract

“…Pseudomonas aeruginosa, after lung tissue resection [51]. In another study, Peyer's patches from mice infected with Yersinia pseudotuberculosis were analyzed [52].…”

Section: Figure 1| Macromolecular Differences Between Cells Of Eukarymentioning

confidence: 99%

Omics in Aid of Host-pathogen Interaction Studies: A Bacterial Perspective

Fels¹,

Gevaert²,

Damme³

2017

Preprint

View full text Add to dashboard Cite

By providing useful tools to study host-pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, the depth of quantitative gene expression profiling has proven to be unsatisfactory when focusing on bacterial pathogens, thus preferentially requiring specific strategies or the development of novel methodologies based on complementary omics approaches. In this review, we focus on the difficulties encountered when making use of omics approaches to study bacterial pathogenesis. Besides, we review different omics strategies (i.e. transcriptomics, proteomics and secretomics) and their applications for studying interactions of pathogens with their host.

show abstract

“…Researchers use RNA-seq to study and monitor transcriptomic dynamics of host-pathogen interaction simultaneously under given conditions, and furthermore examine the strategies applied by the host and pathogen to compete for limited biochemical resources (Damron et al 2016;Darren et al 2017;Westermann et al 2017). For example, Nuss and colleagues (2017) developed an experimental approach that allows simultaneous monitoring of genome-wide infection-linked transcriptional alterations of the host and pathogen.…”

Section: Introductionmentioning

confidence: 99%

“…To differentiate human and mouse expression, the reads that mapped to both human and mouse genomes were removed, which resulted in loss of yields in each species (2-2.5% for human and 17-26% for mouse). Damron et al (2016) In recent investigations into the transcriptomics associated with resistance and susceptibility of wheat against fusarium head blight (FHB), the RNA-seq data contain reads from both wheat and the pathogen, Fusarium graminearum (F. graminearum) , Fauteux et al, 2019. In this paper, we propose a combo-genome alignment approach which is to map RNA-seq data to a combination of both host and pathogen genomes.…”

Section: Introductionmentioning

confidence: 99%

Strategy in wheat-Fusarium dual-genome RNA-seq data processing

Liu

Pan

et al. 2019

Preprint

View full text Add to dashboard Cite

In RNA-seq data processing, short read alignments are usually of one species against its own genome; however, in plant-microbe interaction systems, reads from both host and pathogen samples are blended together. In contrast to single-genome, both pathogen and host reference genomes are involved in the alignment process. In such circumstances, the order of alignment to the host, the pathogen, or simultaneously to both genomes results in differences in read counts of certain genes, especially at the advanced infection stage. It is crucial to have an appropriate strategy for aligning the reads to their respective genomes, yet the existing strategies of either sequential or parallel alignment become a problem when mapping mixed reads to their corresponding reference genomes. The challenge lies in the determination of which reads belong to which species, especially when homology exists between the two genomes.This study proposes a combo-genome alignment strategy after comparing three alignment scenarios. Simulation results demonstrated that the degree of discrepancy in the results is correlated with phylogenetic distance of the two species in the mixture which was attributable to the extent of homology between the two genomes involved. This correlation was also found in the analysis using two real RNA-seq datasets of Fusarium-challenged wheat plants. Comparisons of the three RNA-seq processing strategies on three simulation datasets and two real Fusariuminfected wheat datasets showed that an alignment to a combo-genome, consisting of both host and pathogen genomes, improves mapping quality as compared to sequential alignment procedures.2 Keyword: RNA-seq, host-pathogen interactions, combo-genome, plant-microbe interaction system, sequential alignment, parallel alignment

show abstract

Dual-seq transcriptomics reveals the battle for iron during Pseudomonas aeruginosa acute murine pneumonia

Cited by 130 publications

References 90 publications

Pseudomonas aeruginosa possesses three distinct systems for sensing and using the host molecule haem

Pseudomonas aeruginosa possesses three distinct systems for sensing and using the host molecule haem

Omics in Aid of Host-pathogen Interaction Studies: A Bacterial Perspective

Strategy in wheat-Fusarium dual-genome RNA-seq data processing

Contact Info

Product

Resources

About