scholarly journals Multiplex image-based autophagy RNAi screening identifies SMCR8 as ULK1 kinase activity and gene expression regulator

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Jennifer Jung ◽  
Arnab Nayak ◽  
Véronique Schaeffer ◽  
Tatjana Starzetz ◽  
Achim K Kirsch ◽  
...  
Keyword(s):  
Gene Expression ◽  
Membrane Trafficking ◽  
Gene Locus ◽  
Kinase Activity ◽  
Degradation Pathway ◽  
Rab Gtpase ◽  
Rab Gtpases ◽  
Mrna Expression Analysis ◽  
Different Populations

Autophagy is an intracellular recycling and degradation pathway that depends on membrane trafficking. Rab GTPases are central for autophagy but their regulation especially through the activity of Rab GEFs remains largely elusive. We employed a RNAi screen simultaneously monitoring different populations of autophagosomes and identified 34 out of 186 Rab GTPase, GAP and GEF family members as potential autophagy regulators, amongst them SMCR8. SMCR8 uses overlapping binding regions to associate with C9ORF72 or with a C9ORF72-ULK1 kinase complex holo-assembly, which function in maturation and formation of autophagosomes, respectively. While focusing on the role of SMCR8 during autophagy initiation, we found that kinase activity and gene expression of ULK1 are increased upon SMCR8 depletion. The latter phenotype involved association of SMCR8 with the ULK1 gene locus. Global mRNA expression analysis revealed that SMCR8 regulates transcription of several other autophagy genes including WIPI2. Collectively, we established SMCR8 as multifaceted negative autophagy regulator.

scholarly journals Arf1 orchestrates Rab GTPase conversion at the trans-Golgi network

2021 ◽  
pp. mbc.E20-10-0664
Author(s):  
Laura L. Thomas ◽  
Carolyn M. Highland ◽  
J. Christopher Fromme
Keyword(s):  
Membrane Trafficking ◽  
Rab Gtpase ◽  
Rab Gtpases ◽  
Membrane Domains ◽  
Trans Golgi Network ◽  
Important Regulator ◽  
And Function ◽  
Golgi Network ◽  
New Evidence

Rab family GTPases are key organizers of membrane trafficking and function as markers of organelle identity. Accordingly, Rab GTPases often occupy specific membrane domains and mechanisms exist to prevent the inappropriate mixing of distinct Rab domains. The yeast Golgi complex can be divided into two broad Rab domains: Ypt1 (Rab1) and Ypt6 (Rab6) are present at the early/medial Golgi and sharply transition to Ypt31/32 (Rab11) at the late Golgi/ trans-Golgi network (TGN). This Rab conversion has been attributed to GAP cascades in which Ypt31/32 recruits the Rab-GAPs Gyp1 and Gyp6 to inactivate Ypt1 and Ypt6, respectively. Here we report that Rab transition at the TGN involves additional layers of regulation. We provide new evidence confirming the TRAPPII complex as an important regulator of Ypt6 inactivation and uncover an unexpected role of the Arf1 GTPase in recruiting Gyp1 to drive Ypt1 inactivation at the TGN. Given its established role in directly recruiting TRAPPII to the TGN, Arf1 is therefore a master regulator of Rab conversion on maturing Golgi compartments.

scholarly journals Contrasting patterns in the evolution of the Rab GTPase family in Archaeplastida

2014 ◽  
Vol 83 (4) ◽  
pp. 303-315 ◽  
Author(s):  
Romana Petrželková ◽  
Marek Eliáš
Keyword(s):  
Membrane Trafficking ◽  
Endocytic Pathway ◽  
Rab Gtpase ◽  
Rab Gtpases ◽  
Eukaryotic Diversity ◽  
Limited Sampling ◽  
Primary Plastid ◽  
Core Eudicots ◽  
Stem Lineage

Rab GTPases are a vast group of proteins serving a role of master regulators in membrane trafficking in eukaryotes. Previous studies delineated some 23 Rab and Rab-like paralogs ancestral for eukaryotes and mapped their current phylogenetic distribution, but the analyses relied on a limited sampling of the eukaryotic diversity. Taking advantage of the recent growth of genome and transcriptome resources for phylogenetically diverse plants and algae, we reanalyzed the evolution of the Rab family in eukaryotes with the primary plastid, collectively constituting the presumably monophyletic supergroup Archaeplastida. Our most important novel findings are as follows: (i) the ancestral set of Rabs in Archaeplastida included not only the paralogs Rab1, Rab2, Rab5, Rab6, Rab7, Rab8, Rab11, Rab18, Rab23, Rab24, Rab28, IFT27, and RTW (=Rabl2), as suggested previously, but also Rab14 and Rab34, because Rab14 exists in glaucophytes and Rab34 is present in glaucophytes and some green algae; (ii) except in embryophytes, Rab gene duplications have been rare in Archaeplastida. Most notable is the independent emergence of divergent, possibly functionally novel, in-paralogs of Rab1 and Rab11 in several archaeplastidial lineages; (iii) recurrent gene losses have been a significant factor shaping Rab gene complements in archaeplastidial species; for example, the Rab21 paralog was lost at least six times independently within Archaeplastida, once in the lineage leading to the “core” eudicots; (iv) while the glaucophyte <em>Cyanophora paradoxa</em> has retained the highest number of ancestral Rab paralogs among all archaeplastidial species studied so far, rhodophytes underwent an extreme reduction of the Rab gene set along their stem lineage, resulting in only six paralogs (Rab1, Rab2, Rab6, Rab7, Rab11, and Rab18) present in modern red algae. Especially notable is the absence of Rab5, a virtually universal paralog essential for the endocytic pathway, suggesting that endocytosis has been highly reduced or rewired in rhodophytes.

LRRK2 and Rab GTPases

2018 ◽  
Vol 46 (6) ◽  
pp. 1707-1712 ◽  
Author(s):  
Suzanne R. Pfeffer
Keyword(s):  
Membrane Trafficking ◽  
Protein Function ◽  
Short Review ◽  
Rab Gtpase ◽  
Rab Gtpases ◽  
Rab Protein ◽  
Complex Interactions ◽  
Preferential Binding ◽  
Bona Fide ◽  
Mutant Lrrk2

Leucine-rich repeat kinase 2 (LRRK2) is mutated in familial Parkinson's disease, and pathogenic mutations activate the kinase activity. A tour de force screen by Mann and Alessi and co-workers identified a subset of Rab GTPases as bona fide LRRK2 substrates. Rab GTPases are master regulators of membrane trafficking and this short review will summarize what we know about the connection between LRRK2 and this family of regulatory proteins. While, in most cases, Rab GTPase phosphorylation is predicted to interfere with Rab protein function, the discovery of proteins that show preferential binding to phosphorylated Rabs suggests that more complex interactions may also contribute to mutant LRRK2-mediated pathology.

scholarly journals Rab GTPases: Emerging Oncogenes and Tumor Suppressive Regulators for the Editing of Survival Pathways in Cancer

Cancers ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 259 ◽  
Author(s):  
Priya D. Gopal Krishnan ◽  
Emily Golden ◽  
Eleanor A. Woodward ◽  
Nathan J. Pavlos ◽  
Pilar Blancafort
Keyword(s):  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Intracellular Localization ◽  
Cellular Migration ◽  
Rab Gtpase ◽  
Rab Proteins ◽  
Rab Gtpases ◽  
Aberrant Expression ◽  
Post Translational Modifications ◽  
Survival Pathways

The Rab GTPase family of proteins are mediators of membrane trafficking, conferring identity to the cell membranes. Recently, Rab and Rab-associated factors have been recognized as major regulators of the intracellular positioning and activity of signaling pathways regulating cell growth, survival and programmed cell death or apoptosis. Membrane trafficking mediated by Rab proteins is controlled by intracellular localization of Rab proteins, Rab-membrane interactions and GTP-activation processes. Aberrant expression of Rab proteins has been reported in multiple cancers such as lung, brain and breast malignancies. Mutations in Rab-coding genes and/or post-translational modifications in their protein products disrupt the cellular vesicle trafficking network modulating tumorigenic potential, cellular migration and metastatic behavior. Conversely, Rabs also act as tumor suppressive factors inducing apoptosis and inhibiting angiogenesis. Deconstructing the signaling mechanisms modulated by Rab proteins during apoptosis could unveil underlying molecular mechanisms that may be exploited therapeutically to selectively target malignant cells.

scholarly journals Cell cycle–dependent phosphorylation of Sec4p controls membrane deposition during cytokinesis

2016 ◽  
Vol 214 (6) ◽  
pp. 691-703 ◽  
Author(s):  
Dante Lepore ◽  
Olya Spassibojko ◽  
Gabrielle Pinto ◽  
Ruth N. Collins
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Membrane Trafficking ◽  
Intracellular Trafficking ◽  
Rab Gtpase ◽  
Rab Gtpases ◽  
Positive Regulator ◽  
Physiological Relevance ◽  
A Cell ◽  
Cycle Dependent

Intracellular trafficking is an essential and conserved eukaryotic process. Rab GTPases are a family of proteins that regulate and provide specificity for discrete membrane trafficking steps by harnessing a nucleotide-bound cycle. Global proteomic screens have revealed many Rab GTPases as phosphoproteins, but the effects of this modification are not well understood. Using the Saccharomyces cerevisiae Rab GTPase Sec4p as a model, we have found that phosphorylation negatively regulates Sec4p function by disrupting the interaction with the exocyst complex via Sec15p. We demonstrate that phosphorylation of Sec4p is a cell cycle–dependent process associated with cytokinesis. Through a genomic kinase screen, we have also identified the polo-like kinase Cdc5p as a positive regulator of Sec4p phosphorylation. Sec4p spatially and temporally localizes with Cdc5p exclusively when Sec4p phosphorylation levels peak during the cell cycle, indicating Sec4p is a direct Cdc5p substrate. Our data suggest the physiological relevance of Sec4p phosphorylation is to facilitate the coordination of membrane-trafficking events during cytokinesis.

scholarly journals CDK6 kinase activity is required for thymocyte development

Blood ◽  
2011 ◽  
Vol 117 (23) ◽  
pp. 6120-6131 ◽  
Author(s):  
Miaofen G. Hu ◽  
Amit Deshpande ◽  
Nicolette Schlichting ◽  
Elisabeth A. Hinds ◽  
Changchuin Mao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Kinase Activity ◽  
Thymocyte Development ◽  
Hematopoietic Stem ◽  
Notch Target Gene ◽  
Target Gene Expression ◽  
Lymphoid Malignancies ◽  
Proliferation And Differentiation

Abstract Cyclin-dependent kinase-6 (CDK6) is required for early thymocyte development and tumorigenesis. To mechanistically dissect the role of CDK6 in thymocyte development, we generated and analyzed mutant knock-in mice and found that mice expressing a kinase-dead Cdk6 allele (Cdk6K43M) had a pronounced reduction in thymocytes and hematopoietic stem cells and progenitor cells (Lin−Sca-1+c-Kit+ [LSK]). In contrast, mice expressing the INK4-insensitive, hyperactive Cdk6R31C allele displayed excess proliferation in LSK and thymocytes. However, this is countered at least in part by increased apoptosis, which may limit progenitor and thymocyte expansion in the absence of other genetic events. Our mechanistic studies demonstrate that CDK6 kinase activity contributes to Notch signaling because inactive CDK6 kinase disrupts Notch-dependent survival, proliferation, and differentiation of LSK, with concomitant alteration of Notch target gene expression, such as massive up-regulation of CD25. Further, knockout of CD25 in Cdk6K43M mice rescued most defects observed in young mice. These results illustrate an important role for CDK6 kinase activity in thymocyte development that operates partially through modulating Notch target gene expression. This role of CDK6 as a downstream mediator of Notch identifies CDK6 kinase activity as a potential therapeutic target in human lymphoid malignancies.

scholarly journals Trs65p, a subunit of the Ypt1p GEF TRAPPII, interacts with the Arf1p exchange factor Gea2p to facilitate COPI-mediated vesicle traffic

2011 ◽  
Vol 22 (19) ◽  
pp. 3634-3644 ◽  
Author(s):  
Shuliang Chen ◽  
Huaqing Cai ◽  
Sei-Kyoung Park ◽  
Shekar Menon ◽  
Catherine L. Jackson ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Rab Gtpase ◽  
Vesicle Traffic ◽  
Exchange Factor ◽  
Γ Subunit ◽  
C Terminus ◽  
A Subunit ◽  
Distinct Membrane

The TRAPP complexes are multimeric guanine exchange factors (GEFs) for the Rab GTPase Ypt1p. The three complexes (TRAPPI, TRAPPII, and TRAPPIII) share a core of common subunits required for GEF activity, as well as unique subunits (Trs130p, Trs120p, Trs85p, and Trs65p) that redirect the GEF from the endoplasmic reticulum–Golgi pathway to different cellular locations where TRAPP mediates distinct membrane trafficking events. Roles for three of the four unique TRAPP subunits have been described before; however, the role of the TRAPPII-specific subunit Trs65p has remained elusive. Here we demonstrate that Trs65p directly binds to the C-terminus of the Arf1p exchange factor Gea2p and provide in vivo evidence that this interaction is physiologically relevant. Gea2p and TRAPPII also bind to the yeast orthologue of the γ subunit of the COPI coat complex (Sec21p), a known Arf1p effector. These and previous findings reveal that TRAPPII is part of an Arf1p GEF-effector loop that appears to play a role in recruiting or stabilizing TRAPPII to membranes. In support of this proposal, we show that TRAPPII is more soluble in an arf1Δ mutant.

scholarly journals IκB Kinase α (IKKα) Regulation of IKKβ Kinase Activity

2000 ◽  
Vol 20 (10) ◽  
pp. 3655-3666 ◽  
Author(s):  
Yumi Yamamoto ◽  
Min-Jean Yin ◽  
Richard B. Gaynor
Keyword(s):  
Gene Expression ◽  
Tumor Necrosis Factor ◽  
Tumor Necrosis ◽  
Kinase Activity ◽  
Necrosis Factor Alpha ◽  
Iκb Kinase ◽  
Factor Alpha ◽  
Subsequent Activation ◽  
Necrosis Factor

ABSTRACT Two related kinases, IκB kinase α (IKKα) and IKKβ, phosphorylate the IκB proteins, leading to their degradation and the subsequent activation of gene expression by NF-κB. IKKβ has a much higher level of kinase activity for the IκB proteins than does IKKα and is more critical than IKKα in modulating tumor necrosis factor alpha activation of the NF-κB pathway. These results indicate an important role for IKKβ in activating the NF-κB pathway but leave open the question of the role of IKKα in regulating this pathway. In the current study, we demonstrate that IKKα directly phosphorylates IKKβ. Moreover, IKKα either directly or indirectly enhances IKKβ kinase activity for IκBα. Finally, transfection studies to analyze NF-κB-directed gene expression suggest that IKKα is upstream of IKKβ in activating the NF-κB pathway. These results indicate that IKKα, in addition to its previously described ability to phosphorylate IκBα, can increase the ability of IKKβ to phosphorylate IκBα.

scholarly journals Large-Scale Profiling of Rab GTPase Trafficking Networks: The Membrome

2005 ◽  
Vol 16 (8) ◽  
pp. 3847-3864 ◽  
Author(s):  
Cemal Gurkan ◽  
Hilmar Lapp ◽  
Christelle Alory ◽  
Andrew I. Su ◽  
John B. Hogenesch ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Large Scale ◽  
Building Blocks ◽  
Rab Gtpase ◽  
Rab Gtpases ◽  
Coding System ◽  
Clustering Methods ◽  
Protein Activity ◽  
Organ Systems ◽  
Hierarchical Clustering Methods

Rab GTPases and SNARE fusion proteins direct cargo trafficking through the exocytic and endocytic pathways of eukaryotic cells. We have used steady state mRNA expression profiling and computational hierarchical clustering methods to generate a global overview of the distribution of Rabs, SNAREs, and coat machinery components, as well as their respective adaptors, effectors, and regulators in 79 human and 61 mouse nonredundant tissues. We now show that this systems biology approach can be used to define building blocks for membrane trafficking based on Rab-centric protein activity hubs. These Rab-regulated hubs provide a framework for an integrated coding system, the membrome network, which regulates the dynamics of the specialized membrane architecture of differentiated cells. The distribution of Rab-regulated hubs illustrates a number of facets that guides the overall organization of subcellular compartments of cells and tissues through the activity of dynamic protein interaction networks. An interactive website for exploring datasets comprising components of the Rab-regulated hubs that define the membrome of different cell and organ systems in both human and mouse is available at http://www.membrome.org/ .

scholarly journals Rab1b overexpression modifies Golgi size and gene expression in HeLa cells and modulates the thyrotrophin response in thyroid cells in culture

2013 ◽  
Vol 24 (5) ◽  
pp. 617-632 ◽  
Author(s):  
Nahuel Romero ◽  
Catherine I. Dumur ◽  
Hernán Martinez ◽  
Iris A. García ◽  
Pablo Monetta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hela Cells ◽  
Membrane Trafficking ◽  
Mitogen Activated Protein Kinase ◽  
Thyroid Cell ◽  
Transcriptional Level ◽  
Rab Gtpase ◽  
Mrna Levels ◽  
Consensus Binding Site ◽  
Thyroid Cells

Rab1b belongs to the Rab-GTPase family that regulates membrane trafficking and signal transduction systems able to control diverse cellular activities, including gene expression. Rab1b is essential for endoplasmic reticulum–Golgi transport. Although it is ubiquitously expressed, its mRNA levels vary among different tissues. This work aims to characterize the role of the high Rab1b levels detected in some secretory tissues. We report that, in HeLa cells, an increase in Rab1b levels induces changes in Golgi size and gene expression. Significantly, analyses applied to selected genes, KDELR3, GM130 (involved in membrane transport), and the proto-oncogene JUN, indicate that the Rab1b increase acts as a molecular switch to control the expression of these genes at the transcriptional level, resulting in changes at the protein level. These Rab1b-dependent changes require the activity of p38 mitogen-activated protein kinase and the cAMP-responsive element-binding protein consensus binding site in those target promoter regions. Moreover, our results reveal that, in a secretory thyroid cell line (FRTL5), Rab1b expression increases in response to thyroid-stimulating hormone (TSH). Additionally, changes in Rab1b expression in FRTL5 cells modify the specific TSH response. Our results show, for the first time, that changes in Rab1b levels modulate gene transcription and strongly suggest that a Rab1b increase is required to elicit a secretory response.

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