Molecular switch architecture determines response properties of signaling pathways

Cross-Species Epitope Sequence Analysis for Discovery of Existing Antibodies Useful for Phospho-Specific Protein Detection in Model Species

Signaling pathways play key roles in many important biological processes, such as cell division, differentiation, and migration. Phosphorylation site-specific antibodies specifically target proteins phosphorylated on a given tyrosine, threonine, or serine residue. The use of phospho-specific antibodies facilitates the analysis of signaling pathway regulation and activity. Given the usefulness of phospho-specific antibodies, a number of collections of these antibodies have been generated, typically for the detection of phosphorylated mammalian proteins. Anecdotal evidence shows that some of these are also useful for the detection of phosphorylated forms of orthologous proteins in model organisms. We propose that anti-phospho-mammalian protein antibody collections comprise an untapped resource for research in other species. To systematically analyze the potential utility of anti-phospho-mammalian protein antibodies in other species, we developed the Cross-species Epitope Sequence Analysis software tool (CESA). CESA identifies and aligns orthologous proteins in model species and then analyzes the conservation of antibody target sites. We used CESA to predict what phospho-specific antibodies in a collection from Cell Signaling Technology (CST) might be useful for studies in Drosophila melanogaster and other species. CESA predicts that more than 232 sites on 116 Drosophila proteins can potentially be targeted by the antibodies initially developed at CST to detect human, mouse, or rat phosphoproteins.

CESA: Cross-species Epitope Sequence Analysis for discovery of existing antibodies useful for phospho-specific protein detection in model species

Signaling pathways play key roles in many important biological processes such as cell division, differentiation, and migration. Phosphorylation site-specific antibodies specifically target proteins phosphorylated on a given tyrosine, threonine, or serine residue. Use of phospho-specific antibodies facilitates analysis of signaling pathway regulation and activity. Given the usefulness of phospho-specific antibodies, a number of collections of these antibodies have been generated, typically for detection of phosphorylated mammalian proteins. Anecdotal evidence shows that some of these are also useful for detection of phosphorylated forms of orthologous proteins in model organisms. We propose that anti-phospho-mammalian protein antibody collections comprise an untapped resource for research in other species. To systematically analyze the potential utility of anti-phospho-mammalian protein antibodies in other species, we developed the Cross-species Epitope Sequence Analysis software tool (CESA). CESA identifies and aligns orthologous proteins in model species, then analyzes conservation of antibody target sites. We used CESA to predict what phospho-specific antibodies in a collection from Cell Signaling Technology (CST) might be useful for studies in Drosophila melanogaster and other species. CESA predicts that more than 232 sites on 116 Drosophila proteins can potentially be targeted by the antibodies initially developed at CST to detect human, mouse, or rat phosphoproteins.

A rapid aureochrome opto-switch enables diatom acclimation to dynamic light

Diatoms often outnumber other eukaryotic algae in the oceans, especially in coastal environments characterized by frequent fluctuations in light intensity. The identities and operational mechanisms of regulatory factors governing diatom acclimation to high light stress remain largely elusive. Here, we identified the AUREO1c protein from the coastal diatom Phaeodactylum tricornutum as a crucial regulator of non-photochemical quenching (NPQ), a photoprotective mechanism that dissipates excess energy as heat. AUREO1c detects light stress using a light-oxygen-voltage (LOV) domain and directly activates the expression of target genes, including LI818 genes that encode NPQ effector proteins, via its bZIP DNA-binding domain. In comparison to a kinase-mediated pathway reported in the freshwater green alga Chlamydomonas reinhardtii, the AUREO1c pathway exhibits a faster response and enables accumulation of LI818 transcript and protein levels to comparable degrees between continuous high-light and fluctuating-light treatments. We propose that the AUREO1c-LI818 pathway contributes to the resilience of diatoms under dynamic light conditions.

A computational study of a light-driven artificial device: a third generation rotational photo-molecular motor in dilute solutions

A third-generation artificial photo-molecular motor, featuring two photo-switchable rotating moieties in connection with a pseudoasymmetric molecular centre, is investigated by combining quantum-mechanics (QM) algorithms with classical molecular dynamics (MD) propagators. In particular, in the present contribution we have addressed such a molecular motor in different rotational isomers following the experimental observations arising from the application of multiple spectroscopic techniques in dilute solutions. At first, we focused our attention on the reproduction of the UV/Vis absorption spectrum in two solvents (acetonitrile and cyclohexane) with different gradient-corrected density functional theory (B3LYP, Cam-B3LYP, PBE, PBE0) functionals in conjunction with the conductor-like and polarizable continuum model (C-PCM). Furthermore, we refined the absorption signals by combining a classical MD sampling at room-temperature with DFT-based electronic degrees of freedom to compute perturbed excitation wavelengths driven by thermal fluctuation and solvation effects. In this respect, we have modelled the investigated artificial motor within solution nanodroplets with solvent molecules treated contextually at atomistic level and via a dielectric and polarizable continuum model.

In Vivo Regulation of Signal Transduction Pathways by Vitamin D Stabilizes Homeostasis of Human Immune Cells and Counteracts Molecular Stress

Vitamin D3 is a pre-hormone that regulates hundreds of target genes and dozens of physiological functions, including calcium homeostasis and the activity of the immune system, via its metabolite 1,25-dihydroxyvitamin D3, which is a high-affinity ligand for the transcription factor vitamin D receptor. In this study, we took advantage of data from the VitDHiD vitamin D3 intervention trial (25 healthy individuals) indicating that 442 protein-coding genes were significantly (false discovery rate < 0.05) up- or downregulated in peripheral blood mononuclear cells one day after taking a vitamin D3 bolus. Since more than half of the encoded proteins had "signaling" assigned as a primary biological function, we evaluated their involvement in signal transduction cascades included in the KEGG (Kyoto Encyclopedia of Genes and Genomes) database and found 88 of the vitamin D targets contributing to 16 different pathways. Eight of the pathways show an approximately even contribution of up- and downregulated genes, suggesting that the actions of vitamin D stabilize homeostasis of the physiological processes driven by the respective signaling cascades. Interestingly, vitamin D target genes involved in the signaling pathways of hypoxia-inducible factor 1 (HIF1), tumor necrosis factor (TNF), mitogen-activated protein kinases (MAPKs) and nuclear factor κB (NFκB) are primarily downregulated. This supports the observation that the physiological role of vitamin D in healthy individuals is to tone down certain processes rather than activate them. In conclusion, under in vivo conditions, vitamin D either alleviates the homeostasis of immune cells in healthy individuals or counteracts molecular responses to oxygen deprivation (HIF1), microbe infection (TNF), growth stimulation (MAPKs) and inflammation (NFκB).

Design principles of improving the dose-response alignment in coupled GTPase switches

"Dose-response alignment" (DoRA), where the downstream response of cellular signaling pathways closely matches the fraction of activated receptor, can improve the fidelity of dose information transmission. The negative feedback has been experimentally identified as a key component for DoRA, but numerical simulations indicate that negative feedback is not sufficient to achieve perfect DoRA, i.e., perfect match of downstream response and receptor activation level. Thus a natural question is whether there exist design principles for signaling motifs within only negative feedback loops to improve DoRA to near-perfect DoRA. Here, we investigated several model formulations of an experimentally validated circuit that couples two molecular switches-mGTPase (monomeric GTPase) and tGTPase (heterotrimeric GTPases) - with negative feedback loops. In the absence of feedback, the low and intermediate mGTPase activation levels benefit DoRA in mass action and Hill-function models, respectively. Adding negative feedback has versatile roles on DoRA: it may impair DoRA in the mass action model with low mGTPase activation level and Hill-function model with intermediate mGTPase activation level; in other cases, i.e., the mass action model with a high mGTPase activation level or the Hill-function model with a non-intermediate mGTPase activation level, it improves DoRA. Furthermore, we found that DoRA in a longer cascade (i.e., tGTPase) can be obtained using Hill-function kinetics under certain conditions. In summary, we show how ranges of activity of mGTPase, reaction kinetics, the negative feedback, and the cascade length affect DoRA. This work provides a framework for improving the DoRA performance in signaling motifs with negative feedback.

PEAPOD repressors modulate and coordinate developmental responses to light intensity in Arabidopsis

Higher plants adapt to different light intensities by altering hypocotyl elongation, stomatal density, seed size, and flowering time. Despite the importance of this developmental plasticity, knowledge of the underlying genetic and molecular mechanisms modulating and coordinating responses to light intensity remains incomplete. Here, I report that in Arabidopsis the PEAPOD (PPD) repressors PPD1 and PPD2 prevent exaggerated responses to light intensity. Genetic and transcriptome analyses, of a ppd deletion mutant and a PPD1 overexpression genotype, were used to identify how PPD repressors modulate the light signalling network. A ppd1/ppd2 deletion mutant has elongated hypocotyls, elevated stomatal density, enlarged seed, and delayed flowering, whereas overexpression of PPD1 results in the reverse. Transcription of both PPD1 and PPD2, upregulated in low light and downregulated in higher light, is activated by PHYTOCHROME INTERACTING FACTOR 4. I found PPDs modulate light signalling by negative regulation of SUPPRESSOR OF phyA-105 (SPA1) transcription. Whereas PPDs coordinate many of the responses to light intensity - hypocotyl elongation, flowering time, and stomatal density - by repression/de-repression of SPA1, PPD regulation of seed size occurs independent of SPA1. In conclusion PPD repressors modulate and coordinate developmental responses to light intensity by altering light signal transduction.

Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges

In the past decade, the focus of bottom-up synthetic biology has shifted from the design of complex artificial cell architectures to the design of interactions between artificial cells mediated by physical and chemical cues. Engineering communication between artificial cells is crucial for the realization of coordinated dynamic behaviours in artificial cell populations, which would have implications for biotechnology, advanced colloidal materials and regenerative medicine. In this review, we focus our discussion on molecular communication between artificial cells. We cover basic concepts such as the importance of compartmentalization, the metabolic machinery driving signaling across cell boundaries and the different modes of communication used. The various studies in artificial cell signaling have been classified based on the distance between sender and receiver cells, just like in biology into autocrine, juxtacrine, paracrine and endocrine signaling. Emerging tools available for the design of dynamic and adaptive signaling are highlighted and some recent advances of signaling-enabled collective behaviours, such as quorum sensing, travelling pulses and predator-prey behaviour, are also discussed.

Towards resolution of a paradox in plant G-protein signaling

G-proteins are molecular on-off switches that are involved in transmitting a variety of extracellular signals to their intracellular targets. In animal and yeast systems, the switch property is encoded through nucleotides: a GDP-bound state is the "off-state" and the GTP-bound state is the "on-state". The G-protein cycle consists of the switch turning on through nucleotide exchange facilitated by a G-protein coupled receptor and the switch turning off through hydrolysis of GTP back to GDP, facilitated by a protein designated REGULATOR OF G SIGNALING 1 (RGS). In plants, G-protein signaling dramatically differs from that in animals and yeast. Despite stringent conservation of the nucleotide binding and catalytic structures over the 1.6 billion years that separate the evolution of plants and animals, genetic and biochemical data indicate that nucleotide exchange is less critical for this switch to operate in plants. Also, the loss of the single RGS protein in Arabidopsis (Arabidopsis thaliana) confers unexpectedly weaker phenotypes consistent with a diminished role for the G cycle, at least under static conditions. However, under dynamic conditions, genetic ablation of RGS in Arabidopsis results in a strong phenotype. We explore explanations to this conundrum by formulating a mathematical model that takes into account the accruing evidence for the indispensable role of phosphorylation in G-protein signaling in plants and that the G-protein cycle is needed to process dynamic signal inputs. We speculate that the plant G-protein cycle and its attendant components evolved to process dynamic signals through signaling modulation rather than through on-off, switch-like regulation of signaling. This so-called change detection may impart greater fitness for plants due to their sessility in a dynamic light, temperature, and pest environment.

Heterotrimeric G Proteins in Plants: Canonical and Atypical Gα Subunits

Heterotrimeric GTP-binding proteins (G proteins), consisting of Gα, Gβ and Gγ subunits, transduce signals from a diverse range of extracellular stimuli, resulting in the regulation of numerous cellular and physiological functions in Eukaryotes. According to the classic G protein paradigm established in animal models, the bound guanine nucleotide on a Gα subunit, either guanosine diphosphate (GDP) or guanosine triphosphate (GTP) determines the inactive or active mode, respectively. In plants, there are two types of Gα subunits: canonical Gα subunits structurally similar to their animal counterparts and unconventional extra-large Gα subunits (XLGs) containing a C-terminal domain homologous to the canonical Gα along with an extended N-terminal domain. Both Gα and XLG subunits interact with Gβγ dimers and regulator of G protein signalling (RGS) protein. Plant G proteins are implicated directly or indirectly in developmental processes, stress responses, and innate immunity. It is established that despite the substantial overall similarity between plant and animal Gα subunits, they convey signalling differently including the mechanism by which they are activated. This review emphasizes the unique characteristics of plant Gα subunits and speculates on their unique signalling mechanisms.