pathway expression
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Author(s):  
Gieira S. Jones ◽  
Katherine A. Hoadley ◽  
Halei Benefield ◽  
Linnea T. Olsson ◽  
Alina M. Hamilton ◽  
...  

2022 ◽  
Author(s):  
Joshua R Elmore ◽  
George L Peabody ◽  
Ramesh K Jha ◽  
Gara N Dexter ◽  
Taraka Dale ◽  
...  

Expanding the catabolic repertoire of engineered microbial bioproduction hosts enables more efficient use of complex feedstocks such as lignocellulosic hydrolysates, but the deleterious effects of existing expression systems limit the maximum carry capacity for heterologous catabolic pathways. Here we demonstrate use of a conditionally beneficial oxidative xylose catabolic pathway to improve performance of a Pseudomonas putida strain that has been engineered for growth-coupled bioconversion of glucose into the valuable bioproduct cis,cis-muconic acid. In the presence of xylose, the pathway enhances growth rate, and therefor productivity, by >60%, but the metabolic burden of constitutive pathway expression reduces the its growth rate by >20% in the absence of xylose. To mitigate this growth defect, we develop a xylose biosensor based on the XylR transcription factor from Caulobacter crescentus NA1000 to autonomously regulate pathway expression. We generate a library of engineered xylose-sensitive promoters that cover a three order-of-magnitude range of expression levels to tune pathway expression. Using structural modeling to guide mutations, we engineer XylR with two and three orders-of-magnitude reduced sensitivity to xylose and L-arabinose, respectively. A previously developed heterologous xylose isomerase pathway is placed under control of the biosensor, which improves the growth rate with xylose as a carbon source by 10% over the original constitutively expressed pathway. Finally, the oxidative xylose catabolic pathway is placed under control of the biosensor, enabling the bioproduction strain to maintain the increased growth rate in the presence of xylose, without the growth defect incurred from constitutive pathway expression in the absence of xylose. Utilizing biosensors to autonomously regulate conditionally beneficial catabolic pathways is generalizable, and will be critical for engineering bioproduction hosts bacteria with the wide range of catabolic pathways required for bioconversion of complex feedstocks.


2021 ◽  
Vol 68 ◽  
pp. 152-161
Author(s):  
Yongshuo Ma ◽  
Jingbo Li ◽  
Sanwen Huang ◽  
Gregory Stephanopoulos

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ida Lauritsen ◽  
Pernille Ott Frendorf ◽  
Silvia Capucci ◽  
Sophia A. H. Heyde ◽  
Sarah D. Blomquist ◽  
...  

AbstractThe evolution of microorganisms often involves changes of unclear relevance, such as transient phenotypes and sequential development of multiple adaptive mutations in hotspot genes. Previously, we showed that ageing colonies of an E. coli mutant unable to produce cAMP when grown on maltose, accumulated mutations in the crp gene (encoding a global transcription factor) and in genes involved in pyrimidine metabolism such as cmk; combined mutations in both crp and cmk enabled fermentation of maltose (which usually requires cAMP-mediated Crp activation for catabolic pathway expression). Here, we study the sequential generation of hotspot mutations in those genes, and uncover a regulatory role of pyrimidine nucleosides in carbon catabolism. Cytidine binds to the cytidine regulator CytR, modifies the expression of sigma factor 32 (RpoH), and thereby impacts global gene expression. In addition, cytidine binds and activates a Crp mutant directly, thus modulating catabolic pathway expression, and could be the catabolite modulating factor whose existence was suggested by Jacques Monod and colleagues in 1976. Therefore, transcription factor Crp appears to work in concert with CytR and RpoH, serving a dual role in sensing both carbon availability and metabolic flux towards DNA and RNA. Our findings show how certain alterations in metabolite concentrations (associated with colony ageing and/or due to mutations in metabolic or regulatory genes) can drive the evolution in non-growing cells.


2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Juehan Wang ◽  
Leizhen Huang ◽  
Xi Yang ◽  
Ce Zhu ◽  
Yong Huang ◽  
...  

Aims. Accumulating evidence reported that the microRNA (miRNA) took an important role in intervertebral disc degeneration (IDD). In this study, we revealed a novel miRNA regulatory mechanism in IDD. Main Methods. The miRNA microarray analyses of human degenerated and normal disc samples were employed to screen out the target miRNA. In vitro and in vivo experiments were conducted to verify the regulatory effect of miR-101-3p. Key Findings. The expression level of miR-101-3p was significantly decreased in the degenerated disc samples which were confirmed by qRT-PCR. Moreover, the miR-101-3p expression level was changed dynamically according to the disc degeneration grade. Upregulation of miR-101-3p expression level inhibited cell apoptosis. Furthermore, stanniocalcin-1 (STC1) was selected to be the target gene of miR-101-3p according to the bioinformatic algorithms. Mechanically, upregulation of miR-101-3p significantly decreased the expression of STC1, vascular endothelial growth factor (VEGF), and MAPK pathway expression levels. Therapeutically, in vivo experiment on IDD rat model illustrated that agomir-101-3p could effectively suspend IDD. Significance. Our findings demonstrated that miR-101-3p alleviated IDD process through the STC1/VEGF/MAPK pathway.


Dose-Response ◽  
2021 ◽  
Vol 19 (4) ◽  
pp. 155932582110421
Author(s):  
Huapeng Sun ◽  
Na Zhang ◽  
Yiqiang Jin ◽  
Haisheng Xu

Cardamonin (CAR), a flavone existing in the Alpinia plant, has been found to modulate multiple biological activities, including antioxidant, anti-inflammatory, and anti-tumor effects. Nevertheless, the influence of CAR on pancreatic cancer (PC) is less understood. Here, we conducted in vitro and in vivo experiments to explore the functions of CAR on PC cells’ proliferation, apoptosis and chemosensitivity to gemcitabine (GEM). The growth of PC cells (including PANC-1 and SW1990) was evaluated by the cell counting kit-8 assay, colony formation assay and xenograft tumor experiment. Besides, the apoptosis was determined by flow cytometry and western blot (WB). Moreover, the FOXO3a-FOXM1 pathway expression was tested by reverse transcription-polymerase chain reaction and WB. Our data suggested that CAR restrained cell proliferation, growth and expedited apoptosis both in vitro and in vivo. Moreover, CAR sensitized PC cells to GEM. Mechanistically, CAR heightened FOXO3a while repressed FOXM1. Further loss-of-function assays revealed that down-regulating FOXO3a markedly dampened the anti-tumor effect induced by CAR and accelerated the FOXM1 expression. Our data confirmed that CAR exerted an anti-tumor function in PC dependently by modulating the FOXO3a-FOXM1 axis.


2021 ◽  
Vol 116 (3) ◽  
pp. e208
Author(s):  
Kathryn M. Goldrick ◽  
Jennifer F. Knudtson ◽  
Robert S. Schenken ◽  
Mubeen Sultana ◽  
Randal D. Robinson ◽  
...  

2021 ◽  
Vol 116 (3) ◽  
pp. e202-e203
Author(s):  
Kathryn M. Goldrick ◽  
Jennifer F. Knudtson ◽  
Mubeen Sultana ◽  
Rajeshwar Rao Tekmal ◽  
Robert S. Schenken

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2558
Author(s):  
Ryan S. Pralle ◽  
Wenli Li ◽  
Brianna N. Murphy ◽  
Henry T. Holdorf ◽  
Heather M. White

Lipid-related metabolic disorders (LRMD) are prevalent in early lactation dairy cows, and have detrimental effects on productivity and health. Our objectives were to identify cows resistant or susceptible to LRMD using a ketosis induction protocol (KIP) to discover differentially expressed liver genes and metabolic pathways associated with disposition. Clustering cows based on postpartum lipid metabolite concentrations within dietary treatments identified cows more or less susceptible (MS vs. LS) to LRMD within the control treatment, and more or less resistant (MR vs. LR) within the KIP treatment. Whole-transcriptome RNA sequencing was performed on liver samples (−28, +1, and +14 days relative to calving) to assess differential gene and pathway expression (LS vs. MS; MR vs. LR; n = 3 cows per cluster). Cows within the MS and LR clusters had evidence of greater blood serum β-hydroxybutyrate concentration and liver triglyceride content than the LS and MR clusters, respectively. The inferred metabolism of differentially expressed genes suggested a role of immune response (i.e., interferon-inducible proteins and major histocompatibility complex molecules). Additionally, unique roles for glutathione metabolism and eicosanoid metabolism in modulating susceptibility and resistance, respectively, were implicated. Overall, this research provides novel insight into the role of immunometabolism in LRMD pathology, and suggests the potential for unique control points for LRMD progression and severity.


2021 ◽  
Vol 12 ◽  
Author(s):  
Anshuman Panda ◽  
Shridar Ganesan

Immune checkpoint blockade leads to unprecedented responses in many cancer types. An alternative method of unleashing anti-tumor immune response is to target immunosuppressive metabolic pathways like the indoleamine 2,3-dioxygenase (IDO) pathway. Despite promising results in Phase I/II clinical trials, an IDO-1 inhibitor did not show clinical benefit in a Phase III clinical trial. Since, a treatment can be quite effective in a specific subset without being effective in the whole cancer type, it is important to identify the subsets of cancers that may benefit from IDO-1 inhibitors. In this study, we looked for the genomic and immunologic correlates of IDO pathway expression in cancer using the Cancer Genome Atlas (TCGA) dataset. Strong CD8+ T-cell infiltration, high mutation burden, and expression of exogenous viruses [Epstein-Barr virus (EBV), Human papilloma virus (HPV), and Hepatitis C virus (HCV)] or endogenous retrovirus (ERV3-2) were associated with over-expression of IDO-1 in most cancer types, IDO-2 in many cancer types, and TDO-2 in a few cancer types. High mutation burden in ER+ HER2− breast cancer, and ERV3-2 expression in ER− HER2− and HER2+ breast, colon, and endometrial cancers were associated with over-expression of all three genes. These results may have important implications for guiding development clinical trials of IDO-1 inhibitors.


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