Transition Metals and Virulence in Bacteria.

Transition metals are required trace elements for all forms of life. Due to their unique inorganic and redox properties, transition metals serve as cofactors for enzymes and other proteins. In bacterial pathogenesis, the vertebrate host represents a rich source of nutrient metals, and bacteria have evolved diverse metal acquisition strategies. Host metal homeostasis changes dramatically in response to bacterial infections, including production of metal sequestering proteins and the bombardment of bacteria with toxic levels of metals. In response, bacteria have evolved systems to subvert metal sequestration and toxicity. The coevolution of hosts and their bacterial pathogens in the battle for metals has uncovered emerging paradigms in social microbiology, rapid evolution, host specificity, and metal homeostasis across domains. This review focuses on recent advances and open questions in our understanding of the complex role of transition metals at the host-pathogen interface.

Acinetobacter Metabolism in Infection and Antimicrobial Resistance.

Acinetobacter infections have high rates of mortality due to an increasing incidence of infections by multidrug-resistant (MDR) and extensively-drug-resistant (XDR) strains. Therefore, new therapeutic strategies for the treatment of Acinetobacter infections are urgently needed. Acinetobacter spp. are Gram-negative coccobacilli that are obligate aerobes and can utilize a wide variety of carbon sources. Acinetobacter baumannii is the main cause of Acinetobacter infections, and recent work has identified multiple strategies A. baumannii uses to acquire nutrients and replicate in the face of host nutrient restriction. Some host nutrient sources also serve antimicrobial and immunomodulatory functions. Hence, understanding Acinetobacter metabolism during infection may provide new insights into novel infection control measures. In this review, we focus on the role of metabolism during infection and in resistance to antibiotics and other antimicrobial agents and discuss the possibility that metabolism may be exploited to identify novel targets to treat Acinetobacter infections.

Broad-spectrum suppression of bacterial pneumonia by aminoglycoside-propagated Acinetobacter baumannii.

Antimicrobial resistance is increasing in pathogenic bacteria. Yet, the effect of antibiotic exposure on resistant bacteria has been underexplored and may affect pathogenesis. Here we describe the discovery that propagation of the human pathogen Acinetobacter baumannii in an aminoglycoside antibiotic results in alterations to the bacterium that interact with lung innate immunity resulting in enhanced bacterial clearance. Co-inoculation of mice with A. baumannii grown in the presence and absence of the aminoglycoside, kanamycin, induces enhanced clearance of a non-kanamycin-propagated strain. This finding can be replicated when kanamycin-propagated A. baumannii is killed prior to co-inoculation of mice, indicating the enhanced bacterial clearance results from interactions with innate host defenses in the lung. Infection with kanamycin-propagated A. baumannii alters the kinetics of phagocyte recruitment to the lung and reduces pro- and anti-inflammatory cytokine and chemokine production in the lung and blood. This culminates in reduced histopathologic evidence of lung injury during infection despite enhanced bacterial clearance. Further, the antibacterial response induced by killed aminoglycoside-propagated A. baumannii enhances the clearance of multiple clinically relevant Gram-negative pathogens from the lungs of infected mice. Together, these findings exemplify cooperation between antibiotics and the host immune system that affords protection against multiple antibiotic-resistant bacterial pathogens. Further, these findings highlight the potential for the development of a broad-spectrum therapeutic that exploits a similar mechanism to that described here and acts as an innate immunity modulator.

Change in Mobility Quality Measure for Inpatient Rehabilitation Facilities: Exclusion Criteria and the Risk Adjustment Model.

OBJECTIVE: To describe the exclusion criteria and updated risk adjustment model developed for the Change in Mobility quality measure in the inpatient rehabilitation facility (IRF) quality reporting program. Facility-level quality measures focused on patient outcomes usually require risk adjustment to account for varied admission characteristics of patients across facilities. DESIGN: This cohort study analyzed admission demographic and clinical factors associated with mobility change scores using the Inpatient Rehabilitation Facility Patient Assessment Instrument (IRF-PAI) data for Medicare patients discharged from IRFs in calendar year 2017. SETTING: A total of 1129 IRFs in the United States. PARTICIPANTS: A total of 493,209 (N=493, 209) Medicare fee-for-service and Medicare Advantage IRF patient stays discharged in calendar year 2017. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Mobility change scores using admission and discharge standardized assessment data from the IRF-PAI. RESULTS: Approximately 53% of patients in the study were female, 67% were aged 65-84 years, and nearly 80% were White. In the final risk adjustment model, 105 covariates were included, explaining 20% of variance in mobility change scores. Key risk adjusters included IRF primary diagnosis group, prior indoor ambulation functioning, age older than 90 years, and 14 of the comorbidities. The model showed good calibration across the range of deciles of predicted IRF mobility change scores; the ratio of the average expected to observed change scores ranged from 0.93-1.03, with all but 1 within ±0.03. CONCLUSIONS: The updated risk adjustment model uses IRF patients' demographic and clinical characteristics to predict their mobility change scores. The exclusion criteria and resulting risk model are used to calculate the risk adjusted Change in Mobility quality measure scores, enabling comparisons of Change in Mobility scores across IRFs.

Change in Self-Care Quality Measure for Inpatient Rehabilitation Facilities: Exclusion Criteria and Risk-Adjustment Model.

OBJECTIVE: To describe the exclusion criteria and risk-adjustment model developed for the quality measure Change in Self-Care. The exclusion criteria and risk adjustment model are used to calculate Change in Self-Care scores, allowing scores to be compared across inpatient rehabilitation facilities (IRFs). DESIGN: This national cohort study examined admission demographic and clinical factors associated with IRF patients' self-care change scores using standardized self-care data for Medicare patients discharged in calendar year 2017. SETTING: A total of 1129 IRFs in the United States. PARTICIPANTS: A total of 493,209 (N=493,209) Medicare Fee-for-Service and Medicare Advantage IRF patient stays INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Self-care change scores using admission and discharge standardized assessment data elements from the Inpatient Rehabilitation Facility-Patient Assessment Instrument. RESULTS: Approximately 53% of patients were female, and 67% were between 65 and 84 years old. The final risk-adjustment model contained 93 clinically relevant risk adjusters and explained 23.1% of variance in self-care change scores. Risk adjusters that had the greatest effect on change scores and included IRF primary diagnosis group (ie, binary risk adjusters representing 13 diagnoses), prior self-care functioning, and age older than 90 years. When split by deciles of expected scores, the ratio of the average expected and observed change scores was within 2% of 1.0 across 8 groups and within 8% at the extremes, showing good predictive accuracy. CONCLUSIONS: The risk adjustment model quantifies the relationship between IRF patients' demographic and clinical characteristics and their self-care score changes. The exclusion criteria and model are used to risk-adjust the IRF Change in Self-Care quality measure.

Inpatient Rehabilitation Facility Patients' Functional Abilities and Validity Testing of the Standardized Self-Care and Mobility Data Elements.

OBJECTIVE: To describe the abilities of Medicare patients in inpatient rehabilitation facilities (IRFs) at admission and discharge using the standardized self-care and mobility data elements and examine the validity of the data elements. These data are used in the Center for Medicare & Medicaid's IRF payment and quality reporting programs. DESIGN: Descriptive study reporting IRF patients' self-care and mobility scores. We also examined content validity and the associations between admission scores and length of stay (LOS), discharge scores and discharge destination, and change scores and the number of comorbidities. SETTING: Patients discharged from 1129 IRFs in 2017. PARTICIPANTS: IRF Medicare fee-for-service and Medicare Advantage patient stays (N = 493,209). INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURE(S): Self-care and mobility item scores, IRF LOS, discharge destination, and categories of the number of comorbidities. RESULTS: For each self-care and mobility activity, patients in IRFs overall made substantial improvements in function between admission and discharge. For example, the percentage of patients independent with eating and toilet transfers increased from 29.04% to 66.68% and 0.80% to 39.87%, respectively, between admission and discharge. Activities represented in the standardized data elements are included in other functional assessment instruments addressing content validity. Analyses showed a monotonic relationship between admission scores and LOS and between discharge scores and discharge to community percentages with only a few exceptions. Self-care and mobility scale change scores decreased as the number of comorbidities increased across categories. CONCLUSIONS: Patients in IRFs overall show functional improvement across each of the activities as defined by the standardized self-care and mobility data elements. The results showing the associations between patient functioning and 3 metrics (LOS, discharge to community rates, and number of comorbidities) support the validity of the data elements measuring functional abilities in the IRF Medicare population.

Inpatient Rehabilitation Facility Change in Self-Care and Change in Mobility Quality Measures: Development and Reliability and Validity Testing.

OBJECTIVE: To describe the development, implementation and reliability and validity testing of the inpatient rehabilitation facility (IRF) Change in Self-Care and Change in Mobility quality measures. DESIGN: We describe the activities involved in developing and implementing the 2 facility-level quality measures, including public comment opportunities. We examined facility-level reliability using split-half testing and Pearson product-moment correlations, Spearman rank correlations, and intraclass correlation coefficients (ICC2,1). We examined validity by comparing facility-level quality measure scores and facility disease-specific certification status. SETTING: All 1117 IRFs in the United States with at least 20 Medicare stays that ended in 2017. PARTICIPANTS: Facility-level quality measure scores (N=1117) were derived from data from 427,517 (self-care) and 427,956 (mobility) Medicare fee-for-service and Medicare Advantage IRF patient stays in 2017. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Facility-level Change in Self-Care and Change in Mobility quality measure scores and facility Disease-Specific Certification for Stroke Rehabilitation from The Joint Commission were used in validity analysis. RESULTS: The split-half quality measure scores showed strong, positive correlations for the facility-level self-care (Pearson=0.903, Spearman=0.884, ICC=0.903, P<.0001) and mobility (Pearson=0.903, Spearman=0.884, ICC= 0.903, P<.0001) quality measure scores, providing evidence of reliability. ICCs remained strong when stratifying by provider volume. IRFs with stroke certification had slightly higher mean and median quality measure scores than IRFs without certification, and IRFs with the higher quality measure scores tended to have a higher percentage of certified IRFs. CONCLUSIONS: Our analyses support the reliability and validity of the Change in Self-Care and Change in Mobility quality measure scores in IRFs.

A Postacute Care Function Process Quality Measure for the Collection of Standardized Self-Care and Mobility Data: Development, Implementation, and Quality Measure Scores.

OBJECTIVE: To describe the development of and quality measure scores for the cross-setting postacute care function process quality measure that requires the collection of standardized self-care and mobility data at admission and discharge and at least 1 function goal. DESIGN: Description of the development and implementation of the quality measure and the associated standardized self-care and mobility data elements. Descriptive analyses of quality measure scores for the first calendar year using data from the Minimum Data Set, the Inpatient Rehabilitation Facility Patient Assessment Instrument, the Long-Term Care Hospitals (LTCH) Continuity Assessment Record and Evaluation Data Set, and Outcome and Assessment Information Set. SETTING: 15,127 skilled nursing facilities (SNFs), 1129 inpatient rehabilitation facilities (IRFs), 414 LTCHs, and 10,352 home health agencies (HHAs) in the United States. PARTICIPANTS: In total there were 9,216,943 stays/quality episodes (N = 9,216,943), including 2,084,774 SNF Medicare fee-for-service patient stays, 493,209 IRF Medicare patient stays, 161,714 patient stays, and 6,477,246 Medicare and Medicaid quality episodes. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Scores for the cross-setting postacute care function process quality measure. RESULTS: The mean process quality measure scores for SNFs, IRFs, LTCHs, and HHAs were 95.5%, 99.7%, 99.1%, and 95.8, respectively. The 10th percentile scores for SNFs, IRFs, LTCHs, and HHAs were 88.5%, 99.3%, 98.4%, and 89.4, respectively, indicating that at least 90% of postacute care providers submitted the standardized data for a large proportion of their patients. Mean quality measure scores did not vary by provider characteristics. CONCLUSIONS: Most SNFs, IRFs, LTCHs, and HHAs submitted the self-care and mobility data, resulting in high quality measure scores during the first year of implementation. The availability of the standardized self-care and mobility data across postacute care settings offers the opportunity to compare the characteristics and functional outcomes of patients treated in postacute care.

Identification of Two Variants of Acinetobacter baumannii Strain ATCC 17978 with Distinct Genotypes and Phenotypes.

Acinetobacter baumannii is a nosocomial pathogen that exhibits substantial genomic plasticity. Here, the identification of two variants of A. baumannii ATCC 17978 that differ based on the presence of a 44-kb accessory locus, named AbaAL44 (A. baumannii accessory locus 44 kb), is described. Analyses of existing deposited data suggest that both variants are found in published studies of A. baumannii ATCC 17978 and that American Type Culture Collection (ATCC)-derived laboratory stocks comprise a mix of these two variants. Yet, each variant exhibits distinct interactions with the host in vitro and in vivo. Infection with the variant that harbors AbaAL44 (A. baumannii 17978 UN) results in decreased bacterial burdens and increased neutrophilic lung inflammation in a mouse model of pneumonia, and affects the production of interleukin 1 beta (IL-1ß) and IL-10 by infected macrophages. AbaAL44 harbors putative pathogenesis genes, including those predicted to encode a type I pilus cluster, a catalase, and a cardiolipin synthase. The accessory catalase increases A. baumannii resistance to oxidative stress and neutrophil-mediated killing in vitro. The accessory cardiolipin synthase plays a dichotomous role by promoting bacterial uptake and increasing IL-1ß production by macrophages, but also by enhancing bacterial resistance to cell envelope stress. Collectively, these findings highlight the phenotypic consequences of the genomic dynamism of A. baumannii through the evolution of two variants of a common type strain with distinct infection-related attributes.

Presence of ß-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals.

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum ß-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant ß-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-ß-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

Staphylococcus aureus Glucose-Induced Biofilm Accessory Protein A (GbaA) Is a Monothiol-Dependent Electrophile Sensor.

Staphylococcus aureus is a commensal pathogen that has evolved to protect itself from unfavorable conditions by forming complex community structures termed biofilms. The regulation of the formation of these structures is multifactorial and in S. aureus involves a number of transcriptional regulators. GbaA (glucose-induced biofilm accessory protein A) is a tetracycline repressor (TetR) family regulator that harbors two conserved Cys residues (C55 and C104) and impacts the regulation of formation of poly-N-acetylglucosamine-based biofilms in many methicillin-resistant S. aureus (MRSA) strains. Here, we show that GbaA-regulated transcription of a divergently transcribed operon in a MRSA strain can be induced by potent electrophiles, N-ethylmaleimide and methylglyoxal. Strikingly, induction of transcription in cells requires C55 or C104, but not both. These findings are consistent with in vitro small-angle X-ray scattering, chemical modification, and DNA operator binding experiments, which reveal that both reduced and intraprotomer (C55-C104) disulfide forms of GbaA have very similar overall structures and each exhibits a high affinity for the DNA operator, while DNA binding is strongly inhibited by derivatization of one or the other Cys residues via formation of a mixed disulfide with bacillithiol disulfide or a monothiol derivatization adduct with NEM. While both Cys residues are reactive toward electrophiles, C104 in the regulatory domain is the more reactive thiolate. These characteristics enhance the inducer specificity of GbaA and would preclude sensing of generalized cellular oxidative stress via disulfide bond formation. The implications of the findings for GbaA function in MRSA strains are discussed.

Histidine Utilization Is a Critical Determinant of Acinetobacter Pathogenesis.

Acinetobacter baumannii is a nosocomial pathogen capable of causing a range of diseases, including respiratory and urinary tract infections and bacteremia. Treatment options are limited due to the increasing rates of antibiotic resistance, underscoring the importance of identifying new targets for antimicrobial development. During infection, A. baumannii must acquire nutrients for replication and survival. These nutrients include carbon- and nitrogen-rich molecules that are needed for bacterial growth. One possible nutrient source within the host is amino acids, which can be utilized for protein synthesis or energy generation. Of these, the amino acid histidine is among the most energetically expensive for bacteria to synthesize; therefore, scavenging histidine from the environment is likely advantageous. We previously identified the A. baumannii histidine utilization (Hut) system as being linked to nutrient zinc homeostasis, but whether the Hut system is important for histidine-dependent energy generation or vertebrate colonization is unknown. Here, we demonstrate that the Hut system is conserved among pathogenic Acinetobacter and regulated by the transcriptional repressor HutC. In addition, the Hut system is required for energy generation using histidine as a carbon and nitrogen source. Histidine was also detected extracellularly in the murine lung, demonstrating that it is bioavailable during infection. Finally, the ammonia-releasing enzyme HutH is required for acquiring nitrogen from histidine in vitro, and strains inactivated for hutH are severely attenuated in a murine model of pneumonia. These results suggest that bioavailable histidine in the lung promotes Acinetobacter pathogenesis and that histidine serves as a crucial nitrogen source during infection.

The Innate Immune Protein S100A9 Protects from T-Helper Cell Type 2-mediated Allergic Airway Inflammation.

Calprotectin is a heterodimer of the proteins S100A8 and S100A9, and it is an abundant innate immune protein associated with inflammation. In humans, calprotectin transcription and protein abundance are associated with asthma and disease severity. However, mechanistic studies in experimental asthma models have been inconclusive, identifying both protective and pathogenic effects of calprotectin. To clarify the role of calprotectin in asthma, calprotectin-deficient S100A9-/- and wild-type (WT) C57BL/6 mice were compared in a murine model of allergic airway inflammation. Mice were intranasally challenged with extracts of the clinically relevant allergen, Alternaria alternata (Alt Ext), or PBS every third day over 9 days. On Day 10, BAL fluid and lung tissue homogenates were harvested and allergic airway inflammation was assessed. Alt Ext challenge induced release of S100A8/S100A9 to the alveolar space and increased protein expression in the alveolar epithelium of WT mice. Compared with WT mice, S100A9-/- mice displayed significantly enhanced allergic airway inflammation, including production of IL-13, CCL11, CCL24, serum IgE, eosinophil recruitment, and airway resistance and elastance. In response to Alt Ext, S100A9-/- mice accumulated significantly more IL-13+IL-5+CD4+ T-helper type 2 cells. S100A9-/- mice also accumulated a significantly lower proportion of CD4+ T regulatory (Treg) cells in the lung that had significantly lower expression of CD25. Calprotectin enhanced WT Treg cell suppressive activity in vitro. Therefore, this study identifies a role for the innate immune protein, S100A9, in protection from CD4+ T-helper type 2 cell hyperinflammation in response to Alt Ext. This protection is mediated, at least in part, by CD4+ Treg cell function.

An Integrated, High-Throughput Strategy for Multiomic Systems Level Analysis.

Proteomics, metabolomics, and transcriptomics generate comprehensive data sets, and current biocomputational capabilities allow their efficient integration for systems biology analysis. Published multiomics studies cover methodological advances as well as applications to biological questions. However, few studies have focused on the development of a high-throughput, unified sample preparation approach to complement high-throughput omic analytics. This report details the automation, benchmarking, and application of a strategy for transcriptomic, proteomic, and metabolomic analyses from a common sample. The approach, sample preparation for multi-omics technologies (SPOT), provides equivalent performance to typical individual omic preparation methods but greatly enhances throughput and minimizes the resources required for multiomic experiments. SPOT was applied to a multiomics time course experiment for zinc-treated HL-60 cells. The data reveal Zn effects on NRF2 antioxidant and NFkappaB signaling. High-throughput approaches such as these are critical for the acquisition of temporally resolved, multicondition, large multiomic data sets such as those necessary to assess complex clinical and biological concerns. Ultimately, this type of approach will provide an expanded understanding of challenging scientific questions across many fields.

Defining the interaction of the protease CpaA with its type II secretion chaperone CpaB and its contribution to virulence in Acinetobacter species.

Acinetobacter baumannii, Acinetobacter nosocomialis, and Acinetobacter pittii are a frequent cause of multidrug-resistant, healthcare-associated infections. Our previous work demonstrated that A. nosocomialis M2 possesses a functional type II secretion system (T2SS) that is required for full virulence. Further, we identified the metallo-endopeptidase CpaA, which has been shown previously to cleave human Factor V and deregulate blood coagulation, as the most abundant type II secreted effector protein. We also demonstrated that its secretion is dependent on CpaB, a membrane-bound chaperone. In this study, we show that CpaA expression and secretion are conserved across several medically relevant Acinetobacter species. Additionally, we demonstrate that deletion of cpaA results in attenuation of A. nosocomialis M2 virulence in moth and mouse models. The virulence defects resulting from the deletion of cpaA were comparable with those observed upon abrogation of T2SS activity. The virulence defects resulting from the deletion of cpaA are comparable with those observed upon abrogation of T2SS activity. We also show that CpaA and CpaB strongly interact, forming a complex in a 1:1 ratio. Interestingly, deletion of the N-terminal transmembrane domain of CpaB results in robust secretion of CpaA and CpaB, indicating that the transmembrane domain is dispensable for CpaA secretion and likely functions to retain CpaB inside the cell. Limited proteolysis of spheroplasts revealed that the C-terminal domain of CpaB is exposed to the periplasm, suggesting that this is the site where CpaA and CpaB interact in vivo Last, we show that CpaB does not abolish the proteolytic activity of CpaA against human Factor V. We conclude that CpaA is, to the best of our knowledge, the first characterized, bona fide virulence factor secreted by Acinetobacter species.

Medically Relevant Acinetobacter Species Require a Type II Secretion System and Specific Membrane-Associated Chaperones for the Export of Multiple Substrates and Full Virulence.

Acinetobacter baumannii, A. nosocomialis, and A. pittii have recently emerged as opportunistic human pathogens capable of causing severe human disease; however, the molecular mechanisms employed by Acinetobacter to cause disease remain poorly understood. Many pathogenic members of the genus Acinetobacter contain genes predicted to encode proteins required for the biogenesis of a type II secretion system (T2SS), which have been shown to mediate virulence in many Gram-negative organisms. Here we demonstrate that Acinetobacter nosocomialis strain M2 produces a functional T2SS, which is required for full virulence in both the Galleria mellonella and murine pulmonary infection models. Importantly, this is the first bona fide secretion system shown to be required for virulence in Acinetobacter. Using bioinformatics, proteomics, and mutational analyses, we show that Acinetobacter employs its T2SS to export multiple substrates, including the lipases LipA and LipH as well as the protease CpaA. Furthermore, the Acinetobacter T2SS, which is found scattered amongst five distinct loci, does not contain a dedicated pseudopilin peptidase, but instead relies on the type IV prepilin peptidase, reinforcing the common ancestry of these two systems. Lastly, two of the three secreted proteins characterized in this study require specific chaperones for secretion. These chaperones contain an N-terminal transmembrane domain, are encoded adjacently to their cognate effector, and their disruption abolishes type II secretion of their cognate effector. Bioinformatic analysis identified putative chaperones located adjacent to multiple previously known type II effectors from several Gram-negative bacteria, which suggests that T2SS chaperones constitute a separate class of membrane-associated chaperones mediating type II secretion.

Integrated, High-Throughput, Multiomics Platform Enables Data-Driven Construction of Cellular Responses and Reveals Global Drug Mechanisms of Action.

An understanding of how cells respond to perturbation is essential for biological applications; however, most approaches for profiling cellular response are limited in scope to pre-established targets. Global analysis of molecular mechanism will advance our understanding of the complex networks constituting cellular perturbation and lead to advancements in areas, such as infectious disease pathogenesis, developmental biology, pathophysiology, pharmacology, and toxicology. We have developed a high-throughput multiomics platform for comprehensive, de novo characterization of cellular mechanisms of action. Platform validation using cisplatin as a test compound demonstrates quantification of over 10 000 unique, significant molecular changes in less than 30 days. These data provide excellent coverage of known cisplatin-induced molecular changes and previously unrecognized insights into cisplatin resistance. This proof-of-principle study demonstrates the value of this platform as a resource to understand complex cellular responses in a high-throughput manner.

Induction of the Sugar-Phosphate Stress Response Allows Saccharomyces cerevisiae 2-Methyl-4-Amino-5-Hydroxymethylpyrimidine Phosphate Synthase To Function in Salmonella enterica.

UNLABELLED: Thiamine pyrophosphate is a required cofactor for all forms of life. The pyrimidine moiety of thiamine, 2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate (HMP-P), is synthesized by different mechanisms in bacteria and plants compared to fungi. In this study, Salmonella enterica was used as a host to probe requirements for activity of the yeast HMP-P synthase, Thi5p. Thi5p synthesizes HMP-P from histidine and pyridoxal-5-phosphate and was reported to use a backbone histidine as the substrate, which would mean that it was a single-turnover enzyme. Heterologous expression of Thi5p did not complement an S. enterica HMP-P auxotroph during growth with glucose as the sole carbon source. Genetic analyses described here showed that Thi5p was activated in S. enterica by alleles of sgrR that induced the sugar-phosphate stress response. Deletion of ptsG (encodes enzyme IICB [EIICB] of the phosphotransferase system [PTS]) also allowed function of Thi5p and required sgrR but not sgrS. This result suggested that the role of sgrS in activation of Thi5p was to decrease PtsG activity. In total, the data herein supported the hypothesis that one mechanism to activate Thi5p in S. enterica grown on minimal medium containing glucose (minimal glucose medium) required decreased PtsG activity and an unidentified gene regulated by SgrR. IMPORTANCE: This work describes a metabolic link between the sugar-phosphate stress response and the yeast thiamine biosynthetic enzyme Thi5p when heterologously expressed in Salmonella enterica during growth on minimal glucose medium. Suppressor analysis (i) identified a mutant class of the regulator SgrR that activate sugar-phosphate stress response constitutively and (ii) determined that Thi5p is conditionally active in S. enterica. These results emphasized the power of genetic systems in model organisms to uncover enzyme function and underlying metabolic network structure.

The cysteine desulfhydrase CdsH is conditionally required for sulfur mobilization to the thiamine thiazole in Salmonella enterica.

Thiamine pyrophosphate is a required coenzyme that contains a mechanistically important sulfur atom. In Salmonella enterica, sulfur is trafficked to both thiamine biosynthesis and 4-thiouridine biosynthesis by the enzyme ThiI using persulfide (R-S-S-H) chemistry. It was previously reported that a thiI mutant strain could grow independent of exogenous thiamine in the presence of cysteine, suggesting there was a second mechanism for sulfur mobilization. Data reported here show that oxidation products of cysteine rescue the growth of a thiI mutant strain by a mechanism that requires the transporter YdjN and the cysteine desulfhydrase CdsH. The data are consistent with a model in which sulfide produced by CdsH reacts with cystine (Cys-S-S-Cys), S-sulfocysteine (Cys-S-SO3 (-)), or another disulfide to form a small-molecule persulfide (R-S-S-H). We suggest that this persulfide replaced ThiI by donating sulfur to the thiamine sulfur carrier protein ThiS. This model describes a potential mechanism used for sulfur trafficking in organisms that lack ThiI but are capable of thiamine biosynthesis.

The thiamine biosynthetic enzyme ThiC catalyzes multiple turnovers and is inhibited by S-adenosylmethionine (AdoMet) metabolites.

ThiC (4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase; EC 4.1.99.17) is a radical S-adenosylmethionine (AdoMet) enzyme that uses a [4Fe-4S](+) cluster to reductively cleave AdoMet to methionine and a 5'-deoxyadenosyl radical that initiates catalysis. In plants and bacteria, ThiC converts the purine intermediate 5-aminoimidazole ribotide to 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate, an intermediate of thiamine pyrophosphate (coenzyme B1) biosynthesis. In this study, assay conditions were implemented that consistently generated 5-fold molar excess of HMP, demonstrating that ThiC undergoes multiple turnovers. ThiC activity was improved by in situ removal of product 5'-deoxyadenosine. The activity was inhibited by AdoMet metabolites S-adenosylhomocysteine, adenosine, 5'-deoxyadenosine, S-methyl-5'-thioadenosine, methionine, and homocysteine. Neither adenosine nor S-methyl-5'-thioadenosine had been shown to inhibit radical AdoMet enzymes, suggesting that ThiC is distinct from other family members. The parameters for improved ThiC activity and turnover described here will facilitate kinetic and mechanistic analyses of ThiC.