The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

Type 1 diabetes (T1D) is an autoimmune disease characterized by insulitis and islet β-cell loss. Thus, an effective therapy may require β-cell restoration and immune suppression. Currently, there is no treatment that can achieve both goals efficiently. We report here that GABA exerts antidiabetic effects by acting on both the islet β-cells and immune system. Unlike in adult brain or islet α-cells in which GABA exerts hyperpolarizing effects, in islet β-cells, GABA produces membrane depolarization and Ca 2+ influx, leading to the activation of PI3-K/Akt–dependent growth and survival pathways. This provides a potential mechanism underlying our in vivo findings that GABA therapy preserves β-cell mass and prevents the development of T1D. Remarkably, in severely diabetic mice, GABA restores β-cell mass and reverses the disease. Furthermore, GABA suppresses insulitis and systemic inflammatory cytokine production. The β-cell regenerative and immunoinhibitory effects of GABA provide insights into the role of GABA in regulating islet cell function and glucose homeostasis, which may find clinical application.

AAA-PKB did not prevent actin bundling (membrane ruffling), though this response was PI 3-kinase dependent. Therefore, it is unlikely that AAA-PKB acted by inhibiting PI 3-kinase signaling. These results outline an important role for PKB␣/Akt1 in the stimulation of glucose transport by insulin in muscle cells in culture.Translocation of GLUT4 from an intracellular compartment to the plasma membrane largely accounts for the stimulation of glucose transport by insulin in skeletal muscle (16,31,38), cardiac muscle (48), and adipose cells (23,24). Two insulinresponsive cell lines also express this transporter: L6 rat skeletal myotubes (34, 40) and 3T3-L1 mouse adipocytes (24). Transfection of a molecularly engineered form of this transporter containing an exofacial epitope tag between the first and second transmembrane domains allows for the detection of surface transporters in intact cells. GLUT4 molecules with an exofacial epitope tag have been heterologously expressed in rat adipose cells (44, 51), 3T3-L1 adipocytes (26), CHO cells (12, 26), H9c2 cardiomyocytes (55), and rat 3Y1 cells (22). We have recently shown that stable expression of GLUT4myc in L6 myoblasts (L6-GLUT4myc myoblasts) mimics the response to insulin seen with endogenous GLUT4 in differentiated myotubes (29, 60).Insulin-induced translocation of GLUT4 to the plasma membrane requires the activity of phosphatidylinositol (PI) 3-kinase (47) in rat adipocytes (43, 45), 3T3-L1 adipocytes (8,9,21,27,39,51), L6 muscle cells (53), and rat skeletal muscle (62). Moreover, treatment of intact 3T3-L1 adipocytes with a cell-permeant PI 3,4,5-triphosphate [PI (3,4,5)-P 3 ] compound, which is converted into a product of PI 3-kinase once inside the cell, partly rescued the inhibition of insulin-stimulated glucose transport by wortmannin (25). It is unclear how the lipid products of PI 3-kinase relay the insulin signal to the glucose transporters, but the serine/threonine kinase protein kinase B (PKB)/Akt interacts with the lipid products of PI 3-kinase (19), and activation of PKB/Akt by insulin is prevented by inhibitors of PI 3-kinase (1). To date, three isoforms of PKB/Akt have been identified: PKB␣, -␤, and -␥ (Akt1, -2, and -3) (17). In skeletal muscle and L6 muscle cells, PKB␣ and PKB␥, but not PKB␤, are stimulated by insulin (59). Full activation of PKB/ Akt by insulin requires hierarchical phosphorylation on two residues, Thr308 (Thr309 and Thr305 in the case of PKB␤ and -␥, respectively) and Ser473 (Ser474 in the case of PKB␤; PKB␥ lacks an equivalent site) by 3-phosphoinositide-dependent protein kinase 1 (PDK-1) and PDK-2, respectively (1-3, 14, 50).Recent reports have suggested that activation of PKB/Akt may mediate the stimulation of glucose transport by insulin, since stable overexpression of wild-type PKB␣/Akt1 or constitutively active mutants of PKB␣/Akt1 increased glucose transport and translocation of GLUT4 to levels similar to or greater than those achieved with insulin in rat adipocytes (52), 3T3-L1 adipocytes (33,56), and L6 muscle cells (20,56...

Excessive secretion of glucagon is a major contributor to the development of diabetic hyperglycemia. Secretion of glucagon is regulated by various nutrients, with glucose being a primary determinant of the rate of alpha cell glucagon secretion. The intra-islet action of insulin is essential to exert the effect of glucose on the alpha cells since, in the absence of insulin, glucose is not able to suppress glucagon release in vivo. However, the precise mechanism by which insulin suppresses glucagon secretion from alpha cells is unknown. In this study, we show that insulin induces activation of GABAA receptors in the alpha cells by receptor translocation via an Akt kinase-dependent pathway. This leads to membrane hyperpolarization in the alpha cells and, ultimately, suppression of glucagon secretion. We propose that defects in this pathway(s) contribute to diabetic hyperglycemia.

WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.

Biology relies on functional interplay of proteins in the crowded and heterogeneous environment inside cells, and functional protein interactions are often weak and transient. Thus, methods are needed that preserve these interactions and provide information about them. In-cell NMR spectroscopy is an attractive method to study a protein’s behavior in cells because it may provide residue-level structural and dynamic information. Yet several factors limit the feasibility of protein NMR spectroscopy in cells, and among them slow rotational diffusion has emerged as the most important. In this paper, we seek to elucidate the causes of the dramatically slow protein tumbling in cells and in so doing to gain insight into how the intracellular viscosity and weak, transient interactions modulate protein mobility. To address these questions, we characterized the rotational diffusion of three model globular proteins in E. coli cells using 2D heteronuclear NMR spectroscopy. These proteins have a similar molecular size and globular fold, but very different surface properties, and indeed, they show very different rotational diffusion in the E. coli intracellular environment. Our data are consistent with an intracellular viscosity approximately eight times that of water—too low to be a limiting factor to observing small globular proteins by in-cell NMR spectroscopy. Thus, we conclude that transient interactions with cytoplasmic components significantly and differentially affect the mobility of proteins and therefore their NMR detectability. Moreover, we suggest that an intricate interplay of total protein charge and hydrophobic interactions plays a key role in regulating these weak intermolecular interactions in cells.

On August 3, 2018, an outbreak of African swine fever in pigs was reported in China. We subjected a virus from an African swine fever–positive pig sample to phylogenetic analysis. This analysis showed that the causative strain belonged to the p72 genotype II and CD2v serogroup 8.

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