Time-course data analysis of gene expression profiles reveals purR regulon concerns in organic solvent tolerance in Escherichia coli

Shimizu, Kazunori; Hayashi, Shogo; Doukyu, Noriyuki; Kobayashi, Takeshi; Honda, Hiroyuki

doi:10.1263/jbb.99.72

Cited by 15 publications

(5 citation statements)

References 20 publications

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“…In addition to regulating the co-transcribed genes involved in purine biosynthesis, PurR was found to regulate two other operons, as confirmed in this study. This suggests that PurR may have additional roles in Y. pestis strain 201, consistent with previous findings of PurR having multiple functions in various bacterial species [12,32]. PurR was observed to interact with the promoter regions of ssuE and katG, which belong to the sulfur-starvation utilization (ssu) and katG-cybC-cybB operons [26,33], indicating that PurR could function as a regulator for these genes (Supplementary Figure S3D,E).…”

Section: Purr Regulates Potential Operons In Y Pestis Strain 201supporting

confidence: 89%

“…However, in certain bacteria, Microorganisms 2023, 11, 2801 2 of 18 purR serves additional roles beyond its involvement in purine regulation. For instance, in Escherichia coli, purR contributes to the bacterium's tolerance to organic solvents and enhances its viability when exposed to them [12]. Moreover, mutations in purR have been shown to increase the virulence of Staphylococcus aureus [13].…”

Section: Introductionmentioning

confidence: 99%

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Regulatory Functions of PurR in Yersinia pestis: Orchestrating Diverse Biological Activities

Xiao,

Jin,

Song

et al. 2023

Microorganisms

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The bacterium Yersinia pestis has developed various strategies to sense and respond to the complex stresses encountered during its transmission and pathogenic processes. PurR is a common transcriptional regulator of purine biosynthesis among microorganisms, and it modulates the transcription level of the pur operon to suppress the production of hypoxanthine nucleotide (IMP). This study aims to understand the functions and regulatory mechanisms of purR in Y. pestis. Firstly, we constructed a purR knockout mutant of Y. pestis strain 201 and compared certain phenotypes of the null mutant (201-ΔpurR) and the wild-type strain (201-WT). The results show that deleting purR has no significant impact on the biofilm formation, growth rate, or viability of Y. pestis under different stress conditions (heat and cold shock, high salinity, and hyperosmotic pressure). Although the cytotoxicity of the purR knockout mutant on HeLa and 293 cells is reduced, the animal-challenging test found no difference of the virulence in mice between 201-ΔpurR and 201-WT. Furthermore, RNA-seq and EMSA analyses demonstrate that PurR binds to the promoter regions of at least 15 genes in Y. pestis strain 201, primarily involved in purine biosynthesis, along with others not previously observed in other bacteria. Additionally, RNA-seq results suggest the presence of 11 potential operons, including a newly identified co-transcriptional T6SS cluster. Thus, aside from its role as a regulator of purine biosynthesis, purR in Y. pestis may have additional regulatory functions.

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Section: Purr Regulates Potential Operons In Y Pestis Strain 201supporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Regulatory Functions of PurR in Yersinia pestis: Orchestrating Diverse Biological Activities

Xiao,

Jin,

Song

et al. 2023

Microorganisms

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“…The enrichment of genes such as ompX , which is a part of a complex regulatory network involved in the control of outer membrane adaptability and permeability [29] , and smpA , encoding for the small outer-membrane lipoprotein regulated by σ E [30] , potentially suggest that one mechanism for n-butanol resistance is by preventing n-butanol influx to the cytosol and the disruption of the cell envelope. The xanthine/uracil permease (YjcD), enriched in our experiment, has been predicted to belong to the purR regulon [31] , which has been identified to be involved in organic solvent tolerance [32] . YjaA and YodD are proteins involved in stress response of E. coli to hydrogen peroxide, cadmium and acid [33] , and our data suggests a potential link of those genes with tolerance to n-butanol.…”

Section: Resultsmentioning

confidence: 81%

Genomic Library Screens for Genes Involved in n-Butanol Tolerance in Escherichia coli

2011

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Backgroundn-Butanol is a promising emerging biofuel, and recent metabolic engineering efforts have demonstrated the use of several microbial hosts for its production. However, most organisms have very low tolerance to n-butanol (up to 2% (v/v)), limiting the economic viability of this biofuel. The rational engineering of more robust n-butanol production hosts relies upon understanding the mechanisms involved in tolerance. However, the existing knowledge of genes involved in n-butanol tolerance is limited. The goal of this study is therefore to identify E. coli genes that are involved in n-butanol tolerance.Methodology/Principal FindingsUsing a genomic library enrichment strategy, we identified approximately 270 genes that were enriched or depleted in n-butanol challenge. The effects of these candidate genes on n-butanol tolerance were experimentally determined using overexpression or deletion libraries. Among the 55 enriched genes tested, 11 were experimentally shown to confer enhanced tolerance to n-butanol when overexpressed compared to the wild-type. Among the 84 depleted genes tested, three conferred increased n-butanol resistance when deleted. The overexpressed genes that conferred the largest increase in n-butanol tolerance were related to iron transport and metabolism, entC and feoA, which increased the n-butanol tolerance by 32.8±4.0% and 49.1±3.3%, respectively. The deleted gene that resulted in the largest increase in resistance to n-butanol was astE, which enhanced n-butanol tolerance by 48.7±6.3%.Conclusions/SignificanceWe identified and experimentally verified 14 genes that decreased the inhibitory effect of n-butanol tolerance on E. coli. From the data, we were able to expand the current knowledge on the genes involved in n-butanol tolerance; the results suggest that an increased iron transport and metabolism and decreased acid resistance may enhance n-butanol tolerance. The genes and mechanisms identified in this study will be helpful in the rational engineering of more robust biofuel producers.

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“…The omics analysis indicated that variation of lipid fluidity, activation of a general stress-response system, increased energy production and induction of efflux pumps excreting organic solvents out of the cell were involved in the response of P. putida DOT-T1E to organic solvents [5]. Shimizu et al [6] used DNA microarray to investigate the gene expression profiles in Escherichia coli TK31. They found that the purR regulon was critical in the organic solvent tolerance of E. coli.…”

Section: Introductionmentioning

confidence: 99%

Quantitative proteomic analysis ofRhodococcus ruberresponsive to organic solvents

Kuang

Fan

Ren

2018

Biotechnology & Biotechnological Equipment

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Rhodococcus ruber with organic tolerance has potential applications in biotransformation and bioremediation. To explore the possible organic tolerance mechanism, the response of R. ruber SD3 to toluene and phenol was investigated using a quantitative proteomics approach with isobaric tag for relative and absolute quantification (iTRAQ) and liquid chromatography-tandem mass spectrometry. A total of 362 and 488 differentially expressed proteins were identified in the toluene treatment group and the phenol treatment group as compared to the control group, respectively. Functional annotation and metabolic pathway enrichment showed that transporter, degradation pathway and two-component system were closely related to organic solvent tolerance of R. ruber SD3. The quantitative real-time polymerase chain reaction experiment indicated the mRNA levels of stress proteins with an increased expression of 3.23 times upon toluene stress as compared to the control. The expression of 4-nitrophenol 2-monooxygenase in the phenol treatment group was $123 times higher than the counterpart in the control group. The study revealed the possible tolerance mechanism of R. ruber SD3 to organic solvents stress and provided some potential targets for the engineering of R. ruber SD3 to improve its organic solvent tolerance.

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Time-course data analysis of gene expression profiles reveals purR regulon concerns in organic solvent tolerance in Escherichia coli

Cited by 15 publications

References 20 publications

Regulatory Functions of PurR in Yersinia pestis: Orchestrating Diverse Biological Activities

Regulatory Functions of PurR in Yersinia pestis: Orchestrating Diverse Biological Activities

Genomic Library Screens for Genes Involved in n-Butanol Tolerance in Escherichia coli

Quantitative proteomic analysis ofRhodococcus ruberresponsive to organic solvents

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