A Path to the Atomic-Resolution Structures of Prokaryotic and Eukaryotic Ribosomes

Integrated Omics Approach to Discover Differences in the Metabolism of a New Tibetan Desmodesmus sp. in Two Types of Sewage Treatments

Microalgae are now widely applied in municipal (YH_3) and industrial sewage (YH_4) treatments. Through integrated omics analysis, we studied the similarities and differences at the molecular level between the two different types of sewage treatment processes. The most significantly enriched gene ontology (GO) terms in both types of sewage treatments were the ribosome, photosynthesis, and proteasome pathways. The results show that the pathways of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were enriched for photosynthesis, glyoxylate and dicarboxylate metabolism, and carbon fixation in photosynthetic organisms. Considering YH_3 vs. YH_4, the metabolism of citrate, sedoheptulose-7P, and succinate was significantly upregulated. In addition, the results showed that the pathways of DEGs and DAMs were enriched in terms of amino acid metabolism and carotenoid biosynthesis in YH_4 vs. YH_3. The metabolism of S-Adenosyl-L-homocysteine was significantly downregulated, 2-oxobutanoate was significantly upregulated and downregulated, and the metabolism of abscisic acid glucose ester (ABA-GE) was also significantly upregulated. Overall, the results of this paper will help to improve the basic knowledge of the molecular response of microalgae to sewage treatments, and help design a response strategy based on microalgae for complex, mixed sewage treatments.

How does RNA fold dynamically?

Recent advances in interrogating RNA folding dynamics have shown the classical model of RNA folding to be incomplete. Here, we pose three prominent questions for the field that are at the forefront of our understanding of the importance of RNA folding dynamics for RNA function. The first centers on the most appropriate biophysical framework to describe changes to the RNA folding energy landscape that a growing RNA chain encounters during transcriptional elongation. The second focuses on the potential ubiquity of strand displacement - a process by which RNA can rapidly change conformations - and how this process may be generally present in broad classes of seemingly different RNAs. The third raises questions about the potential importance and roles of cellular protein factors in RNA conformational switching. Answers to these questions will greatly improve our fundamental knowledge of RNA folding and function, drive biotechnological advances that utilize engineered RNAs, and potentially point to new areas of biology yet to be discovered.

Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept

At the turn of the twenty-first century, fundamental changes took place in the understanding of the structure and function of proteins and then in the appreciation of the intracellular space organization. A rather mechanistic model of the organization of living matter, where the function of proteins is determined by their rigid globular structure, and the intracellular processes occur in rigidly determined compartments, was replaced by an idea that highly dynamic and multifunctional "soft matter" lies at the heart of all living things. According this "new view", the most important role in the spatio-temporal organization of the intracellular space is played by liquid-liquid phase transitions of biopolymers. These self-organizing cellular compartments are open dynamic systems existing at the edge of chaos. They are characterized by the exceptional structural and compositional dynamics, and their multicomponent nature and polyfunctionality provide means for the finely tuned regulation of various intracellular processes. Changes in the external conditions can cause a disruption of the biogenesis of these cellular bodies leading to the irreversible aggregation of their constituent proteins, followed by the transition to a gel-like state and the emergence of amyloid fibrils. This work represents a historical overview of changes in our understanding of the intracellular space compartmentalization. It also reflects methodological breakthroughs that led to a change in paradigms in this area of science and discusses modern ideas about the organization of the intracellular space. It is emphasized here that the membrane-less organelles have to combine a certain resistance to the changes in their environment and, at the same time, show high sensitivity to the external signals, which ensures the normal functioning of the cell.