Showing papers in "Trends in Biochemical Sciences in 2016"

TL;DR: Several proposed explanations for the function of Warburg Effect are analyzed, emphasize their rationale, and discuss their controversies.

TL;DR: Current understanding of the mechanism and regulation of NLRP3 inflammasome activation as well as recent advances in the noncanonical and alternative inflammaome pathways are summarized.

TL;DR: Investigating the mechanisms that determine the subcellular fate of lncRNAs has the potential to provide new insights into their biogenesis and specialized functions.

TL;DR: The knowledge of mitochondrial ultrastructural organization and how it impacts mitochondrial metabolism is reviewed.

TL;DR: New regulators of iron metabolism are highlighted, including iron-trafficking proteins [solute carrier family 39, SLC39, also known as ZRT/IRT-like protein, ZIP; and poly-(rC)-binding protein, PCBP] and a cargo receptor (NCOA4) that is crucial for release of ferritin-bound iron.

TL;DR: This review discusses the mechanism of piRNA biogenesis, gives an overview of common themes as well as differences in piRNA-mediated silencing between species, and highlights known and emerging functions of piRNAs.

TL;DR: This review provides a timely update on very recent applications of lipidomics in health and disease and compares mass spectrometry-based techniques for analysis of lipids.

TL;DR: In this review, recent discoveries on the regulation of interorganellar Ca2+ homeostasis and its role in pathophysiology are summarized.

TL;DR: An overview of recent advances in XL-MS, the current state of the field, and a cursory outlook on future challenges is provided.

TL;DR: One class of noncoding small RNAs, tRNA-related fragments (tRFs), which are generated from tRNA, have been suggested to have roles in cell proliferation, priming of viral reverse transcriptases, regulation of gene expression, RNA processing, modulation of the DNA damage response, tumor suppression, and neurodegeneration.

TL;DR: The thermodynamic consequences of excluded-volume and long-range nonspecific intermolecular interactions for macromolecular reactions in volume-occupied media and strategies for extending quantitative analyses of crowding in simple model systems to increasingly complex media up to and including intact cells are proposed.

TL;DR: This review discusses how NPCs gain a remarkable sorting selectivity from non-globular FG domains and their phase separation into dense polymer meshworks, which are effective barriers to normal macromolecules but are at the same time highly permeable to shuttling nuclear transport receptors.

TL;DR: Different models of chaperonin action are reviewed and issues of current debate are discussed, providing insights into how the physical environment of the chaper onin cage actively promotes protein folding, in addition to preventing aggregation.

TL;DR: Current data strongly support efforts to target HSPs in cancer treatment, and mainly focuses on Hsp27, Hsp70, and Hsp90.

TL;DR: This work has shown that loss of cellular control of APOBEC activities leads to DNA hypermutation and promiscuous RNA editing associated with the development of cancer or viral drug resistance, underscoring the importance of understanding how APOBec proteins are regulated.

TL;DR: Following the first report 21 years ago, the field of deoxyribozymes has promise for both fundamental and applied advances in chemistry, biology, and other disciplines.

TL;DR: Cryoelectron microscopy studies are brought together with molecular analyses to describe the principles of proteasome activity and regulation.

TL;DR: A new mechanistic link between metabolic flux and regulation of gene expression is through moonlighting of metabolic enzymes in the nucleus that facilitates delivery of membrane-impermeable or unstable metabolites to the nucleus, including key substrates for epigenetic mechanisms such as acetyl-CoA which is used in histone acetylation.

TL;DR: The spliceosome is a dynamic, reversible, and flexible machine that chaperones small nuclear RNAs and a variety of pre-mRNA sequences into conformations that enable intron removal, and this malleability likely contributes to the regulation of alternative splicing.

TL;DR: The progress made in fungal enzyme technology over the past few years is reviewed with major emphasis on the enzymes needed for the conversion of polysaccharides (cellulose and hemicellulose) into soluble products.

TL;DR: This work summarizes the field and discusses salient topics that cover spurious versus targeted acetylation, the role of SIRT3 deacetylations, nonenzymatic acetylATION, and molecular models for regulatory acetylations that display high and low stoichiometry.

TL;DR: Recent advances highlight Nt-acetylation as a key factor in many biological pathways, including the control of resistance to drought and in regulation of immune responses.

TL;DR: Substrates and intermediates are converted exploiting the catalytic and electron-transfer potentials of c-type heme proteins known from numerous biochemical reactions and that have acquired new functionality in anammox biochemistry.

TL;DR: Recent advances as well as observations made from tissue-specific mTORC2 knockout mice help define TORC2 structure-function relationships and suggest that mammalian TORC 2 may one day also become a bona fide clinical target.

TL;DR: The regulation of RecA filament assembly and the mechanism by which RecA quickly and efficiently searches for and identifies a unique homologous sequence among a vast excess of heterologous DNA are reviewed.

TL;DR: Some major recent developments in the understanding of the mechanisms that regulate these oscillators and their output are discussed, including roles for antisense transcription, intrinsically disordered proteins, codon bias in clock genes, and a more focused discussion of post-transcriptional and translational regulation as a part of both the oscillator and output.

TL;DR: There are multiple conflicting lines of evidence that challenge the biological significance of circulating ex-miRNA, suggesting that they are merely byproducts of cell activity and cell death without any particular function.

TL;DR: Experimental data supporting connections between aging and histone acetylation patterns and key metabolites such as acetyl-CoA and NAD(+) are discussed and a context for the possible medical and physiological relevance is provided.

TL;DR: It is argued that seemingly contradictory data from time-resolved fluorescence resonance energy transfer (FRET) studies can be reconciled, and a model for myosin force generation on actin is put forward.

TL;DR: The current understanding of the injectisome assembly process, secretion hierarchy, and the role of chaperones is presented and future directions essential to revealing mechanistic insight into this fascinating nanomachine are proposed.