The unusual convergence of steroid catabolic pathways in Mycobacterium abscessus.

Mycobacterium abscessus, an opportunistic pathogen responsible for pulmonary infections, contains genes predicted to encode two steroid catabolic pathways: a cholesterol catabolic pathway similar to that of Mycobacterium tuberculosis and a 4-androstenedione (4-AD) catabolic pathway. Consistent with this prediction, M. abscessus grew on both steroids. In contrast to M. tuberculosis, Rhodococcus jostii RHA1, and other Actinobacteria, the cholesterol and 4-AD catabolic gene clusters of the M. abscessus complex lack genes encoding HsaD, the meta-cleavage product (MCP) hydrolase. However, M. abscessus ATCC 19977 harbors two hsaD homologs elsewhere in its genome. Only one of the encoded enzymes detectably transformed steroid metabolites. Among tested substrates, HsaDMab and HsaDMtb of M. tuberculosis had highest substrate specificities for MCPs with partially degraded side chains thioesterified with coenzyme A (kcat/KM = 1.9 × 104 and 5.7 × 103 mM-1s-1, respectively). Consistent with a dual role in cholesterol and 4-AD catabolism, HsaDMab also transformed nonthioesterified substrates efficiently, and a ΔhsaD mutant of M. abscessus grew on neither steroid. Interestingly, both steroids prevented growth of the mutant on acetate. The ΔhsaD mutant of M. abscessus excreted cholesterol metabolites with a fully degraded side chain, while the corresponding RHA1 mutant excreted metabolites with partially degraded side chains. Finally, the ΔhsaD mutant was not viable in macrophages. Overall, our data establish that the cholesterol and 4-AD catabolic pathways of M. abscessus are unique in that they converge upstream of where this occurs in characterized steroid-catabolizing bacteria. The data further indicate that cholesterol is a substrate for intracellular bacteria and that cholesterol-dependent toxicity is not strictly dependent on coenzyme A sequestration.

Cyclic AMP-Mediated Inhibition of Cholesterol Catabolism in Mycobacterium tuberculosis by the Novel Drug Candidate GSK2556286.

Despite the deployment of combination tuberculosis (TB) chemotherapy, efforts to identify shorter, nonrelapsing treatments have resulted in limited success. Recent evidence indicates that GSK2556286 (GSK286), which acts via Rv1625c, a membrane-bound adenylyl cyclase in Mycobacterium tuberculosis, shortens treatment in rodents relative to standard of care drugs. Moreover, GSK286 can replace linezolid in the three-drug, Nix-TB regimen. Given its therapeutic potential, we sought to better understand the mechanism of action of GSK286. The compound blocked growth of M. tuberculosis in cholesterol media and increased intracellular cAMP levels ~50-fold. GSK286 did not inhibit growth of an rv1625c transposon mutant in cholesterol media and did not induce cyclic AMP (cAMP) production in this mutant, suggesting that the compound acts on this adenylyl cyclase. GSK286 also induced cAMP production in Rhodococcus jostii RHA1, a cholesterol-catabolizing actinobacterium, when Rv1625c was heterologously expressed. However, these elevated levels of cAMP did not inhibit growth of R. jostii RHA1 in cholesterol medium. Mutations in rv1625c conferred cross-resistance to GSK286 and the known Rv1625c agonist, mCLB073. Metabolic profiling of M. tuberculosis cells revealed that elevated cAMP levels, induced using either an agonist or a genetic tool, did not significantly affect pools of steroid metabolites in cholesterol-incubated cells. Finally, the inhibitory effect of agonists was not dependent on the N-acetyltransferase MtPat. Together, these data establish that GSK286 is an Rv1625c agonist and sheds light on how cAMP signaling can be manipulated as a novel antibiotic strategy to shorten TB treatments. Nevertheless, the detailed mechanism of action of these compounds remains to be elucidated.

Steryl Ester Formation and Accumulation in Steroid-Degrading Bacteria.

Steryl esters (SEs) are important storage compounds in many eukaryotes and are often prominent components of intracellular lipid droplets. Here, we demonstrate that selected Actino- and Proteobacteria growing on sterols are also able to synthesize SEs and to sequester them in cytoplasmic lipid droplets. We found cholesteryl ester (CE) formation in members of the actinobacterial genera Rhodococcus, Mycobacterium, and Amycolatopsis, as well as several members of the proteobacterial Cellvibrionales order. CEs maximally accumulated under nitrogen-limiting conditions, suggesting that steryl ester formation plays a crucial role for storing excess energy and carbon under adverse conditions. Rhodococcus jostii RHA1 was able to synthesize phytosteryl and cholesteryl esters, the latter reaching up to 7% of its cellular dry weight and 69% of its lipid droplets. Purified lipid droplets from RHA1 contained CEs, free cholesterol, and triacylglycerols. In addition, we found formation of CEs in Mycobacterium tuberculosis when it was grown with cholesterol plus an additional fatty acid substrate. This study provides a basis for the application of bacterial whole-cell systems in the biotechnological production of SEs for use in functional foods and cosmetics.IMPORTANCE Oleaginous bacteria exhibit great potential for the production of high-value neutral lipids, such as triacylglycerols and wax esters. This study describes the formation of steryl esters (SEs) as neutral lipid storage compounds in sterol-degrading oleaginous bacteria, providing a basis for biotechnological production of SEs using bacterial systems with potential applications in the functional food, nutraceutical, and cosmetic industries. We found cholesteryl ester (CE) formation in several sterol-degrading Actino- and Proteobacteria under nitrogen-limiting conditions, suggesting an important role of this process in storing energy and carbon under adverse conditions. In addition, Mycobacterium tuberculosis grown on cholesterol accumulated CEs in the presence of an additional fatty acid substrate.

SbnI is a free serine kinase that generates O -phospho-l-serine for staphyloferrin B biosynthesis in Staphylococcus aureus.

Staphyloferrin B (SB) is an iron-chelating siderophore produced by Staphylococcus aureus in invasive infections. Proteins for SB biosynthesis and export are encoded by the sbnABCDEFGHI gene cluster, in which SbnI, a member of the ParB/Srx superfamily, acts as a heme-dependent transcriptional regulator of the sbn locus. However, no structural or functional information about SbnI is available. Here, a crystal structure of SbnI revealed striking structural similarity to an ADP-dependent free serine kinase, SerK, from the archaea Thermococcus kodakarensis We found that features of the active sites are conserved, and biochemical assays and 31P NMR and HPLC analyses indicated that SbnI is also a free serine kinase but uses ATP rather than ADP as phosphate donor to generate the SB precursor O-phospho-l-serine (OPS). SbnI consists of two domains, and elevated B-factors in domain II were consistent with the open-close reaction mechanism previously reported for SerK. Mutagenesis of Glu20 and Asp58 in SbnI disclosed that they are required for kinase activity. The only known OPS source in bacteria is through the phosphoserine aminotransferase activity of SerC within the serine biosynthesis pathway, and we demonstrate that an S. aureus serC mutant is a serine auxotroph, consistent with a function in l-serine biosynthesis. However, the serC mutant strain could produce SB when provided l-serine, suggesting that SbnI produces OPS for SB biosynthesis in vivo These findings indicate that besides transcriptionally regulating the sbn locus, SbnI also has an enzymatic role in the SB biosynthetic pathway.

Serum bilirubin and the risk of chronic obstructive pulmonary disease exacerbations.

BACKGROUND: Bilirubin is a potent anti-oxidant and higher serum concentrations of bilirubin have been associated with better lung function, slower lung function decline, and lower incidence of chronic obstructive pulmonary disease (COPD). We sought to determine whether elevated bilirubin blood concentrations are associated with lower risk for acute exacerbations of COPD (AECOPD). METHODS: We performed a secondary analyses of data in the Simvastatin for Prevention of Exacerbations in Moderate-to-Severe COPD (STATCOPE) and the Azithromycin for Prevention of Exacerbations of COPD (MACRO) studies. We used time-dependent multivariable Cox proportional hazards analyses, using bilirubin concentrations prior to first AECOPD as the exposure variable and time to first AECOPD as the outcome variable. STATCOPE was used for model development, with validation in MACRO. RESULTS: In STATCOPE (n = 853), higher bilirubin was associated with a lower but statistically insignificant hazard for AECOPD, (adjusted hazard ratio [aHR] 0.89 per log10 increase [95%CI: 0.74 to 1.09; p = 0.26]). In the validation MACRO study (n = 1018), higher bilirubin was associated with a significantly lower hazard for AECOPD (aHR 0.80 per log10 increase [95%CI: 0.67 to 0.94; p = 0.008]). CONCLUSIONS: Bilirubin may be a biomarker of AECOPD risk and may be a novel therapeutic target to reduce AECOPD risk. TRIAL REGISTRATIONS: ClinicalTrials.gov NCT01061671 (registered 02 February 2010) and ClinicalTrials.gov NCT00325897 (registered 12 May 2006).

Cholesterol-Mediated Coenzyme A Depletion in Catabolic Mutants of Mycobacteria Leads to Toxicity.

Cholesterol is a critical growth substrate for Mycobacterium tuberculosis (Mtb) during infection, and the cholesterol catabolic pathway has been targeted for the development of new antimycobacterial agents. A key metabolite in cholesterol catabolism is 3aα-H-4α(3'-propanoate)-7aß-methylhexahydro-1,5-indanedione (HIP). Many of the HIP metabolites are acyl-coenzyme A (CoA) thioesters, whose accumulation in deletion mutants can cause cholesterol-mediated toxicity. We used LC-MS/MS analysis to demonstrate that deletion of genes involved in HIP catabolism leads to acyl-CoA accumulation with concomitant depletion of free CoASH, leading to dysregulation of central metabolic pathways. CoASH and acyl-CoAs inhibited PanK, the enzyme that catalyzes the first step in the transformation of pantothenate to CoASH. Inhibition was competitive with respect to ATP with Kic values ranging from 9 µM for CoASH to 57 µM for small acyl-CoAs and 180 ± 30 µM for cholesterol-derived acyl-CoA. These findings link two critical metabolic pathways and suggest that therapeutics targeting cholesterol catabolic enzymes could both prevent the utilization of an important growth substrate and simultaneously sequester CoA from essential cellular processes, leading to bacterial toxicity.

A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells.

RNA sequencing (RNAseq) has been widely used to generate bulk gene expression measurements collected from pools of cells. Only relatively recently have single-cell RNAseq (scRNAseq) methods provided opportunities for gene expression analyses at the single-cell level, allowing researchers to study heterogeneous mixtures of cells at unprecedented resolution. Tumors tend to be composed of heterogeneous cellular mixtures and are frequently the subjects of such analyses. Extensive method developments have led to several protocols for scRNAseq but, owing to the small amounts of RNA in single cells, technical constraints have required compromises. For example, the majority of scRNAseq methods are limited to sequencing only the 3' or 5' termini of transcripts. Other protocols that facilitate full-length transcript profiling tend to capture only polyadenylated mRNAs and are generally limited to processing only 96 cells at a time. Here, we address these limitations and present a novel protocol that allows for the high-throughput sequencing of full-length, total RNA at single-cell resolution. We demonstrate that our method produced strand-specific sequencing data for both polyadenylated and non-polyadenylated transcripts, enabled the profiling of transcript regions beyond only transcript termini, and yielded data rich enough to allow identification of cell types from heterogeneous biological samples.

Development of a Peer-Reviewed Open-Access Undergraduate Research Journal.

Dissemination of results is a fundamental aspect of the scientific process and requires an avenue for publication that is specifically designed to suit the nature of the research being communicated. Undergraduate research journals provide a unique forum for students to report scientific findings and ideas while learning about the complete scientific process. We have developed a peer-reviewed, open-access, international undergraduate research journal that is linked to a course-based undergraduate research experience. We reflect on lessons learned and recommend effective approaches for the implementation and operation of a successful undergraduate research journal.

Catabolism of the Last Two Steroid Rings in Mycobacterium tuberculosis and Other Bacteria.

Most mycolic acid-containing actinobacteria and some proteobacteria use steroids as growth substrates, but the catabolism of the last two steroid rings has yet to be elucidated. In Mycobacterium tuberculosis, this pathway includes virulence determinants and has been proposed to be encoded by the KstR2-regulated genes, which include a predicted coenzyme A (CoA) transferase gene (ipdAB) and an acyl-CoA reductase gene (ipdC). In the presence of cholesterol, ΔipdC and ΔipdAB mutants of either M. tuberculosis or Rhodococcus jostii strain RHA1 accumulated previously undescribed metabolites: 3aα-H-4α(carboxyl-CoA)-5-hydroxy-7aß-methylhexahydro-1-indanone (5-OH HIC-CoA) and (R)-2-(2-carboxyethyl)-3-methyl-6-oxocyclohex-1-ene-1-carboxyl-CoA (COCHEA-CoA), respectively. A ΔfadE32 mutant of Mycobacterium smegmatis accumulated 4-methyl-5-oxo-octanedioic acid (MOODA). Incubation of synthetic 5-OH HIC-CoA with purified IpdF, IpdC, and enoyl-CoA hydratase 20 (EchA20), a crotonase superfamily member, yielded COCHEA-CoA and, upon further incubation with IpdAB and a CoA thiolase, yielded MOODA-CoA. Based on these studies, we propose a pathway for the final steps of steroid catabolism in which the 5-member ring is hydrolyzed by EchA20, followed by hydrolysis of the 6-member ring by IpdAB. Metabolites accumulated by ΔipdF and ΔechA20 mutants support the model. The conservation of these genes in known steroid-degrading bacteria suggests that the pathway is shared. This pathway further predicts that cholesterol catabolism yields four propionyl-CoAs, four acetyl-CoAs, one pyruvate, and one succinyl-CoA. Finally, a ΔipdAB M. tuberculosis mutant did not survive in macrophages and displayed severely depleted CoASH levels that correlated with a cholesterol-dependent toxicity. Our results together with the developed tools provide a basis for further elucidating bacterial steroid catabolism and virulence determinants in M. tuberculosis.IMPORTANCE Bacteria are the only known steroid degraders, but the pathway responsible for degrading the last two steroid rings has yet to be elucidated. In Mycobacterium tuberculosis, this pathway includes virulence determinants. Using a series of mutants in M. tuberculosis and related bacteria, we identified a number of novel CoA thioesters as pathway intermediates. Analysis of the metabolites combined with enzymological studies establishes how the last two steroid rings are hydrolytically opened by enzymes encoded by the KstR2 regulon. Our results provide experimental evidence for novel ring-degrading enzymes, significantly advance our understanding of bacterial steroid catabolism, and identify a previously uncharacterized cholesterol-dependent toxicity that may facilitate the development of novel tuberculosis therapeutics.

Order Set to Improve the Care of Patients Hospitalized for an Exacerbation of Chronic Obstructive Pulmonary Disease.

RATIONALE: Physicians' adherence to prescribing evidence-based inpatient and outpatient therapies for chronic obstructive pulmonary disease (COPD) is low, and there is a paucity of information about the utility of admission order sets for patients with COPD exacerbations. OBJECTIVES: To determine if implementation of a locally designed, evidence-based, multidisciplinary computer physician order entry set in the electronic health record improves the quality of physician pharmacologic prescribing for patients hospitalized for COPD exacerbations. METHODS: This study was performed before and after implementation of a computerized order set for patients hospitalized for COPD exacerbations. The primary outcome was the rate of zero prescribing errors by physicians for inpatient and discharge drugs for COPD over a 1-year period before implementation and for 6 months after implementation. Errors were defined as no therapy or inappropriate therapy in the following categories: antibiotic, systemic corticosteroid, short-acting bronchodilator, long-acting bronchodilator, and inhaled corticosteroid. Secondary outcomes included mean physician pharmaceutical prescribing error rate; types of errors; hospital lengths of stay; and unscheduled physician visits, emergency department visits, rehospitalizations, and deaths within 30 days from discharge. MEASUREMENTS AND MAIN RESULTS: There were 194 COPD exacerbation admissions during the 1-year preimplementation period and 81 admissions during the 6-month postimplementation period. Compared with the preimplementation period, the percentage of patients receiving all recommended pharmacologic therapies for the 6 months after implementation increased from 18.6% to 54.3% (P < 0.001). The mean number of errors decreased from 1.76 to 0.65 (P < 0.001). Antibiotic and systemic corticosteroid errors decreased from 39% to 16% (P < 0.001) and from 58% to 28% (P < 0.001), respectively. Fewer patients were discharged without a short-acting bronchodilator (13.9% vs. 2.5%; P = 0.005), a long-acting bronchodilator (16.5% vs. 7.4%; P = 0.047), or inhaled corticosteroid (18% vs. 9.9%; P = 0.089). Improvements were sustained over the 6-month postimplementation period. Hospital length of stay decreased from 4 (±3) days preimplementation to 2.9 (±1.9) days postimplementation (P = 0.002). There were no significant differences in 30-day clinical outcomes, including the rates of unscheduled physician or emergency department visits, rehospitalizations, or deaths. CONCLUSIONS: Computerized multidisciplinary admission order set implementation for patients hospitalized for a COPD exacerbation improved physicians' adherence to evidence-based pharmacologic treatment, and they were associated with reductions in length of hospital stay.

STOP-BANG questionnaire performance in a Veterans Affairs unattended sleep study program.

RATIONALE: There are no published data regarding use of the STOP-BANG sleep apnea questionnaire in populations referred to Veterans Affairs (VA) sleep facilities. If a particular STOP-BANG score cutpoint had high positive predictive value in this referral population, it could reduce the need for diagnostic sleep studies. METHODS: STOP-BANG questionnaires were prospectively administered to veterans undergoing unattended sleep studies at a single VA facility. We evaluated the sensitivity, specificity, positive predictive value, and area under the receiver-operating characteristic curve (ROC AUC) of STOP-BANG scores for identifying a Respiratory Disturbance Index (RDI) greater than 15/hour. We also recalibrated the STOP-BANG score to our referral population, using logistic regression models. MEASUREMENTS AND MAIN RESULTS: Of 1,196 consecutive veterans undergoing unattended sleep studies, the mean STOP-BANG score was 5.7 ± 1.4, and 67% had an RDI greater than 15/hour. Sensitivities were excellent at lower STOP-BANG scores, but sharply decreased at scores of 6 and above. Specificity improved in a linear fashion with increasing scores. The ROC AUC was 0.66 (95% confidence interval [CI], 0.64-0.69) and recalibrated models improved the ROC AUC to 0.74 (95% CI, 0.69-0.78). The highest STOP-BANG score of 8 was present in only 7.9% of the sample and had a positive predictive value of 85% (95% CI, 76-92%). CONCLUSIONS: The STOP-BANG questionnaire alone is insufficient to confirm the presence of significant sleep apnea. A maximal score of 8 did not have a high enough positive predictive value to forego confirmatory sleep testing.

A telehealth intervention for veterans on antiviral treatment for the hepatitis C virus.

The standard treatment for chronic hepatitis C (pegylated interferon and ribavirin) causes challenging physical and psychological side effects. The current pilot study evaluated the efficacy of a brief, telephone-based, cognitive-behavioral self-management intervention designed to address mood and quality of life within a sample of veterans on antiviral treatment for hepatitis C. Results from this pilot study support the feasibility of this telehealth intervention, showing that veterans were highly satisfied with the content of the intervention and compliant with the telephone calls. Findings further indicate that symptoms of depression and anxiety and mental health quality of life either remained stable or improved in those participants who received the brief telephone intervention, while those receiving usual care showed significant declines in mood and mental health quality of life. The findings from this study provide evidence that a brief, clinician-administered phone intervention may help individuals on antiviral therapy for hepatitis C to cope more effectively with the negative treatment side effects.

Preoperative psychosocial evaluation of penile prosthesis candidates.

Penile prosthesis surgery is a recommended treatment option for a subset of patients who present with erectile dysfunction (ED). Although treatment outcome research indicates that patients are generally satisfied with this intervention, it remains an invasive procedure with risk for complications. A review of the literature reveals general agreement for the importance of a thorough preoperative evaluation to determine appropriateness for a penile implant; however, there are no known descriptions of such an evaluation in the literature. This article provides an introduction to the domains that are most relevant to assess in a patient who is considering penile implant surgery: sexual history (including organic and psychogenic causes of ED), success and utilization of other treatment interventions, relationship functioning, and patient expectations for and knowledge of the procedure. The advantages to this approach are presented, particularly in enhancing patient satisfaction with treatment outcomes.