Biology subjects

Hogan, D. A.

Publications and source records attributed to Hogan, D. A..

At least 37 records · Page 2Linked to original sources

bioRxiv2021

Tobramycin suppresses cystic fibrosis lung inflammation by increasing 5' tRNA-fMet halves secreted by P. aeruginosa

Although inhaled tobramycin increases lung function in people with cystic fibrosis (pwCF), the density of P. aeruginosa in the lungs is only modestly reduced by tobramycin; hence, the mechanism whereby tobramycin improves lung function is unclear. Here, we demonstrate that tobramycin increases the abundance of two 5' tRNA-fMet halves in outer membrane vesicles (OMVs) secreted by P. aeruginosa and that the 5' tRNA-fMet halves reduce IL-8 secretion by CF bronchial epithelial cells (CF-HBECs). In mouse lung, the 5' tRNA-fMet halves attenuate KC secretion and neutrophil recruitment. We also report that the 5' tRNA-fMet halves suppress pro-inflammatory network gene expression by an Argonaut 2 (AGO2)-mediated gene silencing mechanism, thereby reducing IL-8 secretion in CF-HBECs. Moreover, tobramycin reduces the IL-8 concentration and neutrophil content in bronchoalveolar lavage fluid of pwCF. Thus, we conclude that tobramycin improves lung function in part by reducing chronic inflammation and neutrophil-mediated lung damage in pwCF.

immunology↗

bioRxiv2021

The Candida albicans Cdk8-dependent phosphoproteome reveals repression of hyphal growth through a Flo8-dependent pathway

Ssn3, also known as Cdk8, is a member of the four protein Cdk8 submodule within the multi-subunit Mediator complex involved in the co-regulation of transcription. In Candida albicans, the loss of Ssn3 kinase activity affects multiple phenotypes including cellular morphology, metabolism, nutrient acquisition, immune cell interactions, and drug resistance. In these studies, we generated a strain in which Ssn3 was replaced with a functional variant of Ssn3 that can be rapidly and selectively inhibited by the ATP analog 3-MB-PP1. Consistent with ssn3 null mutant and kinase dead phenotypes, inhibition of Ssn3 kinase activity promoted hypha formation. Furthermore, the increased expression of hypha-specific genes was the strongest transcriptional signal upon inhibition of Ssn3 in transcriptomics analyses. Rapid inactivation of Ssn3 was used for phosphoproteomic studies performed to identify Ssn3 kinase substrates associated with filamentation potential. Both previously validated and novel Ssn3 targets were identified. Protein phosphorylation sites that were reduced specifically upon Ssn3 inhibition included two sites in Flo8 which is a transcription factor known to positively regulate C. albicans morphology. Mutation of the two Flo8 phosphosites (threonine 589 and serine 620) was sufficient to increase Flo8-HA levels and Flo8 dependent activity, suggesting that Ssn3 kinase activity negatively regulates Flo8. Previous work has also shown that loss of Ssn3 activity leads to increased alkalinization of medium with amino acids. Here, we show that FLO8 and STP2, a transcription factor involved in amino acid utilization, are required for ssn3{Delta}/{Delta} phenotype, but that loss of the Ssn3 phosphosites identified in Flo8 was not sufficient to phenocopy the ssn3{Delta}/{Delta} mutant. These data highlight the spectrum of processes affected by the modulation of Ssn3 activity and underscore the importance of considering Ssn3 function in the control of transcription factor activities.

microbiology↗

bioRxiv2021

Generative neural networks separate common and specific transcriptional responses

Genome-wide transcriptome profiling identifies genes that are prone to differential expression across contexts ("common DEGs"), as well as genes with changes specific to the experimental manipulation. Distinguishing common DEGs from those that are specifically changed in a context of interest allows more efficient prediction of which genes are specific to a given biological process under scrutiny. Currently, commonly differentially expressed genes or pathways can only be identified through the laborious manual curation of highly controlled experiments, an inordinately time-consuming and impractical endeavor. Here we pioneer an approach for identifying common patterns using generative neural networks. This approach produces a background set of transcriptomic experiments from which a null distribution of gene and pathway changes can be generated. By comparing the set of differentially expressed genes found in a target experiment against the generated background set, common results can be easily separated from specific ones. This "Specific cOntext Pattern Highlighting In Expression data" (SOPHIE) approach is broadly applicable to new platforms or any species with a large collection of gene expression data. We apply SOPHIE to diverse datasets including those from human, human cancer, and the bacterial pathogen Pseudomonas aeruginosa. SOPHIE identifies common DEGs in concordance with previously described, manually and systematically determined common DEGs. Further, molecular validation indicates that SOPHIE detects highly specific, but low magnitude, biologically relevant, transcriptional changes. SOPHIEs measure of specificity can complement log fold change values generated from traditional differential expression analyses. For example, by filtering the set of differentially expressed genes, one can identify those genes that are specifically relevant to the experimental condition of interest. Consequently, these results can inform future research directions.

bioinformatics↗

bioRxiv2021

Calprotectin-mediated zinc chelation inhibits Pseudomonas aeruginosa protease activity in cystic fibrosis sputum

Pseudomonas aeruginosa induces pathways indicative of low zinc availability in the cystic fibrosis (CF) lung environment. To learn more about P. aeruginosa zinc access in CF, we grew P. aeruginosa strain PAO1 directly in expectorated CF sputum. The P. aeruginosa Zur transcriptional repressor controls the response to low intracellular zinc, and we used the NanoString methodology to monitor levels of Zur-regulated transcripts including those encoding a zincophore system, a zinc importer, and paralogs of zinc containing proteins that do not require zinc for activity. Zur-controlled transcripts were induced in sputum-grown P. aeruginosa compared to control cultures, but not if the sputum was amended with zinc. Amendment of sputum with ferrous iron did not reduce expression of Zur-regulated genes. A reporter fusion to a Zur-regulated promoter had variable activity in P. aeruginosa grown in sputum from different donors, and this variation inversely correlated with sputum zinc concentrations. Recombinant human calprotectin (CP), a divalent-metal binding protein released by neutrophils, was sufficient to induce a zinc-starvation response in P. aeruginosa grown in laboratory medium or zinc-amended CF sputum indicating that CP is functional in the sputum environment. Zinc metalloproteases comprise a large fraction of secreted zinc-binding P. aeruginosa proteins. Here we show that recombinant CP inhibited both LasB-mediated casein degradation and LasA-mediated lysis of Staphylococcus aureus, which was reversible with added zinc. These studies reveal the potential for CP-mediated zinc chelation to post-translationally inhibit zinc metalloprotease activity and thereby impact the protease-dependent physiology and/or virulence of P. aeruginosa in the CF lung environment. ImportanceThe factors that contribute to worse outcomes in individuals with cystic fibrosis (CF) with chronic Pseudomonas aeruginosa infections are not well understood. Therefore, there is a need to understand environmental factors within the CF airway that contribute to P. aeruginosa colonization and infection. We demonstrate that growing bacteria in CF sputum induces a zinc-starvation response that inversely correlates with sputum zinc levels. Additionally, both calprotectin and a chemical zinc chelator inhibit the proteolytic activities of LasA and LasB proteases suggesting that extracellular zinc chelators can influence proteolytic activity and thus P. aeruginosa virulence and nutrient acquisition in vivo.

microbiology↗

bioRxiv2020

Balancing positive and negative selection: in vivo evolution of Candida lusitaniae MRR1

The evolution of pathogens in response to selective pressures present during chronic infections can influence persistence, virulence, and the outcomes of antimicrobial therapy. Because subpopulations within an infection can be spatially separated and the host environment can fluctuate, an appreciation of the pathways under selection may be most easily revealed through the analysis of numerous isolates from single infections. Here, we continued our analysis of a set of clonally-derived Clavispora (Candida) lusitaniae isolates from a single chronic lung infection with a striking enrichment in the number of alleles of MRR1. Genetic and genomic analyses found evidence for repeated acquisition of gain-of-function mutations that conferred constitutive Mrr1 activity. In the same population, there were multiple alleles with both gain-of-function mutations and secondary suppressor mutations that either attenuated or abolished the constitutive activity suggesting the presence of counteracting selective pressures. Our studies demonstrated tradeoffs between high Mrr1 activity, which confers resistance to the antifungal fluconazole, host factors, and bacterial products through its regulation of MDR1, and resistance to hydrogen peroxide, a reactive oxygen species produced in the neutrophilic environment associated with this infection. This inverse correlation between high Mrr1 activity and hydrogen peroxide resistance was observed in multiple Candida species and in serial analysis of populations from this individual collected over three years. These data lead us to propose that dynamic or variable selective pressures can be reflected in population genomics and that these dynamics can complicate the drug resistance profile of the population. ImportanceUnderstanding microbial evolution within patients is critical for managing chronic infections and understanding host-pathogen interactions. Here, our analysis of multiple MRR1 alleles in isolates from a single Clavispora (Candida) lusitaniae infection revealed the selection for both high and low Mrr1 activity. Our studies reveal tradeoffs between high Mrr1 activity, which confers resistance to the commonly used antifungal fluconazole, host antimicrobial peptides and bacterial products, and resistance to hydrogen peroxide. This work suggests that spatial or temporal differences within chronic infections can support a large amount of dynamic and parallel evolution, and that Mrr1 activity is under both positive and negative selective pressure to balance different traits that are important for microbial survival.

microbiology↗

bioRxiv2020

Pseudomonas aeruginosa and Candida albicans both accumulate greater biomass in dual species biofilms under flow

Spatially structured communities of microbes - biofilms - are widespread in nature, and biofilm-dwelling microbes often respond to their environments in ways that are different from their planktonic counterparts. Further, most natural biofilms are multi-species mixtures of microorganisms; the ecology of intra- and inter-species interactions in these consortia, and the resulting effects on total community properties, are often not well understood. A common site of polymicrobial biofilm infections is the lungs of patients with cystic fibrosis (CF). CF is a genetic disorder in humans that leads to colonization of the lungs by a variety of microorganisms, including Pseudomonas aeruginosa and Candida albicans. These opportunistic pathogens are frequently co-isolated from infected lungs, in addition to other infection sites including urinary and intravenous catheters. To study how these microbes behave together in biofilms, we developed a modified artificial sputum medium that is optically clear for use with microfluidic culture. In addition, we engineered strains with optimized fluorescent protein expression constructs allowing for single-cell resolution confocal microscopy. Using these tools and recently developed methods for spatial analysis of 3-D image data, we found that both P. aeruginosa and C. albicans display increased biovolume accumulation in multi-species biofilms relative to single-species biofilms. This pattern did not occur in planktonic co-culture and was thus specific to the biofilm environment. Interestingly, introduction of P. aeruginosa supernatants over dual-species biofilms strongly reduced C. albicans biovolume. This suggests that products that accumulate in batch culture were still inhibitory to C. albicans under a flow regime, but that they their de novo production in mixed species biofilms was not sufficient to inhibit C. albicans biofilm accumulation. Altogether our results indicate a critical impact of flow environment for the outcome of polymicrobial interactions and the need for high-resolution analysis of such communities in future work.

microbiology↗

bioRxiv2020

Mrr1 regulation of methylglyoxal catabolism and methylglyoxal-induced fluconazole resistance in Candida lusitaniae

In Candida species, the transcription factor Mrr1 regulates azole resistance genes in addition to the expression of a suite of other genes including known and putative methylglyoxal reductases. Methylglyoxal (MG) is a toxic metabolic byproduct that is significantly elevated in certain disease states that frequently accompany candidiasis, including diabetes, kidney failure, sepsis, and inflammation. Through the genetic analysis of Candida lusitaniae (syn. Clavispora lusitaniae) strains with different Mrr1 variants with high and low basal activity, we showed that Mrr1 regulates basal and/or induced expression of two highly similar MG reductases, MGD1 and MGD2, and that both participate in MG detoxification and growth on MG as a sole carbon source. We found that exogenous MG increases Mrr1-dependent expression of MGD1 and MGD2 in C. lusitaniae suggesting that Mrr1 is part of the natural response to MG. MG also induced expression of MDR1, which encodes a major facilitator protein involved in fluconazole resistance, in a partially Mrr1-dependent manner. MG significantly improved growth of C. lusitaniae in the presence of fluconazole and strains with hyperactive Mrr1 variants showed greater increases in growth in the presence of fluconazole by MG. In addition to the effects of exogenous MG, we found knocking out GLO1, which encodes another MG detoxification enzyme, led to increased fluconazole resistance in C. lusitaniae. Analysis of isolates other Candida species found heterogeneity in MG resistance and MG stimulation of growth in the presence of fluconazole. Given the frequent presence of MG in human disease, we propose that induction of MDR1 in response to MG is a novel contributor to in vivo resistance of azole antifungals in multiple Candida species. Author SummaryIn Candida species, constitutively active variants of the transcription factor Mrr1 confer resistance to fluconazole, a commonly used antifungal agent. However, the natural role of Mrr1 as well as how its activity is modulated in vivo remain poorly understood. Here, we have shown that, in the opportunistic pathogen Candida lusitaniae, Mrr1 regulates expression and induction of two enzymes that detoxify methylglyoxal, a toxic metabolic byproduct. Importantly, serum methylglyoxal is elevated in conditions that are also associated with increased risk of colonization and infection by Candida species, such as diabetes and kidney failure. We discovered that methylglyoxal causes increased expression of these two Mrr1-regulated detoxification enzymes as well as an efflux pump that causes fluconazole resistance. Likewise, methylglyoxal increased the ability of multiple C. lusitaniae strains to grow in the presence of fluconazole. Several other Candida strains that we tested also exhibited stimulation of growth on fluconazole by methylglyoxal. Given the physiological relevance of methylglyoxal in human disease, we posit that the induction of fluconazole resistance in response to methylglyoxal may contribute to treatment failure.

microbiology↗

bioRxiv2020

Correcting for experiment-specific variability in expression compendia can remove underlying signals

MotivationIn the last two decades, scientists working in different labs have assayed gene expression from millions of samples. These experiments can be combined into compendia and analyzed collectively to extract novel biological patterns. Technical variability, sometimes referred to as batch effects, may result from combining samples collected and processed at different times and in different settings. Such variability may distort our ability to interpret and extract true underlying biological patterns. As more multi-experiment, integrative analysis methods are developed and available data collections increase in size, it is crucial to determine how technical variability affect our ability to detect desired patterns when many experiments are combined ObjectiveWe sought to determine the extent to which an underlying signal was masked by technical variability by simulating compendia comprised of data aggregated across multiple experiments. MethodWe developed a generative multi-layer neural network to simulate compendia of gene expression experiments from large-scale microbial and human datasets. We compared simulated compendia before and after introducing varying numbers of sources of undesired variability. ResultsWe found that the signal from a baseline compendium was obscured when the number of added sources of variability was small. Perhaps as expected, applying statistical correction methods rescued the underlying signal in these cases. As the number of sources of variability increased, surprisingly, we observed that detecting the original signal became increasingly easier even without correction. In fact, applying statistical correction methods reduced our power to detect the underlying signal. ConclusionWhen combining a modest number of experiments, it is best to correct for experiment-specific noise. However, when many experiments are combined, statistical correction reduces ones ability to extract underlying patterns.

bioinformatics↗

bioRxiv2020

Intra-species signaling between distinct Pseudomonas aeruginosa genotypes increases production of quorum sensing controlled virulence factors

The opportunistic pathogen Pseudomonas aeruginosa damages hosts through the production of diverse secreted products, many of which are regulated by quorum sensing. The lasR gene, which encodes a central quorum-sensing regulator, is frequently mutated, and loss of LasR function impairs the activity of downstream regulators RhlR and PqsR. We found that in diverse models, the presence of P. aeruginosa wild type causes LasR loss-of-function strains to hyperproduce RhlR/I-regulated antagonistic factors, and autoinducer production by the wild type is not required for this effect. We uncovered a reciprocal interaction between isogenic wild type and lasR mutant pairs wherein the iron-scavenging siderophore pyochelin, specifically produced by the lasR mutant, induces citrate release and cross-feeding from wild type. Citrate stimulates RhlR signaling and RhlI levels in LasR-but not in LasR+ strains, and the interactions occur in diverse media. Co-culture interactions between strains that differ by the function of a single transcription factor may explain worse outcomes associated with mixtures of LasR+ and LasR loss-of-function strains. More broadly, this report illustrates how interactions within a genotypically diverse population, similar to those that frequently develop in natural settings, can promote net virulence factor production.

microbiology↗

bioRxiv2020

Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: an intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics

Pseudomonas aeruginosa and Candida albicans are opportunistic pathogens whose interactions involve the secreted products ethanol and phenazines. Here we describe the focal role of ethanol in mixed-species co-cultures by dual RNA-seq analyses. P. aeruginosa and C. albicans transcriptomes were assessed after growth in mono-culture or co-culture with either ethanol-producing C. albicans or a C. albicans mutant lacking the primary ethanol dehydrogenase, Adh1. Analyses using KEGG-pathways and the previously published eADAGE method revealed several P. aeruginosa responses to C. albicans-produced ethanol including the induction of a non-canonical low phosphate response mediated by PhoB. C. albicans wild-type, but not C. albicans adh1{Delta}/{Delta}, induces P. aeruginosa production of 5-methyl-phenazine-1-carboxylic acid (5-MPCA), which forms a red derivative within fungal cells. We first demonstrate that PhoB is required for this interaction and that PhoB hyperactivity, via deletion of pstB, leads to increased production of 5-MPCA even when phosphate concentrations are high, but only in the presence of ethanol. Second, we show that ethanol is only sufficient to promote 5-MPCA production at permissive phosphate concentrations. The intersection of ethanol and phosphate in co-culture is mirrored in C. albicans; the adh1{Delta}/{Delta} mutant had increased expression of genes regulated by Pho4, the C. albicans transcription factor that responds to low phosphate which we confirmed by showing the adh1{Delta}/{Delta} strain had elevated Pho4-dependent phosphatase activity. The dual-dependence on ethanol and phosphate concentrations for anti-fungal production highlights how environmental factors modulate microbial interactions and dictate antagonisms such as those between P. aeruginosa and C. albicans. Author SummaryPseudomonas aeruginosa and Candida albicans are opportunistic pathogens that are frequently isolated from co-infections. Using a Dual-Seq approach in combination with genetics approaches, we found that ethanol produced by C. albicans stimulates the PhoB regulon in P. aeruginosa asynchronously with activation of the Pho4 regulon in C. albicans. In doing so, we demonstrate that eADAGE-based analysis can improve the understanding of the P. aeruginosa response to ethanol-producing C. albicans as measured by transcriptomics: we identify a subset of PhoB-regulated genes as differentially expressed in response to ethanol. We validate our result by showing that PhoB is necessary for multiple roles in co-culture including the competition for phosphate and the production of 5-methyl-phenazine-1-carboxylic acid, and that the P. aeruginosa response to C. albicans-produced ethanol depends on phosphate availability. The conditional stimulation of virulence production in response to sub-inhibitory concentrations of ethanol only under phosphate limitation highlights the importance of considering nutrient concentrations in the analysis of co-culture interactions.

microbiology↗

bioRxiv2019

Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin

Pseudomonas aeruginosa strains with loss-of-function mutations in the transcription factor are frequently encountered in the clinic and the environment. Among the characteristics common to LasR-defective (LasR-) strains is increased activity of the transcription factor Anr, relative to their LasR+ counterparts, in low oxygen conditions. One of the Anr-regulated genes that was highly induced in the LasR-strains encoded a putative oxygen-binding hemerythrin encoded by PA14_42860 (PA1673) which we named mhr for microoxic hemerythrin. Purified P. aeruginosa Mhr protein contained the predicted di-iron center and binds oxygen with a Kd of 1 {micro}M. Both Anr and Mhr were necessary for fitness in lasR+ and lasR mutant strains in colony biofilms grown in microoxic conditions, and the effects were more striking in the lasR mutant. Among genes in the Anr regulon, mhr was most closely co-regulated with the Anr-controlled high affinity cytochrome c oxidase genes and in the absence of high affinity cytochrome c oxidase activity, deletion of mhr no longer caused a fitness disadvantage suggesting that Mhr works in concert with microoxic respiration. We demonstrate that Anr and Mhr contribute to LasR-strain fitness even in the normoxic biofilm conditions, and metabolomics data indicate that in a lasR mutant, expression of Anr-regulated mhr leads to differences in metabolism in cells grown on LB and artificial sputum medium. Together these data indicate that increased Anr activity in microoxically-grown lasR mutants confers an advantage in part for its regulation of the O2 binding protein Mhr.\n\nSignificancePseudomonas aeruginosa, a versatile bacterium that both lives in environmental habitats and causes life-threatening opportunistic infections, uses quorum sensing to coordinate gene expression with cell density. The lasR gene, which encodes a quorum sensing regulator, is often deleteriously mutated in clinical isolates. Interestingly, LasR-strains have high activity of the oxygen-sensitive transcription factor Anr in microoxic conditions. This report identifies and characterizes an Anr-regulated microoxic hemerythrin that reversibly binds oxygen. We showed both anr and mhr are critical to fitness in microoxia, and these genes uniquely benefit LasR-strains in normoxia. Our findings enrich our understanding of the success of P. aeruginosa as a pulmonary resident through its propensity to lose LasR functionality in the context of low-oxygen infection environments.

microbiology↗

bioRxiv2019

Phenotypic differences in reversible attachment behavior reveal distinct P. aeruginosa surface colonization strategies

Despite possessing the machinery to sense, adhere to, and proliferate on surfaces, it is commonly observed that bacteria initially have a difficult time attaching to a surface. Before forming a bacterial biofilm, planktonic bacteria exhibit a random period of transient surface attachment known as \"reversible attachment\" which is poorly understood. Using community tracking methods at single-cell resolution, we examine how reversible attachment progresses during initial stages of surface sensing. Pseudomonas aeruginosa strains PAO1 and PA14, which exhibit similar exponential trends of surface cell population increase, show unanticipated differences when the behavior of each cell was considered at the full lineage level and interpreted using the unifying quantitative framework of an exactly solvable stochastic model. Reversible attachment comprises two regimes of behavior, processive and nonprocessive, corresponding to whether cells of the lineage stay on the surface long enough to divide, or not, before detaching. Stark differences between PAO1 and PA14 in the processive regime of reversible attachment suggest the existence of two complementary surface colonization strategies, which are roughly analogous to \"immediate-\" vs \"deferred-gratification\" in a prototypical cognitive-affective processing system. PAO1 lineages commit relatively quickly to a surface compared to PA14 lineages. PA14 lineages allow detaching cells to retain memory of the surface so that they are primed for improved subsequent surface attachment. In fact, it is possible to identify motility suppression events in PA14 lineages in the process of surface commitment. We hypothesize that these contrasting strategies are rooted in downstream differences between Wsp-based and Pil-Chp-based surface sensing systems.

microbiology↗

bioRxiv2019

Pseudomonas aeruginosa ethanol oxidation by AdhA in low oxygen environments

Pseudomonas aeruginosa has a broad metabolic repertoire that facilitates its co-existence with different microbes. Many microbes secrete products that P. aeruginosa can then catabolize, including ethanol, a common fermentation product. Here, we show that under oxygen limiting conditions P. aeruginosa utilizes AdhA, an NAD-linked alcohol dehydrogenase, as a previously undescribed means for ethanol catabolism. In a rich medium containing ethanol, AdhA, but not the previously described PQQ-linked alcohol dehydrogenase, ExaA, oxidizes ethanol and leads to the accumulation of acetate in culture supernatants. AdhA-dependent acetate accumulation, and the accompanying decrease in pH, promotes P. aeruginosa survival in LB-grown stationary phase cultures. The transcription of adhA is elevated by hypoxia and in anoxic conditions, and we show that it is regulated by the Anr transcription factor. We have shown that lasR mutants have higher levels of Anr-regulated transcripts in low oxygen conditions compared to their wild type counterparts. Here, we show that a lasR mutant, when grown with ethanol, has an even larger decrease in pH than WT that is dependent on both anr and adhA. The large increase in AdhA activity similar to that of a strain expressing a hyperactive Anr-D149A variant. Ethanol catabolism in P. aeruginosa by AdhA supports growth on ethanol as a sole carbon source and electron donor in oxygen-limited settings and in cells growing by denitrification in anoxic conditions. This is the first demonstration of a physiological role for AdhA in ethanol oxidation in P. aeruginosa.\n\nImportanceEthanol is a common product of microbial fermentation, and the Pseudomonas aeruginosa response to and utilization of ethanol is relevant to our understanding of its role in microbial communities. Here, we report that the putative alcohol dehydrogenase, AdhA, is responsible for ethanol catabolism and acetate accumulation in low oxygen conditions and that it is regulated by Anr.

microbiology↗

bioRxiv2019

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Here we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility (P. aureginosa only). We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. We conclude that, while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. We finally report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bioontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

bioinformatics↗

bioRxiv2019

Ethanol stimulates trehalose production through a SpoT-DksA-AlgU dependent pathway in Pseudomonas aeruginosa

Pseudomonas aeruginosa frequently resides among ethanol-producing microbes, making its response to these microbially-produced concentrations of ethanol relevant to understanding its biology. Our ranscriptome analysis found that the genes involved in trehalose metabolism were induced by low concentrations of ethanol, and levels of intracellular trehalose increased significantly upon growth with ethanol. The increase in trehalose was dependent on the TreYZ pathway, but not other trehalose metabolic enzymes TreS or TreA. The sigma factor AlgU (AlgT), a homolog of RpoE in other species, was required for increased expression of the treZ gene and trehalose levels, but induction was not controlled by the well-characterized proteolysis of its antisigma factor MucA. Growth with ethanol led to increased SpoT-dependent (p)ppGpp accumulation, which stimulates AlgU-dependent transcription of treZ and other AlgU-regulated genes through DksA, a (p)ppGpp and RNA polymerase binding protein. Ethanol stimulation of trehalose also required acylhomoserine lactone (AHL)-mediated quorum sensing, as induction was not observed in a {Delta}lasR{Delta}rhlR strain. A network analysis using a model, eADAGE, built from publicly available P. aeruginosa transcriptome datasets (1) provided strong support for our model that treZ and co-regulated genes are controlled by both AlgU and AHL-mediated QS (QS). Consistent with (p)ppGpp and AHL-mediated quorum sensing regulation, ethanol, even when added at the time of culture inoculation, stimulated treZ transcript levels and trehalose production in cells from post-exponential phase cultures but not from exponential phase cultures. These data highlight the integration of growth and cell density cues in the P. aeruginosa transcriptional response to ethanol.\n\nImportancePseudomonas aeruginosa is often found with bacteria and fungi that produce fermentation products including ethanol. At concentrations similar to those produced by environmental microbes, we found that ethanol stimulated expression of trehalose biosynthetic genes and cellular levels of trehalose, a disaccharide that protects against environmental stresses. The induction of trehalose by ethanol required the alternative sigma factor AlgU through DksA and SpoT-dependent (p)ppGpp. Trehalose accumulation also required AHL quorum sensing and only occurred in post-exponential phase cultures. This work highlights how cells integrate cell-density and growth cues in their responses to products made by other microbes and a reveals a new role for (p)ppGpp in the regulation of AlgU activity.

microbiology↗

bioRxiv2018

Ethanol decreases Pseudomonas aeruginosa flagellar motility through a cyclic-di-GMP- and stator-dependent pathway

Pseudomonas aeruginosa frequently encounters microbes that produce bioactive metabolites including ethanol. At concentrations that do not affect growth, we found that ethanol reduces P. aeruginosa motility by 30% in a swim agar assay and this decrease is accompanied by a 2.5-fold increase in levels of cyclic diguanylate (c-di-GMP), a second messenger that represses motility, in planktonic cells. A screen of mutants lacking genes involved in c-di-GMP metabolism identified SadC and GcbA as diguanylate cyclases involved in swim zone reduction by ethanol and ethanol-induced c-di-GMP production. The reduction of swimming in response to ethanol also required the stator set, MotAB, two PilZ-domain proteins (FlgZ and PilZ), PilY1-a proposed surface-sensing protein, and PilMNOP, which comprises the pilus alignment complex and these proteins have been previously implicated in the control of motility on agar surfaces. Microscopic analysis of the fraction of quiescent cells in swim medium showed that ethanol decreased the portion of motile cells in the wild type, but had opposite effects in the {triangleup}pilY1, {triangleup}pilMNOP, {triangleup}motAB, and {triangleup}pilZ{triangleup}flgZ mutants. Together, these data indicate ethanol induces a regulated change in motility in planktonic cells at concentrations similar to those produced by other microbes. We propose that this ethanol-responsiveness may contribute to the co-localization of P. aeruginosa with ethanol-producing microbes.

microbiology↗

bioRxiv2018

Refining the application of microbial lipids as tracers of Staphylococcus aureus growth rates in cystic fibrosis sputum

Chronic lung infections in cystic fibrosis (CF) could be treated more effectively if the effect of antimicrobials on pathogens in situ were known. Here, we compared changes in the microbial community composition and pathogen growth rates in longitudinal studies of CF patients undergoing intravenous antibiotic administration during pulmonary exacerbations. Microbial community composition was measured by NanoString DNA analysis and growth rates were obtained by incubating CF sputum with heavy water and tracing incorporation of deuterium into two different anteiso fatty acids (a-C15:0 and a-C17:0) using gas chromatography-mass spectrometry (GC/MS). Prior to this study, both lipids were thought to be specific for Staphylococcaceae and hence their isotopic enrichment was interpreted as a growth proxy for S. aureus. Our experiments revealed, however, that Prevotella is also a relevant microbial producer of a-C17:0 fatty acid in some CF patients, thus deuterium incorporation into these lipids is better interpreted as a more general pathogen growth rate proxy. Even accounting for a small non-microbial background source detected in some patient samples, a-C15:0 fatty acid still appear to be a relatively robust proxy for CF pathogens, revealing a median generation time of ~1.5 days, similar to prior observations. Contrary to our expectations, pathogen growth rates remained relatively stable throughout exacerbation treatment. We suggest two best practices for application of stable isotope probing in CF sputum: (1) parallel determination of microbial community composition in CF sputum using culture-independent tools, and (2) analysis of samples with a minimum a-C15:0 concentration of 0.1 weight percent of saturated fatty acids.\n\nIMPORTANCEIn chronic lung infections, populations of microbial pathogens change and mature in ways that are often unknown, which makes it challenging to identify appropriate treatment options. A promising tool to better understand the physiology of microorganisms in a patient is stable-isotope probing, which we previously developed to estimate the growth rates of S. aureus in cystic fibrosis (CF) sputum. Here, we tracked microbial communities in a cohort of CF patients and found that anteiso fatty acids can also originate from other sources in CF sputum. This awareness led us to develop an new workflow for the application of stable isotope probing in this context, improving our ability to estimate pathogen generation times in clinical samples.

microbiology↗

bioRxiv2018

Profiling of bacterial and fungal microbial communities in cystic fibrosis sputum using RNA

Here, we report an approach to detect diverse bacterial and fungal taxa in complex samples by direct analysis of community RNA in one step using NanoString probe sets. We designed rRNA-targeting probe sets to detect forty two bacterial and fungal genera or species common in cystic fibrosis (CF) sputum, and demonstrated taxon-specificity of these probes as well as a linear response over more than three logs of input RNA. Culture-based analyses correlated qualitatively with relative abundance data on bacterial and fungal taxa obtained by NanoString and the analysis of serial samples demonstrated the use of this method to simultaneously detect bacteria and fungi and to detect microbes at low abundance without an amplification step. The relative abundances of bacterial taxa detected by analysis of RNA correlated with the relative abundances of the same taxa as measured by sequencing of the V4V5 region of the 16S rRNA gene amplified from community DNA from the same sample. We propose that this method may complement other methods designed to understand dynamic microbial communities, may provide information on bacteria and fungi in the same sample with a single assay, and, with further development, may provide quick and easily-interpreted diagnostic information on diverse bacteria and fungi at the genus or species level.\n\nImportanceHere we demonstrate the use of an RNA-based analysis of specific taxa of interest, including bacteria and fungi, within microbial communities. This multiplex method may be useful as a means to identify samples with specific combinations of taxa and to gain information on how specific populations vary over time and space or in response to perturbation. A rapid means to measure bacterial and fungal populations may aid in the study of host response to changes in microbial communities.

microbiology↗