NSUN2‐Mediated m5C Methylation and METTL3/METTL14‐Mediated m6A Methylation Cooperatively Enhance p21 Translation

N6‐methyladenosine (m6A) and m5C methylation are two major types of RNA methylation, but the impact of joint modifications on the same mRNA is unknown. Here, we show that in p21 3′UTR, NSUN2 catalyzes m5C modification and METTL3/METTL14 catalyzes m6A modification. Interestingly, methylation at m6A by METTL3/METTL14 facilitates the methylation of m5C by NSUN2, and vice versa. NSUN2‐mediated m5C and METTL3/METTL14‐mediated m6A methylation synergistically enhance p21 expression at the translational level, leading to elevated expression of p21 in oxidative stress‐induced cellular senescence. Our findings on p21 mRNA methylation and expression reveal that joint m6A and m5C modification of the same RNA may influence each other, coordinately affecting protein expression patterns. J. Cell. Biochem. 118: 2587–2598, 2017. © 2017 Wiley Periodicals, Inc.In p21 3’UTR,NSUN2 catalyzes m5C modification and METTL3/METTL14 catalyzes m6A modification. Methylation at m6A by METTL3/METTL14 facilitates the methylation of m5C by NSUN2, and vice versa. NSUN2‐mediated m5C and METTL3/METTL14‐mediated m6A methylation synergistically enhance p21 expression at the translational level, leading to elevated expression of p21 in oxidative stress‐induced cellular senescence.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137760/1/jcb25957.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137760/2/jcb25957_am.pd

Characterization of a Hyaluronic Acid Utilization Locus and Identification of Two Hyaluronate Lyases in a Marine Bacterium Vibrio alginolyticus LWW-9

Hyaluronic acid (HA) is a negatively charged and linear polysaccharide existing in the tissues and body fluids of all vertebrates. Some pathogenic bacteria target hyaluronic acid for adhesion and/or infection to host cells. Vibrio alginolyticus is an opportunistic pathogen related to infections of humans and marine animals, and the hyaluronic acid-degrading potential of Vibrio spp. has been well-demonstrated. However, little is known about how Vibrio spp. utilize hyaluronic acid. In this study, a marine bacterium V. alginolyticus LWW-9 capable of degrading hyaluronic acid has been isolated. Genetic and bioinformatic analysis showed that V. alginolyticus LWW-9 harbors a gene cluster involved in the degradation, transport, and metabolism of hyaluronic acid. Two novel PL8 family hyaluronate lyases, VaHly8A and VaHly8B, are the key enzymes for the degradation of hyaluronic acid. VaHly8A and VaHly8B have distinct biochemical properties, reflecting the adaptation of the strain to the changing parameters of the aquatic habitats and hosts. Based on genomic and functional analysis, we propose a model for the complete degradation of hyaluronic acid by V. alginolyticus LWW-9. Overall, our study expands our knowledge of the HA utilization paradigm within the Proteobacteria, and the two novel hyaluronate lyases are excellent candidates for industrial applications

let‐7‐repressesed S hc translation delays replicative senescence

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102709/1/acel12176.pd

XGNN: Towards Model-Level Explanations of Graph Neural Networks

Graphs neural networks (GNNs) learn node features by aggregating and combining neighbor information, which have achieved promising performance on many graph tasks. However, GNNs are mostly treated as black-boxes and lack human intelligible explanations. Thus, they cannot be fully trusted and used in certain application domains if GNN models cannot be explained. In this work, we propose a novel approach, known as XGNN, to interpret GNNs at the model-level. Our approach can provide high-level insights and generic understanding of how GNNs work. In particular, we propose to explain GNNs by training a graph generator so that the generated graph patterns maximize a certain prediction of the model.We formulate the graph generation as a reinforcement learning task, where for each step, the graph generator predicts how to add an edge into the current graph. The graph generator is trained via a policy gradient method based on information from the trained GNNs. In addition, we incorporate several graph rules to encourage the generated graphs to be valid. Experimental results on both synthetic and real-world datasets show that our proposed methods help understand and verify the trained GNNs. Furthermore, our experimental results indicate that the generated graphs can provide guidance on how to improve the trained GNNs

Effect of boron deficiency on the photosynthetic performance of sugar beet cultivars with contrasting boron efficiencies

Boron (B) deficiency severely affects the quality of sugar beet production, and the employment of nutrient-efficient varieties for cultivation is a crucial way to solve environmental and resource-based problems. However, the aspect of leaf photosynthetic performance among B-efficient sugar beet cultivars remains uncertain. The B deficient and B-sufficient treatments were conducted in the experiment using KWS1197 (B-efficient) and KWS0143 (B-inefficient) sugar beet cultivars as study materials. The objective of the present study was to determine the impacts of B deficiency on leaf phenotype, photosynthetic capacity, chloroplast structure, and photochemical efficiency of the contrasting B-efficiency sugar beet cultivars. The results indicated that the growth of sugar beet leaves were dramatically restricted, the net photosynthetic rate was significantly decreased, and the energy flux, quantum yield, and flux ratio of PSII reaction centers were adversely affected under B deficiency. Compared to the KWS0143 cultivar, the average leaf area ratio of the KWS1197 cultivar experienced less impact, and its leaf mass ratio (LMR) increased by 26.82% under B deficiency, whereas for the KWS0143 cultivar, the increase was only 2.50%. Meanwhile, the light energy capture and utilization capacity of PSII reaction centers and the proportion of absorbed light energy used for electron transfer were higher by 3.42% under B deficiency; KWS1197 cultivar managed to alleviate the photo-oxidative damage, which results from excessive absorbed energy (ABS/RC), by increasing the dissipated energy (DIo/RC). Therefore, in response to B deprivation, the KWS1197 cultivar demonstrated greater adaptability in terms of morphological indices and photosynthetic functions, which not only explains the improved performance but also renders the measured parameters as the key features for varietal selection, providing a theoretical basis for the utilization of efficient sugar beet cultivars in future

Sp1 Is Essential for p16(INK4a) Expression in Human Diploid Fibroblasts during Senescence

BACKGROUND: p16 (INK4a) tumor suppressor protein has been widely proposed to mediate entrance of the cells into the senescent stage. Promoter of p16 (INK4a) gene contains at least five putative GC boxes, named GC-I to V, respectively. Our previous data showed that a potential Sp1 binding site, within the promoter region from −466 to −451, acts as a positive transcription regulatory element. These results led us to examine how Sp1 and/or Sp3 act on these GC boxes during aging in cultured human diploid fibroblasts. METHODOLOGY/PRINCIPAL FINDINGS: Mutagenesis studies revealed that GC-I, II and IV, especially GC-II, are essential for p16 (INK4a) gene expression in senescent cells. Electrophoretic mobility shift assays (EMSA) and ChIP assays demonstrated that both Sp1 and Sp3 bind to these elements and the binding activity is enhanced in senescent cells. Ectopic overexpression of Sp1, but not Sp3, induced the transcription of p16 (INK4a). Both Sp1 RNAi and Mithramycin, a DNA intercalating agent that interferes with Sp1 and Sp3 binding activities, reduced p16 (INK4a) gene expression. In addition, the enhanced binding of Sp1 to p16 (INK4a) promoter during cellular senescence appeared to be the result of increased Sp1 binding affinity, not an alteration in Sp1 protein level. CONCLUSIONS/SIGNIFICANCE: All these results suggest that GC- II is the key site for Sp1 binding and increase of Sp1 binding activity rather than protein levels contributes to the induction of p16 (INK4a) expression during cell aging

Antibiofilm Activity of an Exopolysaccharide from Marine Bacterium Vibrio sp. QY101

Bacterial exopolysaccharides have always been suggested to play crucial roles in the bacterial initial adhesion and the development of complex architecture in the later stages of bacterial biofilm formation. However, Escherichia coli group II capsular polysaccharide was characterized to exert broad-spectrum biofilm inhibition activity. In this study, we firstly reported that a bacterial exopolysaccharide (A101) not only inhibits biofilm formation of many bacteria but also disrupts established biofilm of some strains. A101 with an average molecular weight of up to 546 KDa, was isolated and purified from the culture supernatant of the marine bacterium Vibrio sp. QY101 by ethanol precipitation, iron-exchange chromatography and gel filtration chromatography. High performance liquid chromatography traces of the hydrolyzed polysaccharides showed that A101 is primarily consisted of galacturonic acid, glucuronic acid, rhamnose and glucosamine. A101 was demonstrated to inhibit biofilm formation by a wide range of Gram-negative and Gram-positive bacteria without antibacterial activity. Furthermore, A101 displayed a significant disruption on the established biofilm produced by Pseudomonas aeruginosa, but not by Staphylococcus aureus. Importantly, A101 increased the aminoglycosides antibiotics' capability of killing P. aeruginosa biofilm. Cell primary attachment to surfaces and intercellular aggregates assays suggested that A101 inhibited cell aggregates of both P. aeruginosa and S. aureus, while the cell-surface interactions inhibition only occurred in S. aureus, and the pre-formed cell aggregates dispersion induced by A101 only occurred in P. aeruginosa. Taken together, these data identify the antibiofilm activity of A101, which may make it potential in the design of new therapeutic strategies for bacterial biofilm-associated infections and limiting biofilm formation on medical indwelling devices. The found of A101 antibiofilm activity may also promote a new recognition about the functions of bacterial exopolysaccharides

HuR and post-transcriptional regulation in vascular aging

HuR (ELAV11 (embryonic lethal, abnormal vision)-like 1), a ubiquitously expressed member of the ELAV-like RNA-binding protein family, has been shown to regulate the stability and translation of mRNAs that encode factors regulating cellular senescence, thereby impacting on aging. In this review, we discuss the current knowledge of HuR's role in vascular cell senescence and vascular aging.BiologySCI(E)[email protected]