Intracellular Products Research Articles

Role of Tumor Cell Intrinsic and Host Autophagy in Cancer.

Macroautophagy (autophagy hereafter) is an intracellular nutrient scavenging pathway induced by starvation and other stressors whereby cellular components such as organelles are captured in double-membrane vesicles (autophagosomes), whereupon their contents are degraded through fusion with lysosomes. Two main purposes of autophagy are to recycle the intracellular breakdown products to sustain metabolism and survival during starvation and to eliminate damaged or excess cellular components to suppress inflammation and maintain homeostasis. In contrast to most normal cells and tissues in the fed state, tumor cells up-regulate autophagy to promote their growth, survival, and malignancy. This tumor-cell-autonomous autophagy supports elevated metabolic demand and suppresses tumoricidal activation of the innate and adaptive immune responses. Tumor-cell-nonautonomous (e.g., host) autophagy also supports tumor growth by maintaining essential tumor nutrients in the circulation and tumor microenvironment and by suppressing an antitumor immune response. In the setting of cancer therapy, autophagy is a resistance mechanism to chemotherapy, targeted therapy, and immunotherapy. Thus, tumor and host autophagy are protumorigenic and autophagy inhibition is being examined as a novel therapeutic approach to treat cancer.

Kinetic modeling of cell growth and value-added products accumulation of Thraustochytrium striatum

A kinetic mathematical model was developed, calibrated, and validated to describe the fermentation performance of a marine protist, Thraustochytrium striatum. This model consists of equations describing substrate consumption, cell growth, and the accumulation of two important intracellular products (lipids and astaxanthin). Moreover, the substrate inhibition and the consumption of product lipids were also considered in the model. After calibration, this model can describe the fermentation performance of T. striatum with high fidelity (R2 values greater than 0.92) over a broad concentration range of individual (glucose 2.5–50 g/L, cellobiose 2.5–10 g/L, and xylose 2.5–10 g/L) and mixed sugar substrates (glucose/cellobiose/xylose, 10.0/2.5/2.5 g/L and 18.0/4.0/4.0 g/L, respectively). Besides synthetic substrates, this model was also proven to be able to simulate the utilization of natural sugar substrates (i.e., glucose, xylose, and cellobiose) generated from the enzymatic hydrolysate of corn stover. However, the presence of toxic compounds in corn stover hydrolysate might have slightly deviated the model prediction, indicating further improvement of this model is needed when it comes to the simulation of natural sugar substrates containing toxic compounds. This model is anticipated to serve as a fundamental framework to simulate and predict the fermentation performance of marine protist for upscaled applications.

Effects of polyethylene terephthalate microplastics on cell growth, intracellular products and oxidative stress of Scenedesmus sp.

Polyethylene terephthalate (PET) has been widely utilized in the synthesis of textile materials and packaging of foods and beverages. In recent years, it has been commonly detected in the form of microplastics (MPs) in wastewater. However, the effects of PET MPs on microalgal intracellular products and their interrelationships have been poorly investigated. In this study, the microalgae Scenedesmus sp. Strain H-1 was exposed to PET MPs to explore their effects on the growth, intracellular products (such as lipids, carbohydrates, and proteins), and antioxidative defense systems of Scenedesmus sp. The results demonstrated that PET MPs significantly reduced Scenedesmus sp. cell growth, with a maximum inhibition rate of 38.25% in the 500 mg L−1 treatment group. PET MPs had negative effects on glucose and nitrate utilization rates and reduced intracellular carbohydrates, intracellular proteins, and photosynthetic pigments. Surprisingly, PET MPs reduced acetyl-CoA carboxylase activity but induced lipid accumulation in microalgae. In addition, PET MPs significantly decreased the essential linoleic acid concentration and increased the palmitic acid content, resulting in reduced biodiesel quality. PET MPs induced the production of reactive oxygen species and malondialdehyde as well as the activities of superoxide dismutase and catalase. The results of the PCA indicated that the response mechanism of Scenedesmus sp. to PET MPs exposure was synergistic. This study provides fundamental data on the impact of MPs on the intracellular products of microalgae.

Co-utilization of glucose and xylose for the production of poly-β-hydroxybutyrate (PHB) by Sphingomonas sanxanigenens NX02

BackgroundPoly-β-hydroxybutyrate (PHB), produced by a variety of microbial organisms, is a good substitute for petrochemically derived plastics due to its excellent properties such as biocompatibility and biodegradability. The high cost of PHB production is a huge barrier for application and popularization of such bioplastics. Thus, the reduction of the cost is of great interest. Using low-cost substrates for PHB production is an efficient and feasible means to reduce manufacturing costs, and the construction of microbial cell factories is also a potential way to reduce the cost.ResultsIn this study, an engineered Sphingomonas sanxanigenens strain to produce PHB by blocking the biosynthetic pathway of exopolysaccharide was constructed, and the resulting strain was named NXdE. NXdE could produce 9.24 ± 0.11 g/L PHB with a content of 84.0% cell dry weight (CDW) using glucose as a sole carbon source, which was significantly increased by 76.3% compared with the original strain NX02. Subsequently, the PHB yield of NXdE under the co-substrate with different proportions of glucose and xylose was also investigated, and results showed that the addition of xylose would reduce the PHB production. Hence, the Dahms pathway, which directly converted D-xylose into pyruvate in four sequential enzymatic steps, was enhanced by overexpressing the genes xylB, xylC, and kdpgA encoding xylose dehydrogenase, gluconolactonase, and aldolase in different combinations. The final strain NX02 (ΔssB, pBTxylBxylCkdpgA) (named NXdE II) could successfully co-utilize glucose and xylose from corn straw total hydrolysate (CSTH) to produce 21.49 ± 0.67 g/L PHB with a content of 91.2% CDW, representing a 4.10-fold increase compared to the original strain NX02.ConclusionThe engineered strain NXdE II could co-utilize glucose and xylose from corn straw hydrolysate, and had a significant increase not only in cell growth but also in PHB yield and content. This work provided a new host strain and strategy for utilization of lignocellulosic biomass such as corn straw to produce intracellular products like PHB.

Salting-out extraction of recombinant κ-carrageenase and phage T7 released from Escherichia coli cells.

Traditional technology of cell disruption has become one of the bottlenecks restricting the industrialization of genetic engineering products due to its high cost and low efficiency. In this study, a novel bioprocess of phage lysis coupled with salting-out extraction (SOE) was evaluated. The lysis effect of T7 phage on genetically engineered Escherichia coli expressing κ-carrageenase was investigated at different multiplicity of infection (MOI), meanwhile the phage and enzyme released into the lysate were separated by SOE. It was found that T7 phage could lyse 99.9% of host cells at MOI=1 and release more than 90.0% of enzyme within 90min. After phage lysis, 87.1% of T7 phage and 71.2% of κ-carrageenase could be distributed at the middle phase and the bottom phase, respectively, in the SOE system composed of 16% ammonium sulfate and 20% ethyl acetate (w/w). Furthermore, κ-carrageenase in the bottom phase could be salted out by ammonium sulfate with a yield of 40.1%. Phage lysis exhibits some advantages, such as mild operation conditions and low cost. While SOE can efficiently separate phage and intracellular products. Therefore, phage lysis coupled with SOE is expected to become a viable alternative to the classical cell disruption and intracellular product recovery.

Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products

BackgroundIntracellular biomacromolecules, such as industrial enzymes and biopolymers, represent an important class of bio-derived products obtained from bacterial hosts. A common key step in the downstream separation of these biomolecules is lysis of the bacterial cell wall to effect release of cytoplasmic contents. Cell lysis is typically achieved either through mechanical disruption or reagent-based methods, which introduce issues of energy demand, material needs, high costs, and scaling problems. Osmolysis, a cell lysis method that relies on hypoosmotic downshock upon resuspension of cells in distilled water, has been applied for bioseparation of intracellular products from extreme halophiles and mammalian cells. However, most industrial bacterial strains are non-halotolerant and relatively resistant to hypoosmotic cell lysis. ResultsTo overcome this limitation, we developed two strategies to increase the susceptibility of non-halotolerant hosts to osmolysis using Cupriavidus necator, a strain often used in electromicrobial production, as a prototypical strain. In one strategy, C. necator was evolved to increase its halotolerance from 1.5% to 3.25% (w/v) NaCl through adaptive laboratory evolution, and genes potentially responsible for this phenotypic change were identified by whole genome sequencing. The evolved halotolerant strain experienced an osmolytic efficiency of 47% in distilled water following growth in 3% (w/v) NaCl. In a second strategy, the cells were made susceptible to osmolysis by knocking out the large-conductance mechanosensitive channel (mscL) gene in C. necator. When these strategies were combined by knocking out the mscL gene from the evolved halotolerant strain, greater than 90% osmolytic efficiency was observed upon osmotic downshock. A modified version of this strategy was applied to E. coli BL21 by deleting the mscL and mscS (small-conductance mechanosensitive channel) genes. When grown in medium with 4% NaCl and subsequently resuspended in distilled water, this engineered strain experienced 75% cell lysis, although decreases in cell growth rate due to higher salt concentrations were observed.ConclusionsOur strategy is shown to be a simple and effective way to lyse cells for the purification of intracellular biomacromolecules and may be applicable in many bacteria used for bioproduction.

Molecular integrative study on interaction domains of nuclear factor erythroid 2-related factor 2 with sirtuin 6

Oxidative stress is one of the elements causing aging and related diseases. Inhibiting Nrf2 activity or increasing oxidative pressure can replicate the deficits of premature aging. SIRT6 is one of the few proteins that can regulate both life span and aging. Deletion of SIRT6 in human cells impairs the antioxidant capacity of cells, which results in the accumulation of intracellular reactive oxygen species and DNA oxidation products. Characterization of the binding of Nrf2 with SIRT6 is critical for understanding the modulation of Nrf2-correlated cell activities by SIRT6. The yeast two-hybrid experiments showed that the binding of Nrf2 with SIRT6 is mediated by Neh1 and Neh3 domains. The elimination of the Neh1 and Neh3 domains decreased the binding stability and free energy, according to the molecular dynamic analysis. The roles of theses domains in mediating the binding were confirmed by co-immunoprecipitation. In cells transfected with the small interfering RNA (siRNA) targeting the Nrf2 Neh1 domain and plasmids overexpressing domain-mutant Nrf2, it was discovered that Nrf2 lost its activity to stimulate the transcription of antioxidant genes in the absence of Neh1 and Neh3 domains.

Monascus Yellow Pigment Production by Coupled Immobilized-Cell Fermentation and Extractive Fermentation in Nonionic Surfactant Micelle Aqueous Solution

Microbial fermentation with immobilized cells possesses many advantages. However, this fermentation mode is restricted to the production of extracellular products. Our previous study demonstrated that the extractive fermentation of Monascus spp. in nonionic surfactant micelle aqueous solution can export Monascus pigments that are supposed to be mainly intracellular products to extracellular culture broth and, in the meantime, extracellularly enhance the production of yellow pigments at a low pH condition; consequently, this makes the continuous production of yellow pigments with immobilized Monascus cells feasible. In this study, immobilized-cell fermentation and extractive fermentation in Triton X-100 micelle aqueous solution were successfully combined to continuously produce Monascus yellow pigments extracellularly. We examined the effects of cell immobilization and Triton X-100 on cell growth, pigment production, and pigment composition. In the repeated-batch extractive fermentation with immobilized cells, the biomass in Ca-alginate gel beads continued to grow and reached 21.2 g/L after seven batches, and dominant yellow pigments were produced extracellularly and stable for each batch. The mean productivity of the extracellular yellow pigments reached up to 22.31 AU410 nm/day within the first four batches (13 days) and 19.7 AU410 nm/day within the first seven batches (25 days). The results also provide a new strategy for producing such intracellular products continuously and extracellularly.

Towards a templated reaction that translates RNA in cells into a proaptotic peptide-PNA conjugate.

Nucleic acid-templated chemistry opens the intriguing prospect of triggering the synthesis of drugs only in diseased cells. Herein, we explore the feasibility of using RNA-templated chemical reactions for the activation of a known Smac peptidomimetic compound (SMC), which has proapoptotic activity. Two peptide nucleic acid (PNA) conjugates were used to enable conditional activation of a masked SMC by reduction of an azide either by Staudinger reduction or catalytic photoreduction using a ruthenium complex. The latter provided ~135 nM SMC-PNA on as little as 10nM (0.01 eq.) template. For the evaluation of the templated azido-SMC reduction system in cellulo, a stable HEK 293 cell line was generated, which overexpressed a truncated, non-functional form of the XIAP mRNA target. We furthermore describe the development of electroporation protocols that enable a robust delivery of PNA conjugates into HEK 293 cells. The action of the reactive PNA conjugates was evaluated by viability and flow cytometric apoptosis assays. In addition, electroporated probes were re-isolated and analyzed by ultra-high performance liquid chromatography (UPLC). Unfortunately, the ruthenium-PNA conjugate proved phototoxic, and treatment of cells with PNA-linked reducing agent and the azido-masked SMC conjugate did not result in a greater viability loss than treatment with scrambled sequence controls. Intracellular product formation was not detectable. A control experiment in total cellular RNA isolate indicated that the templated reaction can in principle proceed in a complex system. The results of this first-of-its-kind study reveal the numerous hurdles that must be overcome if RNA molecules are to trigger the synthesis of pro-apoptotic drugs inside cells.

NF-κB Inhibitor Myrislignan Induces Ferroptosis of Glioblastoma Cells via Regulating Epithelial-Mesenchymal Transformation in a Slug-Dependent Manner.

Glioblastoma (GBM) is the most common malignant tumor of the adult central nervous system. Aberrant regulation of cell death is an important feature of GBM, and investigating the regulatory mechanisms of cell death in GBM may provide insights into development of new therapeutic strategies. We demonstrated that myrislignan has ferroptosis-promoting activity. Myrislignan is a lignan isolated from Myristica fragrans Houtt and an inhibitor of NF-κB signaling pathway. Ferroptosis is an iron-dependent form of programmed cell death characterized by the accumulation of intracellular lipid peroxidation products. Interestingly, ferroptosis was associated with other biological processes in tumor cells such as autophagy and necroptosis. Recently, the crosstalk between epithelial-mesenchymal transition (EMT) and ferroptosis has also been reported, but the mechanisms underlying the crosstalk have not been identified. Our results indicated that myrislignan suppressed growth of GBM through EMT-mediated ferroptosis in a Slug-dependent manner. Myrislignan inhibited the activation of NF-κB signaling by blocking the phosphorylation of p65 protein and induced ferroptosis through the Slug-SLC7A11 signaling pathway in GBM cells. In addition, myrislignan suppressed the progression of GBM in xenograft mouse model. Hence, our findings contribute to the understanding of EMT-induced ferroptosis and provide targets for the development of targeted therapy against GBM.

Development of a Bacterial FhuD-Lysozyme-SsrA Mediated Autolytic (FLSA) System for Effective Release of Intracellular Products

Developing effective bacterial autolytic systems for fast release of intracellular bioproducts could simplify purification procedures and help with the high throughput screening of mutant libraries in protein engineering. Here, we developed a fast and tightly regulated E.coli autolytic system, named the FhuD-lysozyme-SsrA mediated autolytic (FLSA) system, by integrating the secretion signal peptide, T7 lysozyme, and E.coli ClpX/P-SsrA protein degradation machinery. To decrease the cytotoxicity of leaky T7 lysozymes, the SsrA tag was fused to the C-terminus of T7 lysozyme to confer a tight regulation of its production. Using sfGFP as a reporter, we demonstrated that anchoring the Sec-Tat dual pathway signal peptide FhuD to the N-terminus of T7 lysozyme-SsrA could give the highest cell lysing efficiency. The optimization of the FLSA system indicated that weak alkaline conditions (pH 8.0) and 0.5% Triton X-100 could further increase the lysing efficiency by about 24%. The FLSA system was validated by efficient production of sfGFP and human growth hormone 1 (hGH1) in a shake flask, with a cell lytic efficiency of approximately 82% and 80%, respectively. Besides, the FLSA system was applied for large-scale fermentation, in which approximately 90% sGFP was released with a cell density OD600 of 110. Moreover, the FLSA system was also tested for α-amylase mutant library screening in microplates, and the results showed that intracellular α-amylase can be efficiently released out of cells for activity quantitation. In all, the FLSA system can facilitate the release of intracellular recombinant proteins into the cell culture medium, which has the potential to serve as an integrated system for large-scale production of recombinant targets and high throughput enzyme engineering in synthetic biology.

Development and characterization of yeast-incorporated coating films for improving the postharvest shelf-life of snap beans

Snap bean is an important crop species of Leguminosae family, which needs to be stored prior to marketing as it is usually consumed fresh. However, snap bean pods are prone to disease infection during storage, and quickly lose market quality if they store for a long period. One way to tackle this issue is to cover pods with yeast-incorporating coating films. In this research, we assessed incorporation of three strains of yeast Ca63 (Cryptococcus albidus), Ca64 (Cryptococcus albidus) and Yett1006 (Candida parapsilosis) and their intracellular products with naturally-based fruit coating materials. All three strains and their intercellular products could effectively inhibit the growth of Fusarium fujikuroi, the phytopathogenic agent causes pod rot in snap beans, however, the inhibitory impacts of yeast strains were more pronounced than their intercellular products. The snap bean pods treated with either yeast-incorporated films or yeast intracellular products-incorporated films could reduce weight loss rate, decay rate, rust index and color index in pods, leading to longer shelf-life during 15 days of storage at 28 ℃ and relative humidity of 65% ± 5%. In addition, the coating material containing yeasts or their intracellular products positively affected the activity of superoxide dismutase, increased the content of vitamin E, reduced the rate of chlorophyll degradation and effectively inhibited the increase of malondialdehyde content in the treated pods. A metabolomic analysis of the yeasts and their intracellular products revealed that their protective impacts could be due to antioxidant compounds found in their metabolites. Overall, the results of this research provided a basis for the application of the three strains of yeast in postharvest preservation of snap bean pods and laid a foundation for exploring the mechanism underlying postharvest preservation of snap bean pods.

Human Umbilical Cord Mesenchymal Stem Cells-Derived Small Extracellular Vesicles Can Be Considered as Cell-Free Therapeutics for Angiogenesis Promotion.

Angiogenesis has critical roles in several physiological processes. Restoring angiogenesis in some pathological conditions such as a few vascular diseases can be a therapeutic approach to controlling this issue. Mesenchymal stem cells (MSCs) secrete specific intracellular products known as extracellular vesicles (EVs) with high therapeutic potential which compared to their source cells, do not have the limitations of cell therapy. The angiogenic effect of the human umbilical cord MSCs (hUCMSCs)-derived small EVs are evaluated in the present work. Aim of this research is to show that hUCMSCs-derived small EVs cause differentiation of genes involved in angiogenesis like FGFR-1, FGF, VEGF, and VEGFR-2. In this experimental study, MSCs were isolated from the human umbilical cord, and after confirming their identities, their secreted EVs (including exosomes) were extracted by ultracentrifugation. The isolated small EVs were characterized by dynamic light scattering (DLS), transmission electron microscopy (TEM), bicinchoninic acid assay (BCA), and Western Blotting. Then, the human umbilical vein endothelial cells (HUVECs) were treated with derived small EVs for 72 hours, and the expression of the angiogenic factors including FGFR-1, FGF, VEGF, and VEGFR-2 was evaluated by quantitative real-time-polymerase chain reaction (qPCR). Angiogenesis was also evaluated via a tube formation assay. The results demonstrated that FGFR-1, FGF, VEGF, and VEGFR-2 could be elevated 2, 2, 3.5, and 2 times, respectively, in EVs treated HUVECs, and derivative EVs can encourage tube formation in HUVECs. These findings imply that hUCMSCs-derived small EVs are valuable resources in promoting angiogenesis and are very promising in cell-free therapy.

Rhodotorula sp.–based biorefinery: a source of valuable biomolecules

The development of an effective, realistic, and sustainable microbial biorefinery depends on several factors, including as one of the key aspects an adequate selection of microbial strain. The oleaginous red yeast Rhodotorula sp. has been studied as one powerful source for a plethora of high added-value biomolecules, such as carotenoids, lipids, and enzymes. Although known for over a century, the use of Rhodotorula sp. as resource for valuable products has not yet commercialized. Current interests for Rhodotorula sp. yeast have sparked from its high nutritional versatility and ability to convert agro-food residues into added-value biomolecules, two attractive characteristics for designing new biorefineries. In addition, as for other yeast-based bioprocesses, the overall process sustainability can be maximized by a proper integration with subsequent downstream processing stages, for example, by using eco-friendly solvents for the recovery of intracellular products from yeast biomass. This review intends to reflect on the current state of the art of microbial bioprocesses using Rhodotorula species. Therefore, we will provide an analysis of bioproduction performance with some insights regarding downstream separation steps for the extraction of highadded-value biomolecules (specifically using efficient and sustainable platforms), providing information regarding the potential applications of biomolecules produced by Rhodotorula sp, as well as detailing the strengths and limitations of yeast-based biorefinery approaches. Novel genetic engineering technologies are further discussed, indicating some directions on their possible use for maximizing the potential of Rhodotorula sp. as cell factories. KEY POINTS: • Rhodotorula sp. are valuable source of high value-added compounds. • Potential of employing Rhodotorula sp. in a multiple product biorefinery. • Future perspectives in the biorefining of Rhodotorula sp. were discussed.

Computational analysis of peptidoglycan hydrolase genes in Pediococcus acidilactici D3 genome

Peptidoglycan hydrolases (PGH) hydrolyze the covalent bond in peptidoglycans. PGHs are valuable tools for biotechnologists with many applications in medicine, food industry and for recovery of intracellular products from bacteria. Due to their ability to hydrolyze bacterial cell walls, PGHs might be promising in combating multidrug resistant pathogens. Genome of Pediococcus acidilactici D3 was analysed for genes encoding for PGHs. D3 genome encodes for 9 PGHs that might possess different activity. Their physiochemical properties and structure were predicted using computational tools. Functional annotation, physiochemical properties and predicted structures will increase the understanding of PGHs of P. acidilactici D3 in the light of earlier studied PGHs by domain swapping, construction of chimeras and production of engineered lysins with diverse applications.

Heterotrophic Cultivation of Euglena gracilis in Stirred Tank Bioreactor: A Promising Bioprocess for Sustainable Paramylon Production.

Paramylon is a valuable intracellular product of the microalgae Euglena gracilis, and it can accumulate in Euglena cells according to the cultivation conditions. For the sustainable production of paramylon and appropriate cell growth, different bioreactor processes and industrial byproducts can be considered as substrates. In this study, a complex medium with corn steep solid (CSS) was used, and various bioreactor processes (batch, fed batch, semicontinuous and continuous) were performed in order to maximize paramylon production in the microalgae Euglena gracilis. Compared to the batch, fed batch and repeated batch bioprocesses, during the continuous bioprocess in a stirred tank bioreactor (STR) with a complex medium containing 20 g/L of glucose and 25 g/L of CSS, E. gracilis accumulated a competitive paramylon content (67.0%), and the highest paramylon productivity of 0.189 g/Lh was observed. This demonstrated that the application of a continuous bioprocess, with corn steep solid as an industrial byproduct, can be a successful strategy for efficient and economical paramylon production.

Urinary extracellular vesicles carry multiple activators and regulators of coagulation.

Cells shape their extracellular milieu by secreting intracellular products into the environment including extracellular vesicles which are lipid-bilayer limited membrane particles. These vesicles carry out a range of functions, including regulation of coagulation, via multiple contributor mechanisms. Urinary extracellular vesicles are secreted by various cells, lining the urinary space, including the nephron and bladder. They are known to have procoagulant properties, however, the details of this function, beyond tissue factor are not well known. The aim of the study was to access the role of urinary extracellular vesicles in impacting coagulation upon supplementation to plasma. This could indicate their physiological function upon kidney injury or pathology. Supplementation to standard human plasma and plasmas deficient in various coagulation factors was used for this purpose, and calibrated automated thrombogram (CAT®) was the major technique applied. We found that these vesicles contain multiple coagulation-related factors, and their lipid composition affects coagulation activities of plasma upon supplementation. Remarkably, these vesicles can restore thrombin generation in FVII, FVIII, FIX and FXI -deficient plasmas. This study explores the multiple roles of urinary extracellular vesicles in coagulation in in vitro blood coagulation and implies their importance in its regulation by several mechanisms.

Exploring the mechanisms of immunomodulation by a commensal Clostridium species

The microbiome is intricately linked to human health and, when dysregulated, can cause disease. It has been shown that specific members of the intestinal microbiota regulate immunity, a finding that offers an approach for treating autoimmune disease through microbiome engineering. In previously published work, we identified Clostridium immunis, a new human-derived commensal bacterial species that protects mice against colitis. To understand the host immunological response to C. immunis, we performed comprehensive flow cytometric analysis of the colonic immune system of C. immunis-treated mice. We observed a significant decrease in the number of group 3 innate lymphoid cells (ILC3s), a rare but critical tissue-resident immune cell population that has been implicated in autoimmune diseases. We hypothesize that C. immunisproduces a bioactive molecule that downregulates ILC3s. To identify the genetic determinants of ILC3 downregulation by C. immunis, we compared the ability of closely related clostridia to modulate ILC3-produced cytokines in a colonic explant model. By excluding genes encoded by two inactive clostridia strains, we managed to identify 40 genes that are associated with ILC3 modulation. We similarly observed that C. immunis culture supernatant contained activity. By excluding genes that have predicted intracellular products, we further narrowed this list to 8 candidate genes. Critically, we have recently developed a method to perform targeted genetic knockouts in C. immunis, and are currently generating mutants for these genes. This work will therefore identify the gene product required for ILC3 modulation and potentially identify novel classes of bacterially derived molecules to treat ILC3-driven disease.

Rational engineering of natural polyhydroxyalkanoates producing microorganisms for improved synthesis and recovery.

Microbial production of biopolymers derived from renewable substrates and waste streams reduces our heavy reliance on petrochemical plastics. One of the most important biodegradable polymers is the family of polyhydroxyalkanoates (PHAs), naturally occurring intracellular polyoxoesters produced for decades by bacterial fermentation of sugars and fatty acids at the industrial scale. Despite the advances, PHA production still suffers from heavy costs associated with carbon substrates and downstream processing to recover the intracellular product, thus restricting market positioning. In recent years, model-aided metabolic engineering and novel synthetic biology approaches have spurred our understanding of carbon flux partitioning through competing pathways and cellular resource allocation during PHA synthesis, enabling the rational design of superior biopolymer producers and programmable cellular lytic systems. This review describes these attempts to rationally engineering the cellular operation of several microbes to elevate PHA production on specific substrates and waste products. We also delve into genome reduction, morphology, and redox cofactor engineering to boost PHA biosynthesis. Besides, we critically evaluate engineered bacterial strains in various fermentation modes in terms of PHA productivity and the period required for product recovery.

A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics.

Lack of active export system often limits the industrial bio-based production processes accumulating the intracellular product and hence complexing the purification steps. L-lysine, an essential amino acid, is produced biologically in quantities exceeding two million tons per year; yet, L-lysine production is challenged by efficient export system at high titers during fermentation. To address this issue, new exporter candidates for efficient efflux of L-lysine are needed. Using metagenomic functional selection, we identified 58 genes encoded on 28 unique metagenomic fragments from cow gut microbiome library that improved L-lysine tolerance. These genes include a novel L-lysine transporter, belonging to a previously uncharacterized EamA superfamily, which is further in vivo characterized as L-lysine exporter using Xenopus oocyte expression system as well as Escherichia coli host. This novel exporter improved L-lysine tolerance in E. coli by 40% and enhanced yield, titer, and the specific production of L-lysine in an industrial Corynebacterium glutamicum strain by 7.8%, 9.5%, and 12%, respectively. Our approach allows the sequence-independent discovery of novel exporters and can be deployed to increase titers and productivity of toxicity-limited bioprocesses.