Reconstruction of tricarboxylic acid cycle in Corynebacterium glutamicum with a genome-scale metabolic network model for trans-4-hydroxyproline production

trans-4-Hydroxy- l -proline (Hyp) is an abundant component of mammalian collagen and functions as a chiral synthon for the syntheses of anti-inflammatory drugs in the pharmaceutical industry. Proline 4-hydroxylase (P4H) can catalyze the conversion of l -proline to Hyp; however, it is still challenging for the fermentative production of Hyp from glucose using P4H due to the low yield and productivity. Here, we report the metabolic engineering of Corynebacterium glutamicum for the fermentative production of Hyp by reconstructing tricarboxylic acid (TCA) cycle together with heterologously expressing the p4h gene from Dactylosporangium sp. strain RH1. In silico model-based simulation showed that α-ketoglutarate was redirected from the TCA cycle toward Hyp synthetic pathway driven by P4H when the carbon flux from succinyl-CoA to succinate descended to zero. The interruption of the TCA cycle by the deletion of sucCD-encoding the succinyl-CoA synthetase (SUCOAS) led to a 60% increase in Hyp production and had no obvious impact on the growth rate. Fine-tuning of plasmid-borne ProB* and P4H abundances led to a significant increase in the yield of Hyp on glucose. The final engineered Hyp-7 strain produced up to 21.72 g/L Hyp with a yield of 0.27 mol/mol (Hyp/glucose) and a volumetric productivity of 0.36 g·L ⁻¹·hr ⁻¹ in the shake flask fermentation. To our knowledge, this is the highest yield and productivity achieved by microbial fermentation in a glucose-minimal medium for Hyp production. This strategy provides new insights into engineering C. glutamicum by flux coupling for the fermentative production of Hyp and related products.     

Learning the Formation Mechanism of Domain-Level Chromatin States with Epigenomics Data

Epigenetic modifications can extend over long genomic regions to form domain-level chromatin states that play critical roles in gene regulation. The molecular mechanism for the establishment and maintenance of these states is not fully understood and remains challenging to study with existing experimental techniques. Here, we took a data-driven approach and parameterized an information-theoretic model to infer the formation mechanism of domain-level chromatin states from genome-wide epigenetic modification profiles. This model reproduces statistical correlations among histone modifications and identifies well-known states. Importantly, it predicts drastically different mechanisms and kinetic pathways for the formation of euchromatin and heterochromatin. In particular, long, strong enhancer and promoter states grow gradually from short but stable regulatory elements via a multistep process. On the other hand, the formation of heterochromatin states is highly cooperative, and no intermediate states are found along the transition path. This cooperativity can arise from a chromatin looping-mediated spreading of histone methylation mark and supports collapsed, globular three-dimensional conformations rather than regular fibril structures for heterochromatin. We further validated these predictions using changes of epigenetic profiles along cell differentiation. Our study demonstrates that information-theoretic models can go beyond statistical analysis to derive insightful kinetic information that is otherwise difficult to access.     

Interleukin-2 induces extracellular matrix synthesis and TGF-β2 expression in retinal pigment epithelial cells

Macular fibrosis is a vital obstacle of vision acuity improvement of age-related macular degeneration patients. This study was to investigate the effects of interleukin 2 (IL-2) on epithelial-mesenchymal transition (EMT), extracellular matrix (ECM) synthesis and transforming growth factor β2 (TGF-β2) expression in retinal pigment epithelial (RPE) cells. 10 μg/L IL-2 was used to induce fibrosis in RPE cells for various times. Western blot was used to detect the EMT marker α-smooth muscle actin (α-SMA), ECM markers fibronectin (Fn) and type 1 collagen (COL-1), TGF-β2, and the activation of the JAK/STAT3 and NF-κB signaling pathway. Furthermore, JAK/STAT3 and NF-κB signaling pathways were specifically blocked by WP1066 or BAY11-7082, respectively, and the expression of α-SMA, COL-1, Fn and TGF-β2 protein were detected. Wound healing and Transwell assays were used to measure cell migration ability of IL-2 with or without WP1066 or BAY11-7082. After induction of IL-2, the expressions of Fn, COL-1, TGF-β2 protein were significantly increased, and this effect was correlated with IL-2 treatment duration, while α-SMA protein expression did not change significantly. Both WP1066 and BAY11-7082 could effectively downregulate the expression of Fn, COL-1 and TGF-β2 induced by IL-2. What's more, both NF-κB and JAK/STAT3 inhibitors could suppress the activation of the other signaling pathway. Additionally, JAK/STAT3 inhibitor WP1066 and NF-κB inhibitor BAY 11-7082 could obviously decrease RPE cells migration capability induced by IL-2. IL-2 promotes cell migration, ECM synthesis and TGF-β2 expression in RPE cells via JAK/STAT3 and NF-κB signaling pathways, which may play an important role in proliferative vitreoretinopathy.     

p53 Represses the Mevalonate Pathway to Mediate Tumor Suppression

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Ligularia dalaolingensis sp. nov. (Asteraceae–Senecioneae) from central China

Ligularia dalaolingensis, a new species from Hubei and Hunan, China, is described and illustrated. It belongs to L. sect. Ligularia ser. Speciosae on the basis of its palmate leaf venation, racemose synflorescence and pappus which is slightly shorter than the tube of the tubular corolla. In the series, its closest relatives are assumed to be L. fischeri and L. stenocephala. From L. fischeri, L. dalaolingensis is readily distinguished by smaller basal leaves, shorter synflorescence, narrower involucres and fewer phyllaries and florets; from L. stenocephala, L. dalaolingensis differs by smaller basal leaves, shorter synflorescence as well as broader bracts. A diagnostic key to Chinese species of L. ser. Speciosae with broadly ovate, ovate or ovate‐lanceolate bracts is provided.     

Spiradiclis densa sp. nov. (Rubiaceae) from limestone areas in Guangxi,China

A new species of Rubiaceae, Spiradiclis densa, is described and illustrated from southwestern China. It is similar to S. tomentosa, but differs in the elliptic or oblong leaf blades, distylous flowers and inner sides of corolla tube with dense pubescence near throat. The conservation status of the new species is preliminarily assessed as ‘Vulnerable’ according to IUCN categories and criteria.     

Iodine Nutrition and Thyroid Function in Pregnant Women Exposed to Different Iodine Sources

Determination of the public health concern about magnesium (Mg) in health and disease has been confounded by the lack of a practical measure of status. This has resulted in a lack of consistency in associating Mg deficiency with specific pathological conditions. Some attempts at associating Mg with a chronic disease have used the Dietary Reference Intakes (DRIs) as a status assessment measure. Use of current DRIs for Mg is problematic because recent evidence suggests that they should be updated and based on body weight. An evidence-based suggested Estimated Average Requirement (EAR) and Recommended Dietary Allowance (RDA) for a 70-kg individual is 175 and 250 mg/day, respectively. However, numerous dietary and physiological factors can affect the need for Mg and thus affect the use of the current or suggested new DRIs to assess Mg status. Calcium intakes above normal requirements can decrease Mg balance and exacerbate signs of Mg deficiency. Mg deficiency apparently occurs often in obesity because of increased need to counteract the inflammatory stress induced by adipose tissue dysfunction. Deficiency in anti-oxidant nutrients such as vitamin E and selenium can exacerbate a response to low dietary Mg indicated by increased oxidative stress which can lead to chronic disease. Dietary modifiers of Mg absorption and excretion affect balance and thus the need for Mg. Factors decreasing Mg balance include low dietary protein and non-fermentable fiber, while factors that can increase balance include fructose and fermentable fiber and fructose-containing oligosaccharides. Use of the DRIs to assess the Mg status of a population or group needs to consider their physiological characteristics and dietary habits and be aware that the DRIs may need updating. The DRIs only can be considered a component of a toolbox that presently includes serum Mg concentration and the daily urinary Mg excretion to assess the Mg status of an individual.

     

The ABA receptor-like gene VyPYL9 from drought-resistance wild grapevine confers drought tolerance and ABA hypersensitivity in Arabidopsis

Plant Cell, Tissue and Organ Culture (PCTOC) - The PYR/PYL/RCAR (hereafter referred to PYLs) proteins, which act as abscisic acid (ABA) receptors, have been reported to play a crucial role in...     

Effects of starvation on death‐feigning in adult Eucryptorrhynchus brandti (Coleoptera: Curculionidae)

In insects, death‐feigning is an effective defence strategy. Eucryptorrhynchus brandti, a major borer pest in China, has a weak flight ability and exhibits obvious death‐feigning behaviour when disturbed. Despite a large number of studies of its biological and ecological properties as well as control methods, the death‐feigning behaviour has not been specifically described. In laboratory conditions, we recorded the survival rate under starvation and feeding conditions and evaluated the effect of starvation on the duration and occurrence of death‐feigning. In a continuous experiment, we examined variation in the death‐feigning duration every day over 7 day. Then, we evaluated the effects of starvation for 3, 6 and 9 day in a non‐continuous experiment and further observed variation in the death‐feigning intensity. We found that starvation significantly affected the survival rate. Survival time was significantly longer in the starvation group than in the feeding group, and females had longer survival times than males (female: 14 day, male: 8 day). In the continuous experiment, starved E. brandti had the longest duration of death‐feigning at 2 day, followed by a significant decrease. In the non‐continuous experiment, the duration and proportion of death‐feigning decreased significantly as the duration of starvation increased and were significantly lower than feeding. These observations suggest that starvation is a non‐negligible factor in the death‐feigning behaviour of E. brandti adults, facilitating the interpretation of future ecological and behavioural data of thanatosis.