Overcoming heterologous protein interdependency to optimize P450-mediated Taxol precursor synthesis in Escherichia coli.

Recent advances in metabolic engineering have demonstrated the potential to exploit biological chemistry for the synthesis of complex molecules. Much of the progress to date has leveraged increasingly precise genetic tools to control the transcription and translation of enzymes for superior biosynthetic pathway performance. However, applying these approaches and principles to the synthesis of more complex natural products will require a new set of tools for enabling various classes of metabolic chemistries (i.e., cyclization, oxygenation, glycosylation, and halogenation) in vivo. Of these diverse chemistries, oxygenation is one of the most challenging and pivotal for the synthesis of complex natural products. Here, using Taxol as a model system, we use nature's favored oxygenase, the cytochrome P450, to perform high-level oxygenation chemistry in Escherichia coli. An unexpected coupling of P450 expression and the expression of upstream pathway enzymes was discovered and identified as a key obstacle for functional oxidative chemistry. By optimizing P450 expression, reductase partner interactions, and N-terminal modifications, we achieved the highest reported titer of oxygenated taxanes (∼570 ± 45 mg/L) in E. coli. Altogether, this study establishes E. coli as a tractable host for P450 chemistry, highlights the potential magnitude of protein interdependency in the context of synthetic biology and metabolic engineering, and points to a promising future for the microbial synthesis of complex chemical entities.

Differential effects of the soluble fiber inulin in reducing adiposity and altering gut microbiome in aging mice.

Inulin, a soluble dietary fiber, is thought to exert multiple beneficiary effects through promoting growth of bacteria that metabolize the fiber to short-chain fatty acids (SCFAs); however, the effect and efficacy of inulin in aging subjects is unknown. This study aims to systematically evaluate the capacity of SCFAs production and host response in mice of different ages. Male C57BL/6J mice across young (5 months), middle (11 months) and old (26 months) age were subjected to a control diet for 2 weeks, followed by 6 weeks of inulin-containing diet. Inulin-induced increase in fecal butyric acid levels was most prominent in middle-age group compared to other age groups. In addition, inulin-induced increase in fecal propionic acids showed age-dependent decline. Interestingly, the SCFA-producing Roseburia was most abundantly and persistently increased in the middle-age group. Furthermore, inulin intake significantly reduced Firmicutes to Bacteroidetes ratio, and several dysbiotic bacteria associated with pro-inflammatory state. Concomitantly, circulating levels of CXCL1, a chemoattractant for neutrophils, was reduced by inulin intake. Inulin decreased fat mass in all age groups, with middle-aged mice being most responsive to fat-reducing effects of inulin. Moreover, inulin significantly increased energy expenditure and voluntary wheel running in middle-aged mice, but not in old mice. Overall, our data suggest that the efficacy of inulin in altering the microbiome and SCFA production, and the subsequent metabolic response was diminished in old mice, and highlight the importance of including age as a variable in studies determining host-microbe response to diets.

Deletion of ghrelin alters tryptophan metabolism and exacerbates experimental ulcerative colitis in aged mice.

A major component of aging is chronic, low-grade inflammation, attributable in part by impaired gut barrier function. We previously reported that deletion of ghrelin, a peptidergic hormone released mainly from the gut, exacerbates experimental muscle atrophy in aged mice. In addition, ghrelin has been shown to ameliorate colitis in experimental models of inflammatory bowel disease (IBD), although the role of endogenous ghrelin in host-microbe interactions is less clear. Here, we showed that 22-month-old global ghrelin knockout (Ghrl-/-) mice exhibited significantly increased depressive-like behaviors, while anxiety levels and working memory were similar to littermate wild-type (WT) mice. Furthermore, old Ghrl-/- mice showed significantly increased intestinal permeability to fluorescein isothiocyanate (FITC)-dextran, significantly higher colonic interleukin (IL-1ß) levels, and trends for higher colonic IL-6 and tumor necrosis factor-α (TNF-α) compared to WT mice. Interestingly, young Ghrl-/- and WT mice showed comparable depressive-like behavior and gut permeability, suggesting age-dependent exacerbation in gut barrier dysfunction in Ghrl-/- mice. While fecal short-chain fatty acids levels were comparable between old Ghrl-/- and WT mice, serum metabolome revealed alterations in metabolic cascades including tryptophan metabolism. Specifically, tryptophan and its microbial derivatives indole-3-acetic acid and indole-3-lactic acid were significantly reduced in old Ghrl-/-mice. Furthermore, in an experimental model of dextran sulfate sodium (DSS)-induced colitis, Ghrl-/- mice showed exacerbated disease symptoms, and higher levels of chemoattractant and pro-inflammatory cytokines in the colon. Overall, these data demonstrated that ghrelin deficiency is associated with gut barrier dysfunction, alterations in microbially derived tryptophan metabolites, and increased susceptibility to colitis. These data suggested that endogenous ghrelin contributes to maintaining a healthy host-microbe environment, ultimately impacting on brain function.

Ulcerative colitis results in differential metabolism of cranberry polyphenols by the colon microbiome in vitro.

The microbiome plays a major role in polyphenol metabolism, producing metabolites that are bioavailable and potentially more bioactive than the compounds from which they are derived. However, the microbiome can vary among individuals, and especially for those with co-morbidities, such as ulcerative colitis. In subjects with ulcerative colitis, the consequence of a 'dysbiotic' microbiome is characterized by decreased diversity of microbiota that may impact their capability to metabolize polyphenols into bioavailable metabolites. On this premise, the microbiome metabolism of cranberry polyphenols between healthy individuals and those with ulcerative colitis was compared in vitro. Fecal samples from volunteers, with or without diagnosed ulcerative colitis, were cultured anaerobically in the presence of cranberry polyphenols. The resulting metabolites were then quantified via LC-ESI-MS/MS. 16S rRNA metagenomics analysis was also utilized to assess differences in microbiota composition between healthy and ulcerative colitis microbiomes and the modulatory effects of cranberry polyphenols on microbiota composition. Healthy microbiomes produced higher (p < 0.05) concentrations of 5-(3',4'-dihydroxyphenyl)-gamma-valerolactone and 3-hydroxyphenylacetic acid in comparison to ulcerative colitis microbiomes. Additionally, healthy microbiomes contained a higher (p < 0.05) abundance of Ruminococcaceae, which could explain their ability to produce higher concentrations of cranberry polyphenol metabolites. Health status and the presence of cranberry polyphenols also significantly impacted the production of several short-chain and branched-chain fatty acids. These results suggest that efficiency of polyphenol metabolism is dependent on microbiota composition and future works should include metabolite data to account for inter-individual differences in polyphenol metabolism.

Development, validation, and application of a liquid chromatography-tandem mass spectrometry method for quantitative determination of trans-4-hydroxy-l-proline concentration in the serum of dogs with chronic hepatitis.

OBJECTIVE: To develop and analytically validate a liquid chromatography-tandem mass spectrometry method for measurement of endogenous trans-4-hydroxy-l-proline concentrations in canine serum and to assess serum trans-4-hydroxy-l-proline concentrations in dogs with chronic hepatitis. SAMPLE: Serum samples obtained from 20 dogs with histopathologically confirmed chronic hepatitis and 20 healthy control dogs. PROCEDURES: A liquid chromatography-tandem mass spectrometry method for quantification of trans-4-hydroxy-l-proline concentration was developed and assessed for analytic sensitivity, linearity, accuracy, precision, and reproducibility. Serum concentration of trans-4-hydroxy-l-proline in dogs with chronic hepatitis and healthy control dogs was measured. RESULTS: Observed-to-expected ratios for dilutional parallelism ranged from 72.7% to 111.5% (mean ± SD, 91.3 ± 19.6%). Intra-assay and interassay coefficients of variation ranged from 2.1% to 3.0% and 3.2% to 5.3%, respectively. Relative error ranged from -2.3% to 7.8%. Trans-4-hydroxy-l-proline concentrations were significantly lower in serum obtained from dogs with chronic hepatitis (median, 0.24 ng/mL; range, 0.06 to 1.84 ng/mL) than in serum obtained from healthy control dogs (median, 0.78 ng/mL; range, 0.14 to 4.90 ng/mL). CONCLUSIONS AND CLINICAL RELEVANCE: The method described here for the quantification of trans-4-hydroxy-l-proline concentration in canine serum was found to be sensitive, specific, precise, accurate, and reproducible. Dogs with chronic hepatitis had significantly lower serum trans-4-hydroxy-l-proline concentrations than did healthy control dogs, possibly as a result of altered hepatic metabolism of amino acids.