Pathway engineering via quorum sensing and sRNA riboregulators—Interconnected networks and controllers

Beyond Self-Resistance: ABCF ATPase LmrC Is a Signal-Transducing Component of an Antibiotic-Driven Signaling Cascade Accelerating the Onset of Lincomycin Biosynthesis

In natural environments, antibiotics are important means of interspecies competition. At subinhibitory concentrations, they act as cues or signals inducing antibiotic production; however, our knowledge of well-documented antibiotic-based sensing systems is limited. Here, for the soil actinobacterium Streptomyces lincolnensis, we describe a fundamentally new ribosome-mediated signaling cascade that accelerates the onset of lincomycin production in response to an external ribosome-targeting antibiotic to synchronize antibiotic production within the population. The entire cascade is encoded in the lincomycin biosynthetic gene cluster (BGC) and consists of three lincomycin resistance proteins in addition to the transcriptional regulator LmbU: a lincomycin transporter (LmrA), a 23S rRNA methyltransferase (LmrB), both of which confer high resistance, and an ATP-binding cassette family F (ABCF) ATPase, LmrC, which confers only moderate resistance but is essential for antibiotic-induced signal transduction. Specifically, antibiotic sensing occurs via ribosome-mediated attenuation, which activates LmrC production in response to lincosamide, streptogramin A, or pleuromutilin antibiotics. Then, ATPase activity of the ribosome-associated LmrC triggers the transcription of lmbU and consequently the expression of lincomycin BGC. Finally, the production of LmrC is downregulated by LmrA and LmrB, which reduces the amount of ribosome-bound antibiotic and thus fine-tunes the cascade. We propose that analogous ABCF-mediated signaling systems are relatively common because many ribosome-targeting antibiotic BGCs encode an ABCF protein accompanied by additional resistance protein(s) and transcriptional regulators. Moreover, we revealed that three of the eight coproduced ABCF proteins of S. lincolnensis are clindamycin responsive, suggesting that the ABCF-mediated antibiotic signaling may be a widely utilized tool for chemical communication. IMPORTANCE Resistance proteins are perceived as mechanisms protecting bacteria from the inhibitory effect of their produced antibiotics or antibiotics from competitors. Here, we report that antibiotic resistance proteins regulate lincomycin biosynthesis in response to subinhibitory concentrations of antibiotics. In particular, we show the dual character of the ABCF ATPase LmrC, which confers antibiotic resistance and simultaneously transduces a signal from ribosome-bound antibiotics to gene expression, where the 5' untranslated sequence upstream of its encoding gene functions as a primary antibiotic sensor. ABCF-mediated antibiotic signaling can in principle function not only in the induction of antibiotic biosynthesis but also in selective gene expression in response to any small molecules targeting the 50S ribosomal subunit, including clinically important antibiotics, to mediate intercellular antibiotic signaling and stress response induction. Moreover, the resistance-regulatory function of LmrC presented here for the first time unifies functionally inconsistent ABCF family members involving antibiotic resistance proteins and translational regulators.

Engineering an Optogenetic CRISPRi Platform for Improved Chemical Production

Microbial synthesis of chemicals typically requires the redistribution of metabolic flux toward the synthesis of targeted products. Dynamic control is emerging as an effective approach for solving the hurdles mentioned above. As light could control the cell behavior in a spatial and temporal manner, the optogenetic-CRISPR interference (opto-CRISPRi) technique that allocates the metabolic resources according to different optical signal frequencies will enable bacteria to be controlled between the growth phase and the production stage. In this study, we applied a blue light-sensitive protein EL222 to regulate the expression of the dCpf1-mediated CRISPRi system that turns off the competitive pathways and redirects the metabolic flux toward the heterologous muconic acid synthesis in Escherichia coli. We found that the opto-CRISPRi system dynamically regulating the suppression of the central metabolism and competitive pathways could increase the muconic acid production by 130%. These results demonstrated that the opto-CRISPRi platform is an effective method for enhancing chemical synthesis with broad utilities.

Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression

Until recently, engineering strategies for altering gene expression have focused on transcription control using strong inducible promoters or one of several methods to knock down wasteful genes. Recently, synthetic riboregulators have been developed for translational regulation of gene expression. Here, we report a new modular synthetic riboregulator class that has the potential to finely tune protein expression and independently control the concentration of each enzyme in an engineered metabolic pathway. This development is important because the most straightforward approach to altering the flux through a particular metabolic step is to increase or decrease the concentration of the enzyme. Our design includes a cis-repressor at the 5' end of the mRNA that forms a stem-loop helix, occluding the ribosomal binding sequence and blocking translation. A trans-expressed activating-RNA frees the ribosomal-binding sequence, which turns on translation. The overall architecture of the riboregulators is designed using Watson-Crick base-pairing stability. We describe here a cis-repressor that can completely shut off translation of antibiotic-resistance reporters and a trans-activator that restores translation. We have established that it is possible to use these riboregulators to achieve translational control of gene expression over a wide dynamic range. We have also found that a targeting sequence can be modified to develop riboregulators that can, in principle, independently regulate translation of many genes. In a selection experiment, we demonstrated that by subtly altering the sequence of the trans-activator it is possible to alter the ratio of the repressed and activated states and to achieve intermediate translational control.

A 'bioproduction breadboard': programming, assembling, and actuating cellular networks

With advances in synthetic biology and biofabrication, cellular networks can be functionalized and connected with unprecedented sophistication. We describe a platform for the creation of a 'bioproduction breadboard'. This would consist of physically isolated product-producing cell populations, product capture devices, and other unit operations that function as programmed in place, using unique, orthogonal inputs. For product synthesis, customized cell populations would be connected through standardized, generic inputs allowing 'plug and play' functionality and primary, user-mediated regulation. In addition, through autonomous pathway redirection and balancing, the cells themselves would provide secondary, self-directed regulation to optimize bioproduction. By leveraging specialization and division of labor, we envision diverse cell populations linked to create new pathway designs.

Biochemical characterization of a novel bifunctional glycosyl-1-phosphate transferase involved in the exopolysaccharide biosynthesis

Ebosin produced by Streptomyces sp. 139 is a novel exopolysaccharide with anti-rheumatic arthritis activity in vivo and its biosynthesis gene cluster (ste) has been previously identified. In our previous research, ste5 gene has been identified as priming glycosyltransferase involved in Ebosin biosynthesis. However, it remains unclear how ste5 initiated Ebosin biosynthesis in molecular level. Here we show that Ebosin derivative produced by ste5 mutant lost the antagonist activities for IL-1R and Overexpression of ste5 in mutant dramatically enhanced the antagonist activities for IL-1R. For biochemical characterization of Ste5, the ste5 gene was cloned and expressed in Escherichia coli BL21. We identified that the recombinant Ste5 can transfer galactose-1-Phosphate (Gal-1-P) or glucose-1-Phosphate (Glc-1-P) from UDP-galactose and UDP-glucose to the lipid carrier located in the cytoplasmic membrane of Streptomyces sp. 139 (ste5(-)) with a continuous coupled spectrophotometric assay. 12.6 μM of Km was for UDP-galactose and 23.9 μM for UDP-glucose respectively. Our results indicate that Ste5 is bifunctional Gal-1-P and Glc-1-P transferase to initiate Ebosin biosynthesis and may be further applied in remoulding carbohydrate compounds.

Precision metabolic engineering: The design of responsive, selective, and controllable metabolic systems

Metabolic engineering is generally focused on static optimization of cells to maximize production of a desired product, though recently dynamic metabolic engineering has explored how metabolic programs can be varied over time to improve titer. However, these are not the only types of applications where metabolic engineering could make a significant impact. Here, we discuss a new conceptual framework, termed "precision metabolic engineering," involving the design and engineering of systems that make different products in response to different signals. Rather than focusing on maximizing titer, these types of applications typically have three hallmarks: sensing signals that determine the desired metabolic target, completely directing metabolic flux in response to those signals, and producing sharp responses at specific signal thresholds. In this review, we will first discuss and provide examples of precision metabolic engineering. We will then discuss each of these hallmarks and identify which existing metabolic engineering methods can be applied to accomplish those tasks, as well as some of their shortcomings. Ultimately, precise control of metabolic systems has the potential to enable a host of new metabolic engineering and synthetic biology applications for any problem where flexibility of response to an external signal could be useful.

Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data

MOTIVATION

With the advent of meta-'omics' data, the use of metabolic networks for the functional analysis of microbial communities became possible. However, while network-based methods are widely developed for single organisms, their application to bacterial communities is currently limited.

RESULTS

Herein, we provide a novel, context-specific reconstruction procedure based on metaproteomic and taxonomic data. Without previous knowledge of a high-quality, genome-scale metabolic networks for each different member in a bacterial community, we propose a meta-network approach, where the expression levels and taxonomic assignments of proteins are used as the most relevant clues for inferring an active set of reactions. Our approach was applied to draft the context-specific metabolic networks of two different naphthalene-enriched communities derived from an anthropogenically influenced, polyaromatic hydrocarbon contaminated soil, with (CN2) or without (CN1) bio-stimulation. We were able to capture the overall functional differences between the two conditions at the metabolic level and predict an important activity for the fluorobenzoate degradation pathway in CN1 and for geraniol metabolism in CN2. Experimental validation was conducted, and good agreement with our computational predictions was observed. We also hypothesize different pathway organizations at the organismal level, which is relevant to disentangle the role of each member in the communities. The approach presented here can be easily transferred to the analysis of genomic, transcriptomic and metabolomic data.

Anti-Inflammatory Effect of Ebosin on Rat Collagen-Induced Arthritis through Suppressing Production of Interleukin-1β, Interleukin-6 and Tumor Necrosis Factor-α

Reumatoid arthritis (RA) is an autoimmune disease which has been studied experimentally using a wide variety of animal models including collagen-induced arthritis (CIA). Using this CIA model we studied the therapeutic effects and mechanism of action of Ebosin, a novel exopolysaccharide produced by Streptomyces sp. 139, on arthritis. Ebosin at 200, 400 and 600 mg/kg/day was orally administered to rats respectively between day 10 and 30 after immunization with chicken type II collagen. With the treatment arthritic progression was remarkably suppressed. Levels of anti-type II collagen-specific antibody, IL-1β and TNF-α were significantly lower in the Ebosin-treated CIA rats compared with the untreated controls. In cultured fibroblast-like synoviocytes (FLS), remarkable suppression of IL-1β, TNF-α and IL-6 production was detected at both protein and mRNA levels after Ebosin administration. Ebosin also resulted in lower activities of IL-1β-converting enzyme and TNF-α-converting enzyme in FLS. Based on these results, it is concluded that development and progression of rat CIA can be significantly suppressed by orally-administrated Ebosin. The therapeutic effect may be attributed to its inhibition in the production of IL-1β, TNF-α and IL-6 in the CIA rats.

Engineered quorum sensing using pheromone-mediated cell-to-cell communication in Saccharomyces cerevisiae

Population-density-dependent control of gene expression, or quorum sensing, is widespread in nature and is used to coordinate complex population-wide phenotypes through space and time. We have engineered quorum sensing in S. cerevisiae by rewiring the native pheromone communication system that is normally used by haploid cells to detect potential mating partners. In our system, populations consisting of only mating type "a" cells produce and respond to extracellular α-type pheromone by arresting growth and expressing GFP in a population-density-dependent manner. Positive feedback quorum sensing dynamics were tuned by varying α-pheromone production levels using different versions of the pheromone-responsive FUS1 promoter as well as different versions of pheromone genes (mfα1 or mfα2). In a second system, pheromone communication was rendered conditional upon the presence of aromatic amino acids in the growth medium by controlling α-pheromone expression with the aromatic amino acid responsive ARO9 promoter. In these circuits, pheromone communication and response could be fine-tuned according to aromatic amino acid type and concentration. The genetic control programs developed here are responsive to dynamic spatiotemporal and chemical cellular environments, resulting in up-regulation of gene expression. These programs could be used to control biochemical pathways for the production of fuels and chemicals that are toxic or place a heavy metabolic burden on cell growth.