Cellular signalling: Peptide hormones and growth factors

A strategy can be used to analyze intracellular interaction proteomics of cell-surface receptors

Comprehensive knowledge of the intracellular protein interactions of cell-surface receptors will greatly advance our comprehension of the underlying trafficking mechanisms. Hence, development of effective and high-throughput approaches is highly desired. In this work, we presented a strategy aiming to tailor toward the analysis of intracellular protein interactome of cell-surface receptors. We used α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors subunit GluA1 as an example to illustrate the methodological application. To capture intracellular proteins that interact with GluA1, after surface biotinylation of the prepared hippocampal neurons and slices, the non-biotinylated protein components as intracellular protein-enriched fraction were unconventionally applied for the following co-immunoprecipitation. The co-immuno-precipitated proteins were then analyzed through mass spectrometry-based proteomics and bioinformatics platforms. The detailed localizations indicated that intracellular proteins accounted for up to 93.7 and 90.3% of the analyzed proteins in the neurons and slices, respectively, suggesting that our protein preparation was highly effective to characterize intracellular interactome of GluA1. Further, we systematically revealed the protein functional profile of GluA1 intracellular interactome, thereby providing complete overview and better comprehension of diverse intracellular biological processes correlated with the complex GluA1 trafficking. All experimental results demonstrated that our methodology would be applicable and useful for intracellular interaction proteomics of general cell-surface receptors.

Identifying novel antimicrobial peptides from venom gland of spider Pardosa astrigera by deep multi-task learning

Antimicrobial peptides (AMPs) show promises as valuable compounds for developing therapeutic agents to control the worldwide health threat posed by the increasing prevalence of antibiotic-resistant bacteria. Animal venom can be a useful source for screening AMPs due to its various bioactive components. Here, the deep learning model was developed to predict species-specific antimicrobial activity. To overcome the data deficiency, a multi-task learning method was implemented, achieving F1 scores of 0.818, 0.696, 0.814, 0.787, and 0.719 for Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Staphylococcus epidermidis, respectively. Peptides PA-Full and PA-Win were identified from the model using different inputs of full and partial sequences, broadening the application of transcriptome data of the spider Pardosa astrigera. Two peptides exhibited strong antimicrobial activity against all five strains along with cytocompatibility. Our approach enables excavating AMPs with high potency, which can be expanded into the fields of biology to address data insufficiency.

Insights into the Evolution of the Suppressors of Cytokine Signaling (SOCS) Gene Family in Vertebrates

The SOCS family are key negative regulators of cytokine and growth factor signaling. Typically, 8-17 SOCS genes are present in vertebrate species with eight known in mammals, classified as type I (SOCS4-7) and type II (CISH and SOCS1-3) SOCS. It was believed that the type II SOCS were expanded through the two rounds of whole genome duplication (1R and 2R WGDs) from a single CISH/SOCS1-3 precursor. Previously, 12 genes were identified in rainbow trout but here we report 15 additional loci are present, and confirm 26 of the genes are expressed, giving rainbow trout the largest SOCS gene repertoire identified to date. The discovery of the additional SOCS genes in trout has led to a novel model of SOCS family evolution, whereby the vertebrate SOCS gene family was derived from CISH/SOCS2, SOCS1/SOCS3, SOCS4/5, SOCS6, and SOCS7 ancestors likely present before the two WGD events. It is also apparent that teleost SOCS2b, SOCS4, and SOCS5b molecules are not true orthologues of mammalian SOCS2, SOCS4, and SOCS5, respectively. The rate of SOCS gene structural changes increased from 2R vertebrates, to 4R rainbow trout, and the genes with structural changes show large differences and low correlation coefficient of expression levels relative to their paralogues, suggesting a role of structural changes in expression and functional diversification. This study has important impacts in the functional prediction and understanding of the SOCS gene family in different vertebrates, and provides a framework for determining how many SOCS genes could be expected in a particular vertebrate species/lineage.

Monitoring G protein-coupled receptor and β-arrestin trafficking in live cells using enhanced bystander BRET

Endocytosis and intracellular trafficking of receptors are pivotal to maintain physiological functions and drug action; however, robust quantitative approaches are lacking to study such processes in live cells. Here we present new bioluminescence resonance energy transfer (BRET) sensors to quantitatively monitor G protein-coupled receptors (GPCRs) and β-arrestin trafficking. These sensors are based on bystander BRET and use the naturally interacting chromophores luciferase (RLuc) and green fluorescent protein (rGFP) from Renilla. The versatility and robustness of this approach are exemplified by anchoring rGFP at the plasma membrane or in endosomes to generate high dynamic spectrometric BRET signals on ligand-promoted recruitment or sequestration of RLuc-tagged proteins to, or from, specific cell compartments, as well as sensitive subcellular BRET imaging for protein translocation visualization. These sensors are scalable to high-throughput formats and allow quantitative pharmacological studies of GPCR trafficking in real time, in live cells, revealing ligand-dependent biased trafficking of receptor/β-arrestin complexes.

Cellular signaling processes often involve trafficking of receptors and other proteins between subcellular compartments. Here the authors demonstrate a method based on the concept of Enhanced bystander Bioluminescence Resonance Energy Transfer (EbBRET) that allows efficient real time monitoring of endocytosis and trafficking.

Molecular and cellular characterization of GA-Stimulated Transcripts GASA4 and GASA6 in Arabidopsis thaliana

GA and ABA play antagonistic roles in numerous cellular processes essential for growth, development, and stress responses. GASA4 and GASA6 belong to a family of GA-Stimulated transcripts in Arabidopsis, known as GA-inducible and ABA-repressible. We have found that GASA4 and GASA6 expression is likely mediated through a repressor of GA responses, GA INSENSITIVE (GAI) protein. Moreover, GASA4 and GASA6 are in general up regulated by growth hormones (auxin, BR, cytokinin, and GA) and down regulated by stress hormones (ABA, JA, and SA), indicating a role of GASA4 and GASA6 in hormone crosstalk. Genetic analyses show that suppression of both GASA4 and GASA6 causes late flowering, while over-expression of GASA6 causes early flowering in Arabidopsis. GASA family members encode small polypeptides sharing common structural features: an N-terminal signal peptide, a highly divergent intermediate region, and a conserved C-terminal domain containing 12 conserved cysteines. Despite the presence of a signal peptide, it has not been determined whether or not GASA4 and GASA6 can be processed in vivo. By using imaging and immunological analyses, we show that the N-terminal signal peptide is cleaved as predicted, and the cleavage is important for proper sub-cellular localization of GASA4 and GASA6.

[Involvement of the endosomal compartment in cellular insulin signaling]

The insulin receptor and insulin signaling proteins downstream the receptor reside in different subcellular compartments and undergo redistribution within the cell upon insulin activation. Endocytosis of the insulin-receptor complex, by mediating ligand degradation and receptor dephosphorylation, is generally viewed as a mechanism which attenuates or arrests insulin signal transduction. However, several observations suggest that insulin receptor endocytosis and/or recruitement of insulin signaling proteins to endosomes are also involved in a positive regulation of insulin signaling: (1) upon internalization, the insulin receptor remains transiently phosphorylated and activated; (2) in insulin-stimulated cells or tissues, signaling proteins of the PI3K/Akt and Ras/Raf/Mek/Erk pathways are recruited to endosomes or other intracellular compartments, in which they undergo phosphorylation and/or activation; and (3) depletion or overexpression of proteins involved in the regulation of membrane trafficking and endocytosis interfere with insulin signaling. These observations support a spatial and temporal regulation of insulin signal transduction and reinforce the concept that, as for other membrane signaling receptors, endocytosis and signaling are functionally linked.

[Control of insulin signalisation and action by the Grb14 protein]

The action of insulin on metabolism and cell growth is mediated by a specific receptor tyrosine kinase, which, through phosphorylation of several substrates, triggers the activation of two major signaling pathways, the phosphatidylinositol 3-kinase (PI3-K)/Akt pathway and the Ras/extracellular signal-regulated kinase (ERK) pathway. Insulin-induced activation of the receptor and downstream signaling is also subjected to a negative feedback control involving several mechanisms, among which the interaction of the insulin receptor and its substrates with inhibitory proteins. After summarizing the major mechanisms underlying the activation and attenuation of insulin signaling, this review focuses on its control by the Grb14 adaptor protein. Grb14 has been identif-ied as an inhibitor of insulin signaling and action, and is involved in insulin resistance associated with type 2 diabetes and obesity. Studies on the molecular mechanism of action of Grb14 have shown that, through interaction with the activated insulin receptor, Grb14 inhibits its catalytic activity and the activation of downstream signaling. However, the consequences of Grb14 gene invalidation are complex and tissue-specific, and some effects of Grb14 on insulin signaling appear to be linked to its interaction with effector proteins downstream the insulin receptor. Pharmacological inhibition of Grb14 should allow to enhance insulin sensitivity and improve energy homeostasis in insulin-resistant states.

The factor VII-activating protease (FSAP) enhances the activity of bone morphogenetic protein-2 (BMP-2)

Factor VII-activating protease (FSAP) is a circulating protease involved in the pathogenesis of atherosclerosis, calcification, and fibrotic processes. To understand how FSAP controls the balance of local growth factors, we have investigated its effect on the regulation of bone morphogenetic proteins (BMPs). BMP-2 is produced as a large pro-form and secreted as a mature heparin-binding growth factor after intracellular processing by pro-protein convertases (PCs). In this study, we discovered that FSAP enhances the biological activity of mature BMP-2 as well as its pro-form, as shown by osteogenic differentiation of C2C12 myoblasts. These findings were complemented by knockdown of FSAP in hepatocytes, which revealed BMP-2 processing by endogenous FSAP. N-terminal sequencing indicated that pro-BMP-2 was cleaved by FSAP at the canonical PC cleavage site, giving rise to mature BMP-2 (Arg(282)↓Gln(283)), as well as in the N-terminal heparin binding region of mature BMP-2, generating a truncated mature BMP-2 peptide (Arg(289)↓Lys(290)). Similarly, mature BMP-2 was also cleaved to a truncated peptide within its N-terminal region (Arg(289)↓Lys(290)). Plasmin exhibited a similar activity, but it was weaker compared with FSAP. Thrombin, Factor VIIa, Factor Xa, and activated protein C were not effective. These results were further supported by the observation that the mutation of the heparin binding region of BMP-2 inhibited the processing by FSAP but not by PC. Thus, the proteolysis and activation of pro-BMP-2 and mature BMP-2 by FSAP can regulate cell differentiation and calcification in vasculature and may explain why polymorphisms in the gene encoding for FSAP are related to vascular diseases.

Understanding cytokine and growth factor receptor activation mechanisms

Our understanding of the detailed mechanism of action of cytokine and growth factor receptors - and particularly our quantitative understanding of the link between structure, mechanism and function - lags significantly behind our knowledge of comparable functional protein classes such as enzymes, G protein-coupled receptors, and ion channels. In particular, it remains controversial whether such receptors are activated by a mechanism of ligand-induced oligomerization, versus a mechanism in which the ligand binds to a pre-associated receptor dimer or oligomer that becomes activated through subsequent conformational rearrangement. A major limitation to progress has been the relative paucity of methods for performing quantitative mechanistic experiments on unmodified receptors expressed at endogenous levels on live cells. In this article, we review the current state of knowledge on the activation mechanisms of cytokine and growth factor receptors, critically evaluate the evidence for and against the different proposed mechanisms, and highlight other key questions that remain unanswered. New approaches and techniques have led to rapid recent progress in this area, and the field is poised for major advances in the coming years which promise to revolutionize our understanding of this large and biologically and medically important class of receptors.

TBC1D16 is a Rab4A GTPase activating protein that regulates receptor recycling and EGF receptor signaling

Rab4A is a master regulator of receptor recycling from endocytic compartments to the plasma membrane. The protein TBC1D16 is up-regulated in melanoma, and TBC1D16-overexpressing melanoma cells are dependent on TBC1D16. We show here that TBC1D16 enhances the intrinsic rate of GTP hydrolysis by Rab4A. TBC1D16 is both cytosolic and membrane associated; the membrane-associated pool colocalizes with transferrin and EGF receptors (EGFRs) and early endosome antigen 1, but not with LAMP1 protein. Expression of two TBC1D16 isoforms, but not the inactive R494A mutant, reduces transferrin receptor recycling but has no effect on transferrin receptor internalization. Expression of TBC1D16 alters GFP-Rab4A membrane localization. In HeLa cells, overexpression of TBC1D16 enhances EGF-stimulated EGFR degradation, concomitant with decreased EGFR levels and signaling. Thus, TBC1D16 is a GTPase activating protein for Rab4A that regulates transferrin receptor recycling and EGFR trafficking and signaling.

Essential role of endocytosis of the type II transmembrane serine protease TMPRSS6 in regulating its functionality

The type II transmembrane serine protease TMPRSS6 (also known as matriptase-2) controls iron homeostasis through its negative regulation of expression of hepcidin, a key hormone involved in iron metabolism. Upstream of the hepcidin-regulated signaling pathway, TMPRSS6 cleaves its target substrate hemojuvelin (HJV) at the plasma membrane, but the dynamics of the cell-surface expression of the protease have not been addressed. Here, we report that TMPRSS6 undergoes constitutive internalization in transfected HEK293 cells and in two human hepatic cell lines, HepG2 and primary hepatocytes, both of which express TMPRSS6 endogenously. Cell surface-labeled TMPRSS6 was internalized and was detected in clathrin- and AP-2-positive vesicles via a dynamin-dependent pathway. The endocytosed TMPRSS6 next transited in early endosomes and then to lysosomes. Internalization of TMPRSS6 is dependent on specific residues within its N-terminal cytoplasmic domain, as site-directed mutagenesis of these residues abrogated internalization and maintained the enzyme at the cell surface. Cells coexpressing these mutants and HJV produced significantly decreased levels of hepcidin compared with wild-type TMPRSS6 due to the sustained cleavage of HJV at the cell surface by TMPRSS6 mutants. Our results underscore for the first time the importance of TMPRSS6 trafficking at the plasma membrane in the regulation of hepcidin expression, an event that is essential for iron homeostasis.