Linking Ras to myosin function: RasGEF Q, a Dictyostelium exchange factor for RasB, affects myosin II functions

Ras guanine nucleotide exchange factor (GEF) Q, a nucleotide exchange factor from Dictyostelium discoideum, is a 143-kD protein containing RasGEF domains and a DEP domain. We show that RasGEF Q can bind to F-actin, has the potential to form complexes with myosin heavy chain kinase (MHCK) A that contain active RasB, and is the predominant exchange factor for RasB. Overexpression of the RasGEF Q GEF domain activates RasB, causes enhanced recruitment of MHCK A to the cortex, and leads to cytokinesis defects in suspension, phenocopying cells expressing constitutively active RasB, and myosin-null mutants. RasGEF Q− mutants have defects in cell sorting and slug migration during later stages of development, in addition to cell polarity defects. Furthermore, RasGEF Q− mutants have increased levels of unphosphorylated myosin II, resulting in myosin II overassembly. Collectively, our results suggest that starvation signals through RasGEF Q to activate RasB, which then regulates processes requiring myosin II

Role of modulators of small GTPases in chemotaxis, cytokinesis and development in Dictyostelium Discoideum

The work described here shows the complexity of GTPase signalling in an apparently simple organism Dictyostelium discoideum. Ras Guanine nucleotide exchange factor RasGEF Q is one out of at least 25 RasGEFs in D. discoideum. Here we show that it specifically regulates myosin II functions by regulating myosin phosphorylation. RasGEF Q activates the Ras isoform RasB upon stimulation with cAMP. Activated RasB can directly or indirectly activate Myosin Heavy chain kinase A (MHCK A) which then phosphorylates the myosin II heavy chain. Phosphorylated myosin II cannot assemble into filaments and is thus a non-functional form. Furthermore, a DEP domain in RasGEF Q appears to be critical for activating RasGEF Q by release from an autoinhibited state. Studies on the multidomain Rac Guanine nucleotide exchange factor GxcDD show that it is required for the early phases of development in chemotactic migration and streaming behaviour. The characterization of its single domains revealed that the CH domain (Calponin homology domain) of GxcDD functions as a membrane association domain, the RhoGEF domain can physically interact with a subset of Rac GTPases and the ArfGAP-PH tandem accumulates in cortical regions of the cell and in phagosomes. Our results also suggest that a conformational change is required for activation of GxcDD, which would be important for its downstream signaling. Studies on the IQGAP related protein GAPA showed that it associates with two actin-corsslinking protein, namely Filamin and Cortexillin I. GAPA is required for cytokinesis and localizes to the cleavage furrow during cytokinesis in a cortexillin I dependent way. We also observed that GAPA is required for proper phototaxis as is its binding partner Filamin

A cirkadián óramű molekuláris jellemzése: Az oszcillátor fehérje Frequency kifejeződésének transzkripciós és poszttranszkripciós szinten történő szabályozása = Molecular characterization of the circadian clockwork: Regulation of the expression of the oscillator protein on the transcriptional and posttranscriptional level

Kutatási munkánk célja a cirkadián oszcillátor működését biztosító, illetve módosító faktorok megismerése és funkcionális jellemzése volt a Neurospora crassa modellorganizmusban. Eredményeink: 1. Létrehoztunk egy olyan számítógépes programot, amely a Neurospora crassa genomjában képes szekvencia-mintázatokat keresni. A cirkadián óra pozitív komponensének ismert kötőhelyeihez hasonló struktúrákat kerestünk és így azonosítottunk egy új, a cirkadián oszcillátor működését befolyásoló faktort, egy feltehetően RasGEF aktivitású fehérjét. 2. A cirkadián óra egyik pozitív komponensének, a White Collar-1 fehérjének a vizsgálata kapcsán azonosítottunk két, a fehérje foszforilációját és ezen keresztül működését alapvetően meghatározó fehérjerégiót. Az egyik régión belül szekvencia homológia alapján valószínűleg egy MAP kináz foszforilációs hely található. 3. Kimutattuk, hogy a VIVID nevű másodlagos fényreceptor a környezeti fényintenzitásra vonatkozó molekuláris memóriaként működik. A cirkadián óra pozitív faktorával kölcsönhatásba lépve gátolja annak fényfüggő aktiválódását és ezáltal természetes fényperiódusok mellett stabilizálja a cirkadián óra működését. 4. Eredményeink szerint a reaktív oxigén származékok (ROS) szintjének változása fontos tényezője a cirkadián óra szabályozásának. A ROS-szint a molekuláris oszcillátorra hat, emelkedése korábbra helyezi a fázist és rövidíti a periódust. A ROS szint változásának hatását valószínűleg a protein foszfatáz 2A közvetíti. | Aim of our work was to functionally characterize factors involved in the regulation of the circadian clockwork of the model organism Neurospora crassa. Our most important results are summarized below: 1. We designed a computer program that enables one to search the genome of Neurospora for special sequence patterns. By searching for possible binding sites of the positive factor of the Neurospora clock we found a gene coding for a putative RasGEF protein. Our observations on a RasGEF mutant suggest that this protein is a modulator of the molecular clockwork. 2. We characterized two regulatory regions of the White Collar-1 protein. Deletion of these regions alters the phosphorylation of the protein and results in severe circadian phenotypes. One of these regions is a putative binding site of the MAP kinase. 3. We showed that the VIVID protein acting as a molecular memory interacts with and inhibits the positive component of the circadian clock and thus stabilizes the circadian rhythm even in naturally ambiguous photoperiods. 4. We found that reactive oxygen species (ROS) are important factors controlling the circadian clock. Increased ROS production advances the phase and shortens the circadian period. We suggest that the effect of ROS on the molecular oscillator is mediated by the protein phosphatase 2A

Systems level expression correlation of Ras GTPase regulators

Background: Proteins of the ubiquitously expressed core proteome are quantitatively correlated across multiple eukaryotic species. In addition, it was found that many protein paralogues exhibit expression anticorrelation, suggesting that the total level of protein with a given functionality must be kept constant. Methods: We performed Spearman’s rank correlation analyses of gene expression levels for the RAS GTPase subfamily and their regulatory GEF and GAP proteins across tissues and across individuals for each tissue. A large set of published data for normal tissues from a wide range of species, human cancer tissues and human cell lines was analysed. Results: We show that although the multidomain regulatory proteins of Ras GTPases exhibit considerable tissue and individual gene expression variability, their total amounts are balanced in normal tissues. In a given tissue, the sum of activating (GEFs) and deactivating (GAPs) domains of Ras GTPases can vary considerably, but each person has balanced GEF and GAP levels. This balance is impaired in cell lines and in cancer tissues for some individuals. Conclusions: Our results are relevant for critical considerations of knock out experiments, where functionally related homologs may compensate for the down regulation of a protein

The Dictyostelium genome encodes numerous RasGEFs with multiple biological roles

BACKGROUND: Dictyostelium discoideum is a eukaryote with a simple lifestyle and a relatively small genome whose sequence has been fully determined. It is widely used for studies on cell signaling, movement and multicellular development. Ras guanine-nucleotide exchange factors (RasGEFs) are the proteins that activate Ras and thus lie near the top of many signaling pathways. They are particularly important for signaling in development and chemotaxis in many organisms, including Dictyostelium. RESULTS: We have searched the genome for sequences encoding RasGEFs. Despite its relative simplicity, we find that the Dictyostelium genome encodes at least 25 RasGEFs, with a few other genes encoding only parts of the RasGEF consensus domains. All appear to be expressed at some point in development. The 25 genes include a wide variety of domain structures, most of which have not been seen in other organisms. The LisH domain, which is associated with microtubule binding, is seen particularly frequently; other domains that confer interactions with the cytoskeleton are also common. Disruption of a sample of the novel genes reveals that many have clear phenotypes, including altered morphology and defects in chemotaxis, slug phototaxis and thermotaxis. CONCLUSION: These results suggest that the unexpectedly large number of RasGEF genes reflects an evolutionary expansion of the range of Ras signaling rather than functional redundancy or the presence of multiple pseudogenes

Evolutionary expansion of the Ras switch regulatory module in eukaryotes

Ras proteins control many aspects of eukaryotic cell homeostasis by switching between active (GTP-bound) and inactive (GDP-bound) conformations, a reaction catalyzed by GTPase exchange factors (GEF) and GTPase activating proteins (GAP) regulators, respectively. Here, we show that the complexity, measured as number of genes, of the canonical Ras switch genetic system (including Ras, RasGEF, RasGAP and RapGAP families) from 24 eukaryotic organisms is correlated with their genome size and is inversely correlated to their evolutionary distances from humans. Moreover, different gene subfamilies within the Ras switch have contributed unevenly to the module’s expansion and speciation processes during eukaryote evolution. The Ras system remarkably reduced its genetic expansion after the split of the Euteleostomi clade and presently looks practically crystallized in mammals. Supporting evidence points to gene duplication as the predominant mechanism generating functional diversity in the Ras system, stressing the leading role of gene duplication in the Ras family expansion. Domain fusion and alternative splicing are significant sources of functional diversity in the GAP and GEF families but their contribution is limited in the Ras family. An evolutionary model of the Ras system expansion is proposed suggesting an inherent ‘decision making’ topology with the GEF input signal integrated by a homologous molecular mechanism and bifurcation in GAP signaling propagation

GRASP-1 A Neuronal RasGEF Associated with the AMPA Receptor/GRIP Complex

AbstractThe PDZ domain–containing proteins, such as PSD-95 and GRIP, have been suggested to be involved in the targeting of glutamate receptors, a process that plays a critical role in the efficiency of synaptic transmission and plasticity. To address the molecular mechanisms underlying AMPA receptor synaptic localization, we have identified several GRIP-associated proteins (GRASPs) that bind to distinct PDZ domains within GRIP. GRASP-1 is a neuronal rasGEF associated with GRIP and AMPA receptors in vivo. Overexpression of GRASP-1 in cultured neurons specifically reduced the synaptic targeting of AMPA receptors. In addition, the subcellular distribution of both AMPA receptors and GRASP-1 was rapidly regulated by the activation of NMDA receptors. These results suggest that GRASP-1 may regulate neuronal ras signaling and contribute to the regulation of AMPA receptor distribution by NMDA receptor activity

Very-KIND, a KIND domain–containing RasGEF, controls dendrite growth by linking Ras small GTPases and MAP2

The regulation of cytoskeletal components in the dendritic shaft core is critical for dendrite elongation and branching. Here, we report that a brain-specific Ras guanine nucleotide exchange factor (RasGEF) carrying two kinase non-catalytic C-lobe domains (KINDs), very-KIND (v-KIND), regulates microtubule-associated protein 2 (MAP2). v-KIND is expressed in developing mouse brain, predominantly in the cerebellar granule cells. v-KIND not only activates Ras small GTPases via the C-terminal RasGEF domain, but also specifically binds to MAP2 via the second KIND domain (KIND2), leading to threonine phosphorylation of MAP2. v-KIND overexpression suppresses dendritic extension and branching of hippocampal neurons and cerebellar granule cells, whereas knockdown of endogenous v-KIND expression promotes dendrite growth. These findings suggest that v-KIND mediates a signaling pathway that links Ras and MAP2 to control dendrite growth

Whole tumor RNA-sequencing and deconvolution reveal a clinically-prognostic PTEN/PI3K-regulated glioma transcriptional signature

The concept that solid tumors are maintained by a productive interplay between neoplastic and non-neoplastic elements has gained traction with the demonstration that stromal fibroblasts and immune system cells dictate cancer development and progression. While less studied, brain tumor (glioma) biology is likewise influenced by non-neoplastic immune system cells (macrophages and microglia) which interact with neoplastic glioma cells to create a unique physiological state (glioma ecosystem) distinct from that found in the normal tissue. To explore this neoplastic ground state, we leveraged several preclinical mouse models of neurofibromatosis type 1 (NF1) optic glioma, a low-grade astrocytoma whose formation and maintenance requires productive interactions between non-neoplastic and neoplastic cells, and employed whole tumor RNA-sequencing and mathematical deconvolution strategies to characterize this low-grade glioma ecosystem as an aggregate of cellular and acellular elements. Using this approach, we demonstrate that optic gliomas generated by altering the germlin