Molecular dynamics simulation on the allosteric analysis of the c‐di‐GMP class I riboswitch induced by ligand binding

Riboswitches are RNA molecules that regulate gene expression using conformation change, affected by binding of small molecule ligands. Although a number of ligand‐bound aptamer complex structures have been solved, it is important to know ligand‐free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, we use dynamics simulations on a series of models to characterize the ligand‐free and ligand‐bound aptamer domain of the c‐di‐GMP class I (GEMM‐I) riboswitch. The results revealed that the ligand‐free aptamer has a stable state with a folded P2 and P3 helix, an unfolded P1 helix and open binding pocket. The first Mg ions binding to the aptamer is structurally favorable for the successive c‐di‐GMP binding. The P1 helix forms when c‐di‐GMP is successive bound. Three key junctions J1/2, J2/3 and J1/3 in the GEMM‐I riboswitch contributing to the formation of P1 helix have been found. The binding of the c‐di‐GMP ligand to the GEMM‐I riboswitch induces the riboswitch's regulation through the direct allosteric communication network in GEMM‐I riboswitch from the c‐di‐GMP binding sites in the J1/2 and J1/3 junctions to the P1 helix, the indirect ones from those in the J2/3 and P2 communicating to P1 helix via the J1/2 and J1/3 media.     

Changes in seasonal precipitation distribution but not annual amount affect litter decomposition in a secondary tropical forest

In the tropics of South China, climate change induced more rainfall events in the wet season in the last decades. Moreover, there will be more frequently spring drought in the future. However, knowledge on how litter decomposition rate would respond to these seasonal precipitation changes is still limited. In the present study, we conducted a precipitation manipulation experiment in a tropical forest. First, we applied a 60% rainfall exclusion in April and May to defer the onset of wet season and added the same amount of water in October and November to mimic a deferred wet season (DW); second, we increased as much as 25% mean annual precipitation into plots in July and August to simulate a wetter wet season (WW). Five single‐species litters, with their carbon to nitrogen ratio ranged from 27 to 49, and a mixed litter were used to explore how the precipitation change treatments would affect litter decomposition rate. The interaction between precipitation changes and litter species was not significant. The DW treatment marginally accelerated litter decomposition across six litter types. Detailed analysis showed that DW increased litter decomposition rate in the periods of January to March and October to December, when soil moisture was increased by the water addition in the dry season. In contrast, WW did not significantly affect litter decomposition rate, which was consistent with the unchanged soil moisture pattern. In conclusion, the study indicated that regardless of litter types or litter quality, the projected deferred wet season would increase litter decomposition rate, whereas the wetter wet season would not affect litter decomposition rate in the tropical forests. This study improves our knowledge of how tropical forest carbon cycling in response to precipitation change.     

DDX19 Inhibits Type I Interferon Production by Disrupting TBK1-IKKε-IRF3 Interactions and Promoting TBK1 and IKKε Degradation

1. Download high-res image (150KB)
2. Download full-size image

     

Expert consensus on organizing the multidisciplinary team (MDT) diagnosis and treatment of hepato-pancreato-biliary diseases in China

Science China Life Sciences -     

Valproate induces apoptosis by inducing accumulation of neutral lipids which was prevented by disruption of the SIR2 gene in Saccharomyces cerevisiae

We investigated the participation of HDACs in VPA induced apoptosis in Saccharomyces cerevisiae. VPA (20 mM) induced apoptosis in several HDAC mutants, including PRD3 and HDA1-disrupted cells and SIR2 over expressing cells, as well as in wild-type cells but not SIR2-disrupted cells. Intracellular reactive oxygen species and neutral lipid content increased markedly in all kinds of HDAC mutant cells tested except for SIR2-disrupted cells. Thus, these results suggest that 20 mM VPA induces neutral lipid accumulation and apoptosis-like features in S. cerevisiae, and that VPA-induced apoptosis was evaded by deletion of SIR2.     

Stimulation of ATG12-ATG5 conjugation by ribonucleic acid

The ubiquitin-like conjugation reactions, ATG8/microtubule-associated protein 1 light chain 3/MAP1LC3 (LC3) to phosphatidylethanolamine (PE) and ATG12 to ATG5, are biochemical hallmarks for autophagy, a cellular process that degrades bulk cellular proteins and organelles. The two conjugation reactions share the same E1-like enzyme ATG7 but have different E2-like enzymes, ATG3 for LC3-PE and ATG10 for ATG12-ATG5. In cells, ATG12-ATG5 conjugation appears to be required for LC3-PE conjugation. Previously, in vitro reconstitution of LC3-PE conjugation, but not the upstream ATG12-ATG5 conjugation, was reported. In this study, we describe for the first time the de novo reconstitution of mammalian ATG12-ATG5 conjugation by using purified recombinant proteins. We show that ATG7, ATG10 and ATP as an energy source are all essential for ATG12-ATG5 conjugation, and mutation of the specific lysine residue of ATG5 for ATG12 conjugation abrogates the reaction. Furthermore, a potent stimulating activity for ATG12-ATG5 conjugation was detected in mammalian cell extracts, and was surprisingly identified as ribosomes. Our detail biochemical analyses indicate that the ribonucleic acid (RNA) component of ribosomes is both necessary and sufficient for this stimulation.     

Mechanical analysis of deep tissue injury during sitting in patients with spinal cord injury via parametric finite element model

Biomechanics and Modeling in Mechanobiology - Spinal cord injury patients are prone to develop deep tissue injury because of long-term mechanical load. However, there is a lack of statistical...