Prediction of Burkholderia pseudomallei DsbA substrates identifies potential virulence factors and vaccine targets

Vezina, Ben; Petit, Guillaume A.; Martin, Jennifer L.; Halili, Maria A.

doi:10.1371/journal.pone.0241306

Cited by 5 publications

(7 citation statements)

References 98 publications

(156 reference statements)

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“…Additionally, given the susceptibility to non-β-lactam antibiotics (e.g. ERY, CHX, NOV), the Dsb system may be important for the function of other resistance mechanisms, such as efflux pumps (Hayashi et al 2000; Vezina et al 2020). Thus, we suggest that antibiotic susceptibility caused by defects in the DSB system is multifactorial.…”

Section: Resultsmentioning

confidence: 99%

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

Hogan

Maydaniuk

Natarajan

et al. 2022

Preprint

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The cell envelope of the Gram-negativeBurkholderia cepaciacomplex (Bcc) presents unique restrictions to antibiotic penetration. As a consequence, Bcc species are notorious for causing recalcitrant multidrug-resistant infections in immunocompromised individuals, such as those living with cystic fibrosis. To systematically identify cell envelope-associated resistance and susceptibility determinants at the genome level, we constructed a high-density, randomly-barcoded transposon mutant library in the clinical isolateB. cenocepaciaK56-2 and exposed it to a panel of more than twenty cell envelope-targeting antibiotics. By quantifying relative mutant fitness with BarSeq, followed by validation with CRISPR-interference, we profiled over a hundred new chemical-genetic interactions and identified novel mediators of antibiotic susceptibility in the Bcc cell envelope. We first reveal new connections between broad-spectrum β-lactam susceptibility, peptidoglycan synthesis, and blockages in undecaprenyl phosphate metabolism, highlighting a β-lactam critical vulnerability associated with sharing this common lipid intermediate. We then show that the clinically relevant synergy of the β-lactam/ β-lactamase inhibitor combination ceftazidime/avibactam is primarily mediated by inhibition of the PenB carbapenemase, over more than twenty other putative β-lactamases. Importantly, avibactam more strongly potentiates the activity of aztreonam and meropenem than ceftazidime in a panel of Bcc clinical isolates. Finally, we characterize for first time in the Bcc the iron and receptor-dependent activity of the novel siderophore cephalosporin antibiotic, cefiderocol. Overall, our work has implications for antibiotic target prioritization, and for using additional combinations of β-lactam/ β-lactamase inhibitors that can extend the utility of our current clinical arsenal of antibacterial therapies.

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Section: Resultsmentioning

confidence: 99%

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

Hogan

Maydaniuk

Natarajan

et al. 2022

Preprint

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“…Moreover, the ScsB and ScsC proteins share similarities with the DSB proteins DsbD and DsbC, respectively. Because they are essential for the folding of several virulence factors in the periplasm of bacteria, DSB proteins have been investigated as potential targets for drug discovery (Landeta et al, 2017;Bocian-Ostrzycka et al, 2017;Halili et al, 2015;Duprez et al, 2015;Vezina et al, 2020;Nebl et al, 2020;Furniss et al, 2022). Expanding our understanding of the related SCS proteins, including their mode of action and structural variation, may contribute to the identification of new druggable targets to fight bacterial infections.…”

Section: Discussionmentioning

confidence: 99%

The suppressor of copper sensitivity protein C from Caulobacter crescentus is a trimeric disulfide isomerase that binds copper(I) with subpicomolar affinity

Petit¹,

Hong²,

Djoko³

et al. 2022

Acta Cryst Sect D Struct Biol

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The introduction of disulfide bonds into periplasmic proteins is a critical process in many Gram-negative bacteria. The formation and regulation of protein disulfide bonds have been linked to the production of virulence factors. Understanding the different pathways involved in this process is important in the development of strategies to disarm pathogenic bacteria. The well characterized disulfide bond-forming (DSB) proteins play a key role by introducing or isomerizing disulfide bonds between cysteines in substrate proteins. Curiously, the suppressor of copper sensitivity C proteins (ScsCs), which are part of the bacterial copper-resistance response, share structural and functional similarities with DSB oxidase and isomerase proteins, including the presence of a catalytic thioredoxin domain. However, the oxidoreductase activity of ScsC varies with its oligomerization state, which depends on a poorly conserved N-terminal domain. Here, the structure and function of Caulobacter crescentus ScsC (CcScsC) have been characterized. It is shown that CcScsC binds copper in the copper(I) form with subpicomolar affinity and that its isomerase activity is comparable to that of Escherichia coli DsbC, the prototypical dimeric bacterial isomerase. It is also reported that CcScsC functionally complements trimeric Proteus mirabilis ScsC (PmScsC) in vivo, enabling the swarming of P. mirabilis in the presence of copper. Using mass photometry and small-angle X-ray scattering (SAXS) the protein is demonstrated to be trimeric in solution, like PmScsC, and not dimeric like EcDsbC. The crystal structure of CcScsC was also determined at a resolution of 2.6 Å, confirming the trimeric state and indicating that the trimerization results from interactions between the N-terminal α-helical domains of three CcScsC protomers. The SAXS data analysis suggested that the protomers are dynamic, like those of PmScsC, and are able to sample different conformations in solution.

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“…pseudomallei based on a high number of discriminating peptides can increase the confidence in the diagnoses of melioidosis and glanders. Moreover, until now, diagnosis of these diseases is often cumbersome because of the diverse clinical manifestations, inadequacy of conventional diagnostic methods and lack of diagnostic facilities [13,14].…”

Section: Plos Neglected Tropical Diseasesmentioning

confidence: 99%

“…Melioidosis is a neglected tropical disease, which may spread, creating the risk that this disease will become endemic in more parts of the world. Furthermore, it is considered a potential biological threat for which no vaccine is available [2,13].…”

Section: Introductionmentioning

confidence: 99%

“…Diagnosis can be cumbersome because the clinical manifestations of the disease varies between patients, isolation of the bacterium can be complicated in some clinical specimens and trustworthy identification to the species level is sometimes challenging [13,14]. With proteome analysis, B. mallei and B. pseudomallei can be identified quickly and with certainty [15].…”

Section: Introductionmentioning

confidence: 99%

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Expression of virulence and antimicrobial related proteins in Burkholderia mallei and Burkholderia pseudomallei

et al. 2023

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Background Burkholderia mallei and Burkholderia pseudomallei are both potential biological threat agents. Melioidosis caused by B. pseudomallei is endemic in Southeast Asia and Northern Australia, while glanders caused by B. mallei infections are rare. Here we studied the proteomes of different B. mallei and B. pseudomallei isolates to determine species specific characteristics. Methods The expressed proteins of 5 B. mallei and 6 B. pseudomallei strains were characterized using liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). Subsequently, expression of potential resistance and virulence related characteristics were analyzed and compared. Results Proteome analysis can be used for the identification of B. mallei and B. pseudomallei. Both species were identified based on >60 discriminative peptides. Expression of proteins potentially involved in antimicrobial resistance, AmrAB–OprA, BpeAB–OprB, BpeEF–OprC, PenA as well as several other efflux pump related proteins and putative β-lactamases was demonstrated. Despite, the fact that efflux pump BpeAB–OprB was expressed in all isolates, no clear correlation with an antimicrobial phenotype and the efflux-pump could be established. Also consistent with the phenotypes, no amino acid mutations in PenA known to result in β-lactam resistance could be identified. In all studied isolates, the expression of virulence (related) factors Capsule-1 and T2SS was demonstrated. The expression of T6SS-1 was demonstrated in all 6 B. pseudomallei isolates and in 2 of the 5 B. mallei isolates. In all, except one B. pseudomallei isolate, poly-beta-1,6 N-acetyl-D-glucosamine export porin (Pga), important for biofilm formation, was detected, which were absent in the proteomes of B. mallei. Siderophores, iron binding proteins, malleobactin and malleilactone are possibly expressed in both species under standard laboratory growth conditions. Expression of multiple proteins from both the malleobactin and malleilactone polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) clusters was demonstrated in both species. All B. pseudomallei expressed at least seven of the nine proteins of the bactobolin synthase cluster (bactobolin, is a ribosome targeting antibiotic), while only in one B. mallei isolate expression of two proteins of this synthase cluster was identified. Conclusions Analyzing the expressed proteomes revealed differences between B. mallei and B. pseudomallei but also between isolates from the same species. Proteome analysis can be used not only to identify B. mallei and B. pseudomallei but also to characterize the presence of important factors that putatively contribute to the pathogenesis of B. mallei and B. pseudomallei.

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Prediction of Burkholderia pseudomallei DsbA substrates identifies potential virulence factors and vaccine targets

Cited by 5 publications

References 98 publications

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

The suppressor of copper sensitivity protein C from Caulobacter crescentus is a trimeric disulfide isomerase that binds copper(I) with subpicomolar affinity

Expression of virulence and antimicrobial related proteins in Burkholderia mallei and Burkholderia pseudomallei

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