Abstract Protein kinase dynamics play key roles in regulation of cell differentiation, growth, development and in diverse cell signaling networks. Protein kinase sensors enable visualization of protein kinase activity in living cells and tissues in time and space. These sensors have therefore become important and powerful molecular tools for investigation of diverse kinase activities and can resolve long-standing and challenging biological questions. In the present Update, we review new advanced approaches for genetically encoded protein kinase biosensor designs developed in animal systems together with the basis of each biosensor’s working principle and components. In addition, we review recent first examples of real time plant protein kinase activity biosensor development and application. We discuss how these sensors have helped to resolve how stomatal signal transduction in response to elevated CO2 merges with abscisic acid signaling downstream of a resolved basal SnRK2 kinase activity in guard cells. Furthermore, recent advances, combined with the new strategies described in this Update, can help deepen the understanding of how signaling networks regulate unique functions and responses in distinct plant cell types and tissues and how different stimuli and signaling pathways can interact.
more »
« less
Quantitative insights in tissue growth and morphogenesis with optogenetics
Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through the spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis of organs. While many of the molecular components and physical interactions have been identified in key model developmental systems, there are still many unresolved questions related to the dynamics involved due to challenges in precisely perturbing and quantitatively measuring signaling dynamics. Recently, a broad range of synthetic optogenetic tools have been developed and employed to quantitatively define relationships between signal transduction and downstream cellular responses. These optogenetic tools can control intracellular activities at the single cell or whole tissue scale to direct subsequent biological processes. In this brief review, we highlight a selected set of studies that develop and implement optogenetic tools to unravel quantitative biophysical mechanisms for tissue growth and morphogenesis across a broad range of biological systems through the manipulation of morphogens, signal transduction cascades, and cell mechanics. More generally, we discuss how optogenetic tools have emerged as a powerful platform for probing and controlling multicellular development.
more » « less- Award ID(s):
- 2225601
- NSF-PAR ID:
- 10466046
- Publisher / Repository:
- IOP Publishing
- Date Published:
- Journal Name:
- Physical Biology
- Volume:
- 20
- Issue:
- 6
- ISSN:
- 1478-3967
- Format(s):
- Medium: X Size: Article No. 061001
- Size(s):
- ["Article No. 061001"]
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Iakoucheva, Lilia M. (Ed.)The complexity of biological processes such as cell differentiation is reflected in dynamic transitions between cellular states. Trajectory inference arranges the states into a progression using methodologies propelled by single-cell biology. However, current methods, all returning a best trajectory, do not adequately assess statistical significance of noisy patterns, leading to uncertainty in inferred trajectories. We introduce a tree dimension test for trajectory presence in multivariate data by a dimension measure of Euclidean minimum spanning tree, a test statistic, and a null distribution. Computable in linear time to tree size, the tree dimension measure summarizes the extent of branching more effectively than globally insensitive number of leaves or tree diameter indifferent to secondary branches. The test statistic quantifies trajectory presence and its null distribution is estimated under the null hypothesis of no trajectory in data. On simulated and real single-cell datasets, the test outperformed the intuitive number of leaves and tree diameter statistics. Next, we developed a measure for the tissue specificity of the dynamics of a subset, based on the minimum subtree cover of the subset in a minimum spanning tree. We found that tissue specificity of pathway gene expression dynamics is conserved in human and mouse development: several signal transduction pathways including calcium and Wnt signaling are most tissue specific, while genetic information processing pathways such as ribosome and mismatch repair are least so. Neither the tree dimension test nor the subset specificity measure has any user parameter to tune. Our work opens a window to prioritize cellular dynamics and pathways in development and other multivariate dynamical systems.more » « less
-
more » « less
Abstract A number of hormones and growth factors stimulate target cells via the second messenger pathways, which in turn regulate cellular phenotypes. Cyclic adenosine monophosphate (cAMP) is a ubiquitous second messenger that facilitates numerous signal transduction pathways; its production in cells is tightly balanced by ligand‐stimulated receptors that activate adenylate cyclases (ACs), that is, “source” and by phosphodiesterases (PDEs) that hydrolyze it, that is, “sinks.” Because it regulates various cellular functions, including cell growth and differentiation, gene transcription and protein expression, the cAMP signaling pathway has been exploited for the treatment of numerous human diseases. Reduction in cAMP is achieved by blocking “sources”; however, elevation in cAMP is achieved by either stimulating “source” or blocking “sinks.” Here we discuss an alternative paradigm for the regulation of cellular cAMP via GIV/Girdin, the prototypical member of a family of modulators of trimeric GTPases, Guanine nucleotide Exchange Modulators (GEMs). Cells upregulate or downregulate cellular levels of GIV‐GEM, which modulates cellular cAMP via spatiotemporal mechanisms distinct from the two most often targeted classes of cAMP modulators, “sources” and “sinks.” A network‐based compartmental model for the paradigm of GEM‐facilitated cAMP signaling has recently revealed that GEMs such as GIV serve much like a “tunable valve” that cells may employ to finetune cellular levels of cAMP. Because dysregulated signaling via GIV and other GEMs has been implicated in multiple disease states, GEMs constitute a hitherto untapped class of targets that could be exploited for modulating aberrant cAMP signaling in disease states.
This article is categorized under:
Models of Systems Properties and Processes > Mechanistic Models
Biological Mechanisms > Cell Signaling
-
Mitogen-activated protein kinase (MAPK) signaling pathways are highly conserved regulators of eukaryotic cell function. These enzymes regulate many biological processes, including the cell cycle, apoptosis, differentiation, protein biosynthesis, and oncogenesis; therefore, tight control of the activity of MAPK is critical. Kinases and phosphatases are well established as MAPK activators and inhibitors, respectively. Kinases phosphorylate MAPKs, initiating and controlling the amplitude of the activation. In contrast, MAPK phosphatases (MKPs) dephosphorylate MAPKs, downregulating and controlling the duration of the signal. In addition, within the past decade, pseudoenzymes of these two families, pseudokinases and pseudophosphatases, have emerged as bona fide signaling regulators. This review discusses the role of pseudophosphatases in MAPK signaling, highlighting the function of phosphoserine/threonine/tyrosine-interacting protein (STYX) and TAK1-binding protein (TAB 1) in regulating MAPKs. Finally, a new paradigm is considered for this well-studied cellular pathway, and signal transduction pathways in general.more » « less
-
Mechanical forces generated by dynamic cellular activities play a crucial role in the morphogenesis and growth of biological tissues. While the influence of mechanics is clear, many questions arise regarding the way by which mechanical forces communicate with biological processes at the level of a confluent cell population. Some answers may be found in the development of mathematical models that are capable of describing the emerging behavior of a large population of active agents based on individualistic rules (single-cell response). In this perspective, the present work presents a continuum-scale model that can capture, in an average sense, the active mechanics and evolution of a confluent tissue with or without external mechanical constraints. For this, we conceptualize a confluent cell population (in a monolayer) as a deformable dynamic network, where a single cell can modify the topology of its neighborhood by swapping neighbors or dividing. With this description, we use concepts from statistical mechanics and the transient network theory to derive an equivalent active visco-elastic continuum model, which can recapitulate some of the salient features of the underlying network at the macroscale. Without loss of generality, the cell network is here assumed to follow well-known rules used in vertex model simulations, which are: (a) cell elasticity based on its bulk and cortical elasticity, (b) cell intercalation (or T1 transition), and (c) cell proliferation (expansion and division). We show, through examples and illustrations, that the model is able to characterize complex cross-talk between mechanical forces and biological processes, which are likely to drive the emergent growth and deformation of cell aggregates.more » « less
