Genetically engineered probiotic E. coli Nissle to consume amino acids associated with orphan metabolic diseases

Orphan metabolic diseases are rare genetic defects that interfere with metabolism due to ineffective or missing enzymes. Two of them, Phenylketonuria (PKU) and Maple Syrup Urine Disease (MSUD) are defined by accumulation of amino acids to toxic levels due to defective metabolism of protein break down products. PKU is caused by a defect in the gene encoding phenylalanine hydroxylase (PAH). MSUD is caused by a defect in a multi-enzyme complex found in mitochondria called branched chain ɑ-ketoacid dehydrogenase “BCKDH”. Without the activity of these enzymes, the amino acid phenylalanine (Phe) in the case of PKU or the branched-chain amino acids leucine (Leu), isoleucine and valine for MSUD build up to neurotoxic levels in the blood and brain, leading to neurological deficits. Current treatment options focus on dietary protein restriction, are insufficient and, unfortunately, can lead to a failure to thrive. Lifelong compliance with a prescription diet is also a concern. We have genetically engineered Nissle, a probiotic strain of E. coli, to reduce serum phenylalanine and leucine levels in patients with PKU or MSUD; preclinical data supporting the activity of these strains are described. Please click Additional Files below to see the full abstract

Engineering and manufacturing of probiotic E. Coli to treat metabolic disorder

The fields of synthetic biology and microbiome research developed greatly over the last decade. The convergence of those two disciplines is now enabling the development of new therapeutic strategies, using engineered microbes that operate from within the gut as living medicines. Inborn errors of metabolism represent candidate diseases for these therapeutics, particularly those disorders where a toxic metabolite causing a syndrome is also present in the intestinal lumen. Phenylketonuria (PKU), a rare inherited disease caused by a defect in phenylalanine hydroxylase (PAH) activity, is one such disease and is characterized by the accumulation of systemic phenylalanine (Phe) that can lead to severe neurological deficits unless patients are placed on a strict low-Phe diet. As an alternative treatment, Escherichia coli Nissle (EcN), a well-characterized probiotic, was genetically modified to efficiently import and degrade Phe (SYNB1618). The coupled expression of a Phe transporter with a Phe ammonia lyase (PAL) allows rapid conversion of Phe into trans-cinnamic acid (TCA) in vitro, which is then further metabolized by the host to hippuric acid (HA) and excreted in the urine. Experiments conducted in the enu2-/- PKU mouse model showed that the oral administration of SYNB1618 is able to significantly reduce blood Phe levels triggered by subcutaneous Phe injection. Decreases in circulating Phe levels were associated with proportional increases in urinary HA, confirming that Phe metabolism was caused by the engineered pathway in SYNB1618. Subsequent studies have shown that SYNB1618 is similarly operative in a non-human primate model, providing a translational link to inform future human clinical studies. Consistent with preclinical studies, recent Phase 1/2a clinical data demonstrate that oral administration of SYNB1618 resulted in significant dose-dependent production of biomarkers specifically associated with SYNB1618 activity, demonstrating proof-of-mechanism of this cell therapy

Engineering of probiotic E.coli to treat metabolic disorders

The fields of synthetic biology and microbiome research developed greatly over the last decade. The convergence of those two disciplines is now enabling the development of new therapeutic strategies, using engineered microbes that operate from within the gut as living medicines. Inborn errors of metabolism represent candidate diseases for these therapeutics, particularly those disorders where a toxic metabolite causing a syndrome is also present in the intestinal lumen. Phenylketonuria (PKU), a rare inherited disease caused by a defect in phenylalanine hydroxylase (PAH) activity, is one such disease and is characterized by the accumulation of systemic phenylalanine (Phe) that can lead to severe neurological deficits unless patients are placed on a strict low-Phe diet. As an alternative treatment, Escherichia coli Nissle (EcN), a well-characterized probiotic, was genetically modified to efficiently import and degrade Phe (SYN-PKU). The coupled expression of a Phe transporter with a Phe ammonia lyase (PAL) allows rapid conversion of Phe into trans-cinnamic acid (TCA) in vitro, which is then further metabolized by the host to hippuric acid (HA) and excreted in the urine. Experiments conducted in the enu2-/- PKU mouse model showed that the oral administration of SYN-PKU is able to significantly reduce blood Phe levels triggered by subcutaneous Phe injection. Decreases in circulating Phe levels were associated with proportional increases in urinary HA, confirming that Phe metabolism was caused by the engineered pathway in SYN-PKU. Subsequent studies have shown that SYN-PKU is similarly operative in a non-human primate model, providing a translational link to inform future human clinical studies. In addition to SYN-PKU, a second EcN strain was genetically engineered to rapidly import and degrade branched-chain amino acids (BCAAs) for the treatment of maple syrup urine disease (SYN-MSUD). MSUD, similar to PKU, is a rare genetic disorder caused by a defect in branched-chain ketoacid dehydrogenase activity leading to the toxic accumulation of BCAAs, particularly leucine, and their ketoacid derivatives. The controlled expression in SYN-MSUD of two BCAA transporters, a leucine dehydrogenase, a ketoacid decarboxylase and an alcohol dehydrogenase, result in the efficient degradation of BCAAs into branched-chain alcohols. In a mouse model of MSUD, the oral delivery of SYN-MSUD suppressed the increase in blood BCAAs level induced by a high-protein challenge and prevented the associated moribund phenotype, as measured by locomotor activity. In conclusion, the therapeutic effects observed with SYN-PKU and SYN-MSUD in pre-clinical studies support the further evaluation of engineered microbes as promising approaches for serious inborn errors of metabolism

Transplantability of a circadian clock to a noncircadian organism

Circadian oscillators are posttranslationally regulated and affect gene expression in autotrophic cyanobacteria. Oscillations are controlled by phosphorylation of the KaiC protein, which is modulated by the KaiA and KaiB proteins. However, it remains unclear how time information is transmitted to transcriptional output. We show reconstruction of the KaiABC oscillator in the noncircadian bacterium Escherichia coli. This orthogonal system shows circadian oscillations in KaiC phosphorylation and in a synthetic transcriptional reporter. Coexpression of KaiABC with additional native cyanobacterial components demonstrates a minimally sufficient set of proteins for transcriptional output from a native cyanobacterial promoter in E. coli. Together, these results demonstrate that a circadian oscillator is transplantable to a heterologous organism for reductive study as well as wide-ranging applications

Reprogramming Probiotic Lactobacillus reuteri as a Biosensor for Staphylococcus aureus Derived AIP-I Detection

10.1021/acssynbio.8b00063ACS SYNTHETIC BIOLOGY751229123

Reprogramming Probiotic <i>Lactobacillus reuteri</i> as a Biosensor for <i>Staphylococcus aureus</i> Derived AIP‑I Detection

Gram-positive <i>Staphylococcus aureus</i> infection that results in pneumonia, urinary tract infection, and in severe cases, sepsis, has recently been classified as a serious threat to public health. Rapid and cost-effective detection of these infections are costly and time-consuming. Here, we present probiotic lactic acid bacteria engineered to detect autoinducer peptide-I (AIP-I), a quorum sensing molecule produced by <i>Staphylococcus</i> sp. during pathogenesis. We achieved this by adapting the well-characterized <i>agr</i> quorum sensing (<i>agr</i>QS) from <i>Staphylococcus aureus</i> into <i>Lactobacillus reuteri</i>. The engineered biosensor is able to detect AIP-I levels in the nanomolar to micromolar range. We further investigated the function of the biosensor to detect real-time changes in AIP-I levels to understand the dynamics of <i>Staphylococcus aureus</i> under various strenuous conditions. The developed sensors would be useful for detection of <i>Staphylococcus</i> contamination in hospital settings and for high-throughput drug screening

An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria

Abstract Enteric hyperoxaluria (EH) is a metabolic disease caused by excessive absorption of dietary oxalate leading to the formation of chronic kidney stones and kidney failure. There are no approved pharmaceutical treatments for EH. SYNB8802 is an engineered bacterial therapeutic designed to consume oxalate in the gut and lower urinary oxalate as a potential treatment for EH. Oral administration of SYNB8802 leads to significantly decreased urinary oxalate excretion in healthy mice and non‐human primates, demonstrating the strain's ability to consume oxalate in vivo. A mathematical modeling framework was constructed that combines in vitro and in vivo preclinical data to predict the effects of SYNB8802 administration on urinary oxalate excretion in humans. Simulations of SYNB8802 administration predict a clinically meaningful lowering of urinary oxalate excretion in healthy volunteers and EH patients. Together, these findings suggest that SYNB8802 is a promising treatment for EH