Characterization of the Burkholderia thailandensis SOS Response by Using Whole-Transcriptome Shotgun Sequencing

Ulrich, Ricky L.; DeShazer, David; Kenny, Tara; Ulrich, Melanie; Moravusova, Anna; Opperman, Timothy J.; Bavari, Sina; Bowlin, Terry L.; Moir, Donald T.; Panchal, Rekha G.

doi:10.1128/aem.00538-13

Cited by 15 publications

(19 citation statements)

References 52 publications

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“…Further evidence for the association between the Gallionellales and Gram-positive LexA-binding motifs is provided by the fact that purified B. subtilis LexA binds canonical SOS targets (lexA and recA promoters) of both organisms. In contrast, E. coli LexA, which targets a LexA-binding motif very similar to that reported in the Betaproteobacteria B. thailandensis, Bordetella pertussis, and Ralstonia solanacearum (12,16,55), does not bind canonical target promoters in the Gallionellales. In spite of the overall similarity of their binding motifs, B. subtilis and G. capsiferriformans LexA proteins show distinct binding specificities (see Fig.…”

Section: Resultssupporting

confidence: 52%

“…In the Betaproteobacteria, in vivo and in silico studies have established that the SOS response is regulated by a LexA protein targeting a binding motif closely related to that observed in E. coli and other Gammaproteobacteria (12,15,16). Comparative genomic and transcriptomic data, however, indicate that the SOS regulon of the Betaproteobacteria displays some fundamental differences from that reported for many Gammaproteobacteria.…”

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confidence: 96%

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An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria

et al. 2015

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The SOS response is a transcriptional regulatory network governed by the LexA repressor that activates in response to DNA damage. In the Betaproteobacteria, LexA is known to target a palindromic sequence with the consensus sequence CTGT-N 8 -ACAG. We report the characterization of a LexA regulon in the iron-oxidizing betaproteobacterium Sideroxydans lithotrophicus. In silico and in vitro analyses show that LexA targets six genes by recognizing a binding motif with the consensus sequence GAACGaaCGTTC, which is strongly reminiscent of the Bacillus subtilis LexA-binding motif. We confirm that the closely related Gallionella capsiferriformans shares the same LexA-binding motif, and in silico analyses indicate that this motif is also conserved in the Nitrosomonadales and the Methylophilales. Phylogenetic analysis of LexA and the alpha subunit of DNA polymerase III (DnaE) reveal that the organisms harboring this noncanonical LexA form a compact taxonomic cluster within the Betaproteobacteria. However, their lexA gene is unrelated to the standard Betaproteobacteria lexA, and there is evidence of its spread through lateral gene transfer. In contrast to other reported cases of noncanonical LexA-binding motifs, the regulon of S. lithotrophicus is comparable in size and function to that of many other Betaproteobacteria, suggesting that a convergent SOS regulon has reevolved under the control of a new LexA protein. Analysis of the DNA-binding domain of S. lithotrophicus LexA reveals little sequence similarity with that of other LexA proteins targeting similar binding motifs, suggesting that network structure may limit site evolution or that structural constrains make the B. subtilis-type motif an optimal interface for multiple LexA sequences. IMPORTANCEUnderstanding the evolution of transcriptional systems enables us to address important questions in microbiology, such as the emergence and transfer potential of different regulatory systems to regulate virulence or mediate responses to stress. The results reported here constitute the first characterization of a noncanonical LexA protein regulating a standard SOS regulon. This is significant because it illustrates how a complex transcriptional program can be put under the control of a novel transcriptional regulator. Our results also reveal a substantial degree of plasticity in the LexA recognition domain, raising intriguing questions about the space of protein-DNA interfaces and the specific evolutionary constrains faced by these elements.

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Section: Resultssupporting

confidence: 52%

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confidence: 96%

An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria

et al. 2015

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“…To determine genes that are induced in other bacterial species as part of the SOS response (including sulA ), other groups have used Mitomycin C (MMC) or other DNA damaging agents (e.g. UV light) [46]–[50]. To assess whether DNA damage induces expression of argR-sulA in NTHI, we exposed an NTHI GFP reporter strain (GFP under control of the argR-sulA promoter) to increasing concentrations of MMC and monitored fluorescence intensity as a measure of promoter activity.…”

Section: Resultsmentioning

confidence: 99%

Haemophilus Responses to Nutritional Immunity: Epigenetic and Morphological Contribution to Biofilm Architecture, Invasion, Persistence and Disease Severity

et al. 2013

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In an effort to suppress microbial outgrowth, the host sequesters essential nutrients in a process termed nutritional immunity. However, inflammatory responses to bacterial insult can restore nutritional resources. Given that nutrient availability modulates virulence factor production and biofilm formation by other bacterial species, we hypothesized that fluctuations in heme-iron availability, particularly at privileged sites, would similarly influence Haemophilus biofilm formation and pathogenesis. Thus, we cultured Haemophilus through sequential heme-iron deplete and heme-iron replete media to determine the effect of transient depletion of internal stores of heme-iron on multiple pathogenic phenotypes. We observed that prior heme-iron restriction potentiates biofilm changes for at least 72 hours that include increased peak height and architectural complexity as compared to biofilms initiated from heme-iron replete bacteria, suggesting a mechanism for epigenetic responses that participate in the changes observed. Additionally, in a co-infection model for human otitis media, heme-iron restricted Haemophilus, although accounting for only 10% of the inoculum (90% heme-iron replete), represented up to 99% of the organisms recovered at 4 days. These data indicate that fluctuations in heme-iron availability promote a survival advantage during disease. Filamentation mediated by a SulA-related ortholog was required for optimal biofilm peak height and persistence during experimental otitis media. Moreover, severity of disease in response to heme-iron restricted Haemophilus was reduced as evidenced by lack of mucosal destruction, decreased erythema, hemorrhagic foci and vasodilatation. Transient restriction of heme-iron also promoted productive invasion events leading to the development of intracellular bacterial communities. Taken together, these data suggest that nutritional immunity, may, in fact, foster long-term phenotypic changes that better equip bacteria for survival at infectious sites.

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“…The role of stress has been implicated in the establishment of persistence, including the stringent response to starvation, DNA damage, SOS signaling, and oxidative stress. Genes that encode stress response mechanisms were activated in persisters enriched by exposure to antibiotics (5)(6)(7)(8). Furthermore, low acidity, temperature variations, and osmotic stress were also shown to significantly increase the number of persisters in bacteria (9)(10)(11)(12)(13).…”

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confidence: 99%

“…Disrupted equilibrium of toxin-antitoxin (TA) systems, which regulate essential cellular activities, including protein translation, DNA stability, and cell membrane integrity, leads to metabolic shutdown similar to that of the stringent response to stress (14)(15)(16)(17)(18). Other studies have profiled persister transcriptomes using various enrichment methods, including antibiotic lysis of susceptible bacterial populations (5,19,20), flow cytometry based on dormancy markers (6), and analysis of stationary-phase bacteria (8,11,21). However, the already highly heterogeneous nature of persisters has been further confounded by the different stressor conditions used between the experimental groups, thus generating transcriptomic data sets that were biased to the particular phenotypic assay.…”

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confidence: 99%

A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis

et al. 2020

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Persister cells are genetically identical variants in a bacterial population that have phenotypically modified their physiology to survive environmental stress. In bacterial pathogens, persisters are able to survive antibiotic treatment and reinfect patients in a frustrating cycle of chronic infection. To better define core persistence mechanisms for therapeutics development, we performed transcriptomics analyses of Burkholderia thailandensis populations enriched for persisters via three methods: flow sorting for low proton motive force, meropenem treatment, and culture aging. Although the three persister-enriched populations generally displayed divergent gene expression profiles that reflect the multimechanistic nature of stress adaptations, there were several common gene pathways activated in two or all three populations. These include polyketide and nonribosomal peptide synthesis, Clp proteases, mobile elements, enzymes involved in lipid metabolism, and ATP-binding cassette (ABC) transporter systems. In particular, identification of genes that encode polyketide synthases (PKSs) and fatty acid catabolism factors indicates that generation of secondary metabolites, natural products, and complex lipids could be part of the metabolic program that governs the persistence state. We also found that loss-of-function mutations in the PKS-encoding gene locus BTH_I2366, which plays a role in biosynthesis of histone deacetylase (HDAC) inhibitors, resulted in increased sensitivity to antibiotics targeting DNA replication. Furthermore, treatment of multiple bacterial pathogens with a fatty acid synthesis inhibitor, CP-640186, potentiated the efficacy of meropenem against the persister populations. Altogether, our results suggest that bacterial persisters may exhibit an outwardly dormant physiology but maintain active metabolic processes that are required to maintain persistence. IMPORTANCE The discovery of antibiotics such as penicillin and streptomycin marked a historic milestone in the 1940s and heralded a new era of antimicrobial therapy as the modern standard for medical treatment. Yet, even in those early days of discovery, it was noted that a small subset of cells (∼1 in 105) survived antibiotic treatment and continued to persist, leading to recurrence of chronic infection. These persisters are phenotypic variants that have modified their physiology to survive environmental stress. In this study, we have performed three transcriptomic screens to identify persistence genes that are common between three different stressor conditions. In particular, we identified genes that function in the synthesis of secondary metabolites, small molecules, and complex lipids, which are likely required to maintain the persistence state. Targeting universal persistence genes can lead to the development of clinically relevant antipersistence therapeutics for infectious disease management.

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Characterization of the Burkholderia thailandensis SOS Response by Using Whole-Transcriptome Shotgun Sequencing

Cited by 15 publications

References 52 publications

An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria

An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria

Haemophilus Responses to Nutritional Immunity: Epigenetic and Morphological Contribution to Biofilm Architecture, Invasion, Persistence and Disease Severity

A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis

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