Architectural principles for Hfq/Crc-mediated regulation of gene expression

Pei, X.Y.; Dendooven, Tom; Sonnleitner, Elisabeth; Chen, Shao-Xia; Bläsi, Udo; Luisi, B.F.

doi:10.7554/elife.43158

Cited by 48 publications

(92 citation statements)

References 62 publications

(116 reference statements)

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“…Repression of the Hfq-Crc complex by CrcZ, a small non-coding RNA, permits translation of genes encoding proteins for non-preferred substrates in P. aeruginosa strain PAO1. 16,45,46 Table 3 shows five proteins with lower abundances in LCSP vs. CSP for planktonic cultivation and the one protein with higher abundance during biofilm cultivation whose transcripts were reported to be upregulated or downregulated by mutation of this Hfq-Crc-CrcZ CCR system. 46,47 Furthermore, the HupA transcript in P. aeruginosa has been associated with stress acclimation, 48,49 while HupA has a regulatory role in E. coli by increasing aggregation and adhesion.…”

Section: Resultsmentioning

confidence: 99%

Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics

Yung

McGill

Chen

et al. 2019

npj Biofilms Microbiomes

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Microorganisms enhance fitness by prioritizing catabolism of available carbon sources using a process known as carbon catabolite repression (CCR). Planktonically grown Pseudomonas aeruginosa is known to prioritize the consumption of organic acids including lactic acid over catabolism of glucose using a CCR strategy termed “reverse diauxie.” P. aeruginosa is an opportunistic pathogen with well-documented biofilm phenotypes that are distinct from its planktonic phenotypes. Reverse diauxie has been described in planktonic cultures, but it has not been documented explicitly in P. aeruginosa biofilms. Here a combination of exometabolomics and label-free proteomics was used to analyze planktonic and biofilm phenotypes for reverse diauxie. P. aeruginosa biofilm cultures preferentially consumed lactic acid over glucose, and in addition, the cultures catabolized the substrates completely and did not exhibit the acetate secreting “overflow” metabolism that is typical of many model microorganisms. The biofilm phenotype was enabled by changes in protein abundances, including lactate dehydrogenase, fumarate hydratase, GTP cyclohydrolase, L-ornithine N(5)-monooxygenase, and superoxide dismutase. These results are noteworthy because reverse diauxie-mediated catabolism of organic acids necessitates a terminal electron acceptor like O2, which is typically in low supply in biofilms due to diffusion limitation. Label-free proteomics identified dozens of proteins associated with biofilm formation including 16 that have not been previously reported, highlighting both the advantages of the methodology utilized here and the complexity of the proteomic adaptation for P. aeruginosa biofilms. Documenting the reverse diauxic phenotype in P. aeruginosa biofilms is foundational for understanding cellular nutrient and energy fluxes, which ultimately control growth and virulence.

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Section: Resultsmentioning

confidence: 99%

Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics

Yung

McGill

Chen

et al. 2019

npj Biofilms Microbiomes

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“…One answer may come from recent structural analysis of the association of Crc as the fourth partner with the sRNA-Hfq-mRNA ternary regulatory complex. Crc itself does not interact with sRNAs through Rho-independent terminators; however, it does enhance the association between Hfq and A-rich target sequences via an Hfq (distal surface)-RNA-Crc sandwich conformation (27, 56), perhaps thus potentially selecting for the AAN triplet motif. It may be interesting to consider the possibility that sRNAs with AAN motifs tend to regulate mRNAs with U-rich motifs.…”

Section: Discussionmentioning

confidence: 99%

Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing

et al. 2019

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The Gram-negative bacterium P. aeruginosa is ubiquitously distributed in diverse environments and can cause severe biofilm-related infections in at-risk individuals. Although the presence of a large number of putative sRNAs and widely conserved RNA chaperones in this bacterium implies the importance of posttranscriptional regulatory networks for environmental fluctuations, limited information is available regarding the global role of RNA chaperones such as Hfq in the P. aeruginosa transcriptome, especially under different environmental conditions. Here, we characterize Hfq-dependent differences in gene expression and biological processes in two physiological states: the planktonic and biofilm forms. A combinatorial comparative CLIP-seq and total RNA-seq approach uncovered condition-dependent association of RNAs with Hfq in vivo and expands the potential direct regulatory targets of Hfq in the P. aeruginosa transcriptome.

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“…6B), indicating a possible release of CCR. We then examined the translation efficiency of amiE (encoding the aliphatic amidase), which is inhibited by Crc and Hfq in CCR (11,34). We constructed a translational fusion between a lacZ reporter gene and the CRC regulatory sequence of amiE (amiE=-lacZ) (11) as well as a C-terminal 6ϫHis-tagged amiE (amiE-His), which are driven by an exogenous P tac promoter and P BAD promoter, respectively.…”

Section: Fig 1 Legend (Continued)mentioning

confidence: 99%

TpiA is a Key Metabolic Enzyme That Affects Virulence and Resistance to Aminoglycoside Antibiotics through CrcZ in Pseudomonas aeruginosa

Xia

Wang

Pan

et al. 2020

mBio

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Carbon metabolism plays an essential role in bacterial pathogenesis and susceptibility to antibiotics. In Pseudomonas aeruginosa, Crc, Hfq, and a small RNA, CrcZ, are central regulators of carbon metabolism. By screening mutants of genes involved in carbon metabolism, we found that mutation of the tpiA gene reduces the expression of the type III secretion system (T3SS) and bacterial resistance to aminoglycoside antibiotics. TpiA is a triosephosphate isomerase that reversibly converts glyceraldehyde 3-phosphate to dihydroxyacetone phosphate, a key step connecting glucose metabolism with glycerol and phospholipid metabolisms. We found that mutation of the tpiA gene enhances the bacterial carbon metabolism, respiration, and oxidative phosphorylation, which increases the membrane potential and promotes the uptake of aminoglycoside antibiotics. Further studies revealed that the level of CrcZ is increased in the tpiA mutant due to enhanced stability. Mutation of the crcZ gene in the tpiA mutant background restored the expression of the T3SS genes and the bacterial resistance to aminoglycoside antibiotics. Overall, this study reveals an essential role of TpiA in the metabolism, virulence, and antibiotic resistance in P. aeruginosa. IMPORTANCE The increase in bacterial resistance against antibiotics imposes a severe threat to public health. It is urgent to identify new drug targets and develop novel antimicrobials. Metabolic homeostasis of bacteria plays an essential role in their virulence and resistance to antibiotics. Recent studies demonstrated that antibiotic efficacies can be improved by modulating the bacterial metabolism. Pseudomonas aeruginosa is an important opportunistic human pathogen that causes various infections. The bacterium is intrinsically resistant to antibiotics. In this study, we provide clear evidence that TpiA (triosephosphate isomerase) plays an essential role in the metabolism of P. aeruginosa and influences bacterial virulence and antibiotic resistance. The significance of this work is in identifying a key enzyme in the metabolic network, which will provide clues as to the development of novel treatment strategies against infections caused by P. aeruginosa.

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Architectural principles for Hfq/Crc-mediated regulation of gene expression

Cited by 48 publications

References 62 publications

Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics

Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics

Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing

TpiA is a Key Metabolic Enzyme That Affects Virulence and Resistance to Aminoglycoside Antibiotics through CrcZ in Pseudomonas aeruginosa

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