диафрагмированные волноводные фильтры / e95144be-d686-417c-8bc3-3525c73c4572

I. INTRODUCTION

Although antibiotics are known for eliminating pathogens through a variety of mechanisms, antibiotics may also promote the formation of persisters, which are dormant variants of regular cells that are highly tolerant to antibiotics [1]. For example, antibiotic pretreatment to E. coli, including rifampicin, tetracycline, and carbonyl cyanide m- chlorophenyl hydrazine, increased the microbial persistence dramatically by halting protein synthesis. The presence of persister-speci c tolerance is suggested to account for the recalcitrance of infectious diseases. It is thus important to study the mechanisms via which antibiotics cause pathogens to change their metabolism and form persister cells. In experimental studies, screening knockout libraries has not produced mutants that lack persisters, indicating that dormancy is not regulated by one single gene or enzyme [1]. Although research has been conducted on the reactionux distribution upon the antibiotic treatment [2], no genome-scale modeling

approach has been published to incorporate the interaction of multiple genes, enzymes, and metabolites to investigate potential persister-forming mechanisms triggered by antibiotics. This motivates us to develop the rst genome-scale modeling approach to quantify the effect of antibiotics on the metabolic ux redistribution, and thus investigate potential mechanisms for the persister formation that is triggered by antibiotics.

The enzyme-dependent reactions can be generally identi ed from the metabolic pathways according to the upregulated genes in the experimental data. However, existing studies show that the correlation between mRNA or protein levels and metabolic uxes levels is not necessarily high for all metabolic reactions [3], Kim et al. [3] developed therst in silico approach to capture the relationship between mRNA levels and metabolic uxes. This approach, calledux-coupled genes, requires transcriptome and uxome data under different conditions. Since uxome data are mostly

limited to the central carbon metabolism, this approach cannot be applied to metabolic pathways for other metabolisms in genome-scale models. The ux balance analysis (FBA) is one of the most commonly used approaches to quantify microbial growth under speci c nutrient conditions from genomescale models. On the basis of the FBA platform, several approaches, including GIMME [4], iMAT [5], MADE [6], E-FLUX [2], Lee-12 [7], RELATCH [8], and GX-FBA [9], have been developed to integrate gene expression data with genome-scale models to predict metabolism. Most of these methods place tight constraints on metabolic uxes from mRNA data so that the change in metabolic uxes matches the change in mRNA levels. However, the performances of these methods are not as good as traditional FBA and probabilistic FBA (pFBA) [10] in which no constraints from gene expression data were imposed to metabolic uxes. One potential reason for this is that not all of reactions rates are enzyme-dependent, as some of them depend on the availability of reactants instead (i.e., substrate-dependent). In many cases, mRNA or protein levels in the same metabolic branch might engage alteration in the opposite directions. Therefore, assigning a tight constraint or objective function to t the uxes to microarray data, as shown in the aforementioned approaches, might not exhibit good prediction capability. We hypothesize that adding a loose constraint to metabolic uxes based upon gene expression data may return a better correlation between the metabolic uxes and mRNA levels than FBA and pFBA. Hence, the reactions identi ed as mRNA/enzyme-dependent were constrained here in a way that mimics the stress imposed by antibiotics to the bacteria. The reactions with large ux change and the metabolites with large exchange rates are determined to provide a systemslevel investigation of potential persister formation mechanisms of P. aeruginosa. This pathogen was selected in this letter, as it is one of the leading causes of nosocomial infections in hospitalized patients and it displays resistance to a wide array of antibiotics by forming a bio lm in chronic infectious processes [11].

II. METHOD

A. ILLUSTRATIVE EXAMPLE OF OVERALL APPROACH

Gene expression data of microorganisms under the control condition and other experimental conditions were rst obtained [Fig. 1(A)]. The changes in gene expression levels were used to constrain metabolic uxes, which were then used to identify the metabolic reactions that mainly depend on the enzyme levels instead of the reactant/substrate levels. For example, it can be concluded from Fig. 1(A) that theuxes of Reaction 1 are positively correlated with the expression levels of Gene 1, while the uxes of Reaction 2 are not correlated with Gene 2 expression levels. Reaction 2 may be substrate-dependent instead of enzyme-dependent. Since substrates are constrained by mass balance, the uxes of substrate-dependent reactions may be negatively correlative with gene express levels.

The reactions whose uxes are positively associated with gene expression levels were then further constrained with

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FIGURE 1. Schematic of the proposed approach to quantify the metabolism alteration imposed by the treatment of antibiotics on pathogens.

limited metabolic uxes, as shown in the red color reactions in Fig. 1(B). This can mimic the inhibition of the antibiotics on the protein synthesis, which can be re ected by the low activity levels of the metabolic reactions associated with these proteins/genes. For example, the ux through Reaction 1 is limited to a small value. On the other hand, the ux of Reaction 2 was not constrained as it is not positively correlated with the expression levels of Gene 2, that is, it may not be in uenced by the antibiotics that inhibit the protein synthesis.

The ux change of each metabolic reaction was further investigated. In particular, the ux distributions of each metabolic reaction before and after the treatment with antibiotics [i.e., the black and red curves shown in Fig. 1(B), respectively] were compared to identify the reactions with the largest ux changes. On the basis of these reactions, we can further study how the antibiotic may change the microbial metabolism and possibly induce the persister pathogen formation. The detail of the developed method can be found in the Supplemental Document 1.

III. RESULTS

A. DETERMINATION OF CORRELATION FACTOR BETWEEN GENE EXPRESSION LEVELS AND METABOLIC FLUXES BY INTEGRATING GENE EXPRESSION DATA INTO THE METABOLIC NETWORK

In order to test the performance of our approach for integrating gene expression data into metabolic models, theuxomics data set obtained by C13 labeling in [15] was utilized as the experimental data. In addition, our approach was compared with pFBA and FBA (Fig. 2), as these two methods have been approved to predict higher correlation between metabolic uxes and gene express levels than other aforementioned existing approaches. The experimental data were obtained with different dilution rates: 0.1, 0.4, 0.5, and 0.7 h 1. The 0.1-h 1 condition was treated as the control. As shown in Fig. 2(A), the prediction by our approach for the 0.4-h 1 dilution rate generated a correlation factor R of 0.81, which is higher than 0.75 and 0.76 predicted from FBA and

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FIGURE 2. Prediction of the intracellular fluxes from the gene expression data measured at (A) 0.4-h 1 dilution rate, (B) 0.5-h 1 dilution rate, and

(C) 0.7-h 1 dilution rate. The X-axis shows the measured fluxes, while the Y-axis represents the predicted fluxes through individual reactions of the central carbon metabolism.

pFBA, respectively. For the data obtained with the 0.5-h 1 dilution rate, our approach generated R equal to 0.75, while R for pFBA and FBA are 0.71 and 0.70, respectively. Our approach remained the best for the 0.7-h 1 dilution rate (R equal to 0.75), while pFBA outperformed FBA again (R equal to 0.73 versus 0.72).

Among the 28 intracellular reactions in central carbon metabolism, 18 reactions demonstrated a positive correlation in their uxes to the expression levels of their corresponding genes. Meanwhile, the rate limiting steps in central carbon metabolism have large positive correlation with their genes. For example, the reaction in which isocitrate is converted into 2-oxoglutarate is the rate limiting step in the TCA cycle. Its correlation factor was predicted to be 0.95 according to our approach, and 0.79 according to uxomics data. Other rate limiting enzymes, such as pyruvate kinase and -ketoglutarate dehydrogenase, were inferred to have a strong correlation between reaction rate and gene expression level by both our approach and the uxomics data. This also indicates a good prediction ability of our approach.

B. INVESTIGATING THE METABOLIC ALTERATION OF P. AERUGINOSA UPON THE TREATMENT OF RIBOSOME TARGETED ANTIBIOTICS

Our approach was applied to the microarray data presented by Dotsch et al. [16] to determine the metabolic reactions that are positively correlated with the gene expression levels in P. aeruginosa. In particular, gene expression data of P. aeruginosa at multiple time points (4, 12, 24, 48, and 4 h as control) in planktonic growth and bio lm formation were used to determine the correlation factors between gene expression levels and reaction rates. Expression patterns of metabolic genes were extracted and then integrated with the metabolic model for P. aeruginosa. Results revealed that 112 reactions out of all 1110 reactions are associated with positive correlation factors. As mentioned-above, the activities of reactions depend on both the enzyme levels and the reactant (or substrate) availability. The latter is constrained by the topology of the metabolic network. The reactions with higher correlation factors are more enzyme-dependent,

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while the reactions with lower correlation factors are more substrate-dependent or network-dependent. Thus, the reactions with higher correlation factors should be more sensitive to the ribosome-targeted antibiotics.

The obtained correlation factors were applied to constrain metabolic uxes, as shown in Fig. 1(B) to predict the metabolism variation. It turned out that ten reversible reactions changed their ux directions, 171 reactions increased their uxes, 372 reactions had decreased ux values, and 558 reactions did not change their uxes. Supplementary Document 2 shows the distribution of ux variation among different metabolic pathways. The categories of metabolic pathways were de ned by Oberhardt et al. [12]. Some of the metabolic pathways with large ux change have been found important by experiment for the persister cell formation of P. aeruginosa. These metabolic pathways will be discussed in detail in the next sections.

Some of the reactions with large ux change were found to be involved in persister cell formation and the antibiotic resistance of P. aeruginosa. These reactions were mainly related to the homoserine metabolism, the production of 2-heptyl-4-quinolone (HHQ), isocitrate lyase, and indole derivatives, and exchange reactions of some extracellular components. The detail of these reactions was given in this section.

FIGURE 3. Flux adjustment of the homoserine metabolism upon the treatment of antibiotics.

Acyl-homoserine-lactone behaves as a quorum-sensing molecule and triggers persister cell formation in P. aeruginosa [17]. Our approach predicted the ux change in the homoserine metabolism that was consistent with this observation. Fig. 3 illustrated the change of uxes in the metabolic reactions for the synthesis of L-Homocysteine. Speci cally, the uxes of the synthesis reactions for L-Threonine and L- Homocysteine were enhanced, while the synthesis rate of L- Cystathinonine was decreased. L-Homocysteine is a precursor of acyl-homoserine-lactone, as it leads to the synthesis of S-adenosylmethionine, a reactant for acyl-homoserine- lactone synthesis. According to the FBA results, the enhanced L-Homocysteine synthesis results in the enhancement of the acyl-homoserine-lactone. This provides a possible explanation for the presence of antibiotics triggering the formation of P. aeruginosa persister cells.

Wei et al. [18] reported that 2-heptyl-3-hydroxy-4- quinolone (PQS) production was strongly reduced in persister strains PAO-SCV. The production rates of HHQ and PQS were predicted to be downregulated to 0.0559 of their nominal values, which is consistent with the data shown in [18].

It has been suggested that the persistence of Mycobacterium tuberculosis, which shares orthologous genes for

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FIGURE 4. Metabolites, which the exchange rates are significantly increased after antibiotic treatment.

energy production and conversion with P. aeruginosa [19], requires the elevation of the intracellular level of isocitrate lyase, which is a key anaplerotic enzyme for the glyoxylate bypass [20]. Our results showed that the ux of the reaction catalyzed by isocitrate lyase was enhanced to 5.89 fold of its nominal value upon the treatment of ribosome-targeting antibiotics, such as rifampicin. In addition to this enzyme, enzymes acetyl-CoA C-acetyltransferase and putrescine aminotransferase were found to be positively related to the persister cell formation of P. aeruginosa [21]. Our results indicated that the uxes of the reactions catalyzed by these enzymes were increased by 1.26 and 1.28 folds of their nominal values.

The ux change in the exchange reactions was further analyzed, and Fig. 4 showed the metabolites whose exchange rates were signi cantly increased compared with the control condition. Some of them are related to microbial persister formation. For instance, acetate enhances protein aggregation and the generation of persisters [23]. The data of Fig. 4 indicate that the exchange rate of acetate increased more than ninefold in P. aeruginosa upon addition of antibiotics. Agmatine was reported to induce antibiotic resistance [24], and our results showed an increase in production of agmatine after antibiotics treatment. Ma et al. [25] demonstrated that oxoglutarate metabolism was important for antibiotic tolerance in E. coli showing that a sucB mutant de cient in 2-oxoglutarate dehydrogenase complex had decreased viability when exposed to antibiotics. Our results support this result since the exchange rate of oxoglutarate was signi cantly enhanced. Amato et al. [26] demonstrated that the switch from glucose to fumarate promoted persister cell formation of E. coli. This is shown in our results as there was an increase in fumarate exchange rate. Cava et al. [27] demonstrated that D-alanine was able to inhibit the spore germination. Our results about D-alanine support the nding.

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