Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Microcolony-seq applied on a clinical urinary tract infection

ABSTRACT: Urine was obtained from a patient with a urinary tract infection and frozen in 15% glycerol at -80C. For the Microcolony-seq experiment a sample from the frozen urine was serially diluted four times 10-fold and plated on an LB agar plates and incubated at 37C. After 8 hours of incubated microcolonies were visible. Twenty microcolonies were picked and subjected to the Microcolony-seq pipeline and four additional microcolonies were mixed and separated to four Eppendorf tubes and served as the technical replicates of the experiment. RNA was extracted with 1 mL TriReagent (Sigma-Aldrich) per sample. RNA quality was assessed by Nanodrop and by Bioanalyzer using the Agilent RNA 6000 Pico Kit (5067-1513). rRNA depletion was done by using the DIY rRNA depletion method, using the rRNA sequence probe set designed for E. coli K-12. RNA-seq libraries were constructed based on the RNAtag-Seq protocol with several modifications. The rRNA depletion step was done first following by the fragmentation step in the RNAtag-Seq protocol. Then the first ligation was carried out and the rest of the RNAtag-Seq protocol was followed. Libraries were single-end sequenced using the Nextseq500 Sequencer (Illumina).

INSTRUMENT(S): NextSeq 550, RNAtag-Seq protocol (Shishkin et al., 2015), Bench work, TriReagent

ORGANISM(S): mixed sample

SUBMITTER: Raya Faigenbaum-Romm

PROVIDER: E-MTAB-13892 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Candida albicans is an opportunistic fungal pathogen that can infect oral mucosal surfaces despite being under continuous flow from saliva. Previous studies have shown that under specific conditions C. albicans will form microcolonies that more closely resemble the biofilms formed in vivo than standard in vitro biofilm models. However, very little is known about these microcolonies, particularly genomic differences between these specialized biofilm structures and the traditional in vitro biofilms. In this study, we used a novel flow system, in which C. albicans spontaneously forms microcolonies, to further characterize the architecture of fungal microcolonies and their genomics compared to non-microcolony conditions. Fungal microcolonies arise from radially branching filamentous hyphae that increasingly intertwine with one another to form extremely dense biofilms, and closely resemble the architecture of in vivo oropharyngeal candidiasis. We identified 20 core microcolony genes that were differentially regulated in flow-induced microcolonies using RNA-seq. These genes included HWP1, ECE1, IHD1, PLB1, HYR1, PGA10, and SAP5. To better understand the regulatory elements for microcolonies, we utilized a predictive algorithm to discover ten transcriptional regulators potentially involved in microcolony formation. Of these transcription factors, we found that six played a key role in microcolony formation and development (Rob1, Ndt80, Efg1, Sfl1, Sfl2, and Nrg1). We also found that Hwp1, Sap5, Pga10, and all the microcolony regulators promoted adhesion and invasion of the microcolonies to oral epithelium. Furthermore, epithelial cells infected with deletion mutants of ROB1, NDT80, SFL2, EFG1, and MCM1 had reduced immune response, evidenced by reduced phosphorylation of MKP1 and c-Fos, key signal transducers in the hyphal invasion response. This profile of microcolony transcriptional regulators more closely reflects Sfl1 and Sfl2 hyphal regulatory networks than biofilm regulatory networks, suggesting that hyphal morphogenesis plays a more central role in the development of flow-induced microcolonies.

Project description:A hallmark of the biofilm architecture is the presence of microcolonies. However, little is known about the underlying mechanisms governing microcolony formation. In the human pathogen Pseudomonas aeruginosa, microcolony formation is dependent on the two-component regulator MifR, with mifR mutant biofilms exhibiting an overall thin structure lacking microcolonies, and overexpression of mifR resulting in hyper-microcolony formation. Here, we made use of the distinct MifR-dependent phenotypes to elucidate mechanisms associated with microcolony formation. Using global transcriptomic and proteomic approaches, we demonstrate that cells located within microcolonies experience stressful, oxygen limited, and energy starving conditions, as indicated by the activation of stress response mechanisms and anaerobic and fermentative processes, in particular pyruvate fermentation. Inactivation of genes involved in pyruvate utilization including uspK, acnA and ldhA abrogated microcolony formation in a manner similar to mifR inactivation. Moreover, depletion of pyruvate from the growth medium impaired biofilm and microcolony formation, while addition of pyruvate significantly increased microcolony formation. Addition of pyruvate partly restored microcolony formation in M-bM-^HM-^FmifR biofilms. Moreover, addition of pyruvate to or expression of mifR in lactate dehydrogenase (ldhA) mutant biofilms did not restore microcolony formation. Consistent with the finding of denitrification genes not demonstrating distinct expression patterns in biofilms forming or lacking microcolonies, addition of nitrate did not alter microcolony formation. Our findings indicate the fermentative utilization of pyruvate to be a microcolony-specific adaptation to the oxygen limitation and energy starvation of the P. aeruginosa biofilm environment. For biofilm growth experiments, three independent replicates of P. aeruginosa strains PAO1 and M-NM-^TmifR were grown as biofilms in a flow-through system using a once-through continuous flow tube reactor system for biofilm sample collection and in flow cells (BioSurface Technologies) for the analysis of biofilm architecture as previously described (Sauer et al., 2002, Sauer et al., 2004, Petrova & Sauer, 2009). Cells were treated with RNAprotect (Qiagen) and total RNA was extracted using an RNeasy mini purification kit (Qiagen) per the manufacturerM-bM-^@M-^Ys instructions. RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNase treatment. Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol. Sauer, K., A. K. Camper, G. D. Ehrlich, J. W. Costerton & D. G. Davies, (2002) Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm. J. Bacteriol. 184: 1140-1154. Sauer, K., M. C. Cullen, A. H. Rickard, L. A. H. Zeef, D. G. Davies & P. Gilbert, (2004) Characterization of nutrient-induced dispersion in Pseudomonas aeruginosa PAO1 biofilm. J. Bacteriol. 186: 7312-7326. Petrova, O. E. & K. Sauer, (2009) A novel signaling network essential for regulating Pseudomonas aeruginosa biofilm development. PLoS Pathogens 5: e1000668.

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Microcolony-seq applied on a clinical urinary tract infection

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