1
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Chakraborty S, Kanade M, Gayathri P. Mechanism of GTPase activation of a prokaryotic small Ras-like GTPase MglA by an asymmetrically interacting MglB dimer. J Biol Chem 2024; 300:107197. [PMID: 38508314 PMCID: PMC11016934 DOI: 10.1016/j.jbc.2024.107197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Cell polarity oscillations in Myxococcus xanthus motility are driven by a prokaryotic small Ras-like GTPase, mutual gliding protein A (MglA), which switches from one cell pole to the other in response to extracellular signals. MglA dynamics is regulated by MglB, which functions both as a GTPase activating protein (GAP) and a guanine nucleotide exchange factor (GEF) for MglA. With an aim to dissect the asymmetric role of the two MglB protomers in the dual GAP and GEF activities, we generated a functional MglAB complex by coexpressing MglB with a linked construct of MglA and MglB. This strategy enabled us to generate mutations of individual MglB protomers (MglB1 or MglB2 linked to MglA) and delineate their role in GEF and GAP activities. We establish that the C-terminal helix of MglB1, but not MglB2, stimulates nucleotide exchange through a site away from the nucleotide-binding pocket, confirming an allosteric mechanism. Interaction between the N-terminal β-strand of MglB1 and β0 of MglA is essential for the optimal GEF activity of MglB. Specific residues of MglB2, which interact with Switch-I of MglA, partially contribute to its GAP activity. Thus, the role of the MglB2 protomer in the GAP activity of MglB is limited to restricting the conformation of MglA active site loops. The direct demonstration of the allosteric mechanism of GEF action provides us new insights into the regulation of small Ras-like GTPases, a feature potentially present in many uncharacterized GEFs.
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Affiliation(s)
- Sukanya Chakraborty
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
| | - Manil Kanade
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
| | - Pananghat Gayathri
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India.
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2
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Tran LT, Akıl C, Senju Y, Robinson RC. The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea. Commun Biol 2024; 7:273. [PMID: 38472392 DOI: 10.1038/s42003-024-05888-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.
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Affiliation(s)
- Linh T Tran
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Caner Akıl
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
- Division of Structural Biology, University of Oxford, Oxford, England
| | - Yosuke Senju
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan.
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.
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3
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Yang D, Wang J, Qin Z, Feng J, Mao C, Chen Y, Huang X, Ruan Y. Phenotypic and genotypic characterization of NPRL3-related epilepsy: Two case reports and literature review. Epilepsia Open 2024; 9:33-40. [PMID: 37902097 PMCID: PMC10839296 DOI: 10.1002/epi4.12856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/20/2023] [Indexed: 10/31/2023] Open
Abstract
Nitrogen permease regulator-like 3 (NPRL3) has been reported to play a role in seizure onset. The principal manifestation of NPRL3-related epilepsy is a range of epilepsy-associated syndromes, such as familial focal epilepsy with variable foci (FFEVF), sleep-related hypermotor epilepsy (SHE), and temporal lobe epilepsy (TLE). The association between phenotype and genotype of NPRL3 mutations remains inadequately described. This study aimed to explore the phenotypic and genotypic spectra of NPRL3-related epilepsy. We reported two novel NPRL3 variants in two unrelated epilepsy cases, including a nonsense (c.1174C > T, p.Gln392*) and a missense variant (c.1322C > T, p.Thr441Met). Following a review of the literature, a total of 116 cases of NPRL3-related epilepsy were assessed, mostly with nonsense and frameshift mutations. Our findings suggest that patients harboring various NPRL3 variants exhibit variable clinical manifestations. In addition, it may be worthwhile to consider theexistence of NPRL3 mutations in epilepsy patients with a family history. This study provides useful information for the treatment and prognosis by expanding the phenotypic and genotypic spectrum of NPRL3-related epilepsy. PLAIN LANGUAGE SUMMARY: This study expands the phenotypic and genotypic spectra of NPRL3-related epilepsy by reporting two cases with different novel variants. Following a review of the literature, it was observed that patients harboring various NPRL3 variants exhibited a variability of clinical manifestations. Also, patients carrying nonsense mutations are frequently prone to drug resistance and other severe comorbidities such as developmental delay, but more cases need to be collected to confirm these findings.
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Affiliation(s)
- Dongling Yang
- Ruikang Clinical Medical CollegeGuangxi University of Chinese MedicineNanningChina
- Department of Pediatric Neurology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionGuangxi Clinical Research Center for Pediatric DiseasesNanningChina
| | - Jinqiu Wang
- Department of Pediatric Neurology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionGuangxi Clinical Research Center for Pediatric DiseasesNanningChina
| | - Zailong Qin
- Guangxi Key Laboratory of Precision Medicine for Genetic DiseasesMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Genetic and Metabolic Central LaboratoryGuangxi Birth Defects Research and Prevention InstituteNanningChina
| | - Juntan Feng
- Department of Pediatric Neurology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionGuangxi Clinical Research Center for Pediatric DiseasesNanningChina
| | - Chengyun Mao
- Department of Pediatric Neurology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionGuangxi Clinical Research Center for Pediatric DiseasesNanningChina
| | - Yuyi Chen
- Department of Pediatric Neurology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionGuangxi Clinical Research Center for Pediatric DiseasesNanningChina
| | - Xuelin Huang
- Department of Pediatric Neurology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionGuangxi Clinical Research Center for Pediatric DiseasesNanningChina
| | - Yiyan Ruan
- Department of Pediatric Neurology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionGuangxi Clinical Research Center for Pediatric DiseasesNanningChina
- Guangxi Key Laboratory of Precision Medicine for Genetic DiseasesMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
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4
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Carreira LAM, Szadkowski D, Lometto S, Hochberg GKA, Søgaard-Andersen L. Molecular basis and design principles of switchable front-rear polarity and directional migration in Myxococcus xanthus. Nat Commun 2023; 14:4056. [PMID: 37422455 PMCID: PMC10329633 DOI: 10.1038/s41467-023-39773-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
During cell migration, front-rear polarity is spatiotemporally regulated; however, the underlying design of regulatory interactions varies. In rod-shaped Myxococcus xanthus cells, a spatial toggle switch dynamically regulates front-rear polarity. The polarity module establishes front-rear polarity by guaranteeing front pole-localization of the small GTPase MglA. Conversely, the Frz chemosensory system, by acting on the polarity module, causes polarity inversions. MglA localization depends on the RomR/RomX GEF and MglB/RomY GAP complexes that localize asymmetrically to the poles by unknown mechanisms. Here, we show that RomR and the MglB and MglC roadblock domain proteins generate a positive feedback by forming a RomR/MglC/MglB complex, thereby establishing the rear pole with high GAP activity that is non-permissive to MglA. MglA at the front engages in negative feedback that breaks the RomR/MglC/MglB positive feedback allosterically, thus ensuring low GAP activity at this pole. These findings unravel the design principles of a system for switchable front-rear polarity.
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Affiliation(s)
| | - Dobromir Szadkowski
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Stefano Lometto
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University, 35043, Marburg, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University, 35043, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
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5
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Diab R, Pilotto F, Saxena S. Autophagy and neurodegeneration: Unraveling the role of C9ORF72 in the regulation of autophagy and its relationship to ALS-FTD pathology. Front Cell Neurosci 2023; 17:1086895. [PMID: 37006471 PMCID: PMC10060823 DOI: 10.3389/fncel.2023.1086895] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
The proper functioning of the cell clearance machinery is critical for neuronal health within the central nervous system (CNS). In normal physiological conditions, the cell clearance machinery is actively involved in the elimination of misfolded and toxic proteins throughout the lifetime of an organism. The highly conserved and regulated pathway of autophagy is one of the important processes involved in preventing and neutralizing pathogenic buildup of toxic proteins that could eventually lead to the development of neurodegenerative diseases (NDs) such as Alzheimer’s disease or Amyotrophic lateral sclerosis (ALS). The most common genetic cause of ALS and frontotemporal dementia (FTD) is a hexanucleotide expansion consisting of GGGGCC (G4C2) repeats in the chromosome 9 open reading frame 72 gene (C9ORF72). These abnormally expanded repeats have been implicated in leading to three main modes of disease pathology: loss of function of the C9ORF72 protein, the generation of RNA foci, and the production of dipeptide repeat proteins (DPRs). In this review, we discuss the normal physiological role of C9ORF72 in the autophagy-lysosome pathway (ALP), and present recent research deciphering how dysfunction of the ALP synergizes with C9ORF72 haploinsufficiency, which together with the gain of toxic mechanisms involving hexanucleotide repeat expansions and DPRs, drive the disease process. This review delves further into the interactions of C9ORF72 with RAB proteins involved in endosomal/lysosomal trafficking, and their role in regulating various steps in autophagy and lysosomal pathways. Lastly, the review aims to provide a framework for further investigations of neuronal autophagy in C9ORF72-linked ALS-FTD as well as other neurodegenerative diseases.
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Affiliation(s)
- Rim Diab
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Federica Pilotto
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Smita Saxena
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- *Correspondence: Smita Saxena,
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6
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Regulation of mTORC1 by the Rag GTPases. Biochem Soc Trans 2023; 51:655-664. [PMID: 36929165 DOI: 10.1042/bst20210038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023]
Abstract
The Rag GTPases are an evolutionarily conserved family that play a crucial role in amino acid sensing by the mammalian target of rapamycin complex 1 (mTORC1). mTORC1 is often referred to as the master regulator of cell growth. mTORC1 hyperactivation is observed in multiple diseases such as cancer, obesity, metabolic disorders, and neurodegeneration. The Rag GTPases sense amino acid levels and form heterodimers, where RagA or RagB binds to RagC or RagD, to recruit mTORC1 to the lysosome where it becomes activated. Here, we review amino acid signaling to mTORC1 through the Rag GTPases.
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7
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Dinet C, Mignot T. Unorthodox regulation of the MglA Ras-like GTPase controlling polarity in Myxococcus xanthus. FEBS Lett 2023; 597:850-864. [PMID: 36520515 DOI: 10.1002/1873-3468.14565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Motile cells have developed a large array of molecular machineries to actively change their direction of movement in response to spatial cues from their environment. In this process, small GTPases act as molecular switches and work in tandem with regulators and sensors of their guanine nucleotide status (GAP, GEF, GDI and effectors) to dynamically polarize the cell and regulate its motility. In this review, we focus on Myxococcus xanthus as a model organism to elucidate the function of an atypical small Ras GTPase system in the control of directed cell motility. M. xanthus cells direct their motility by reversing their direction of movement through a mechanism involving the redirection of the motility apparatus to the opposite cell pole. The reversal frequency of moving M. xanthus cells is controlled by modular and interconnected protein networks linking the chemosensory-like frizzy (Frz) pathway - that transmits environmental signals - to the downstream Ras-like Mgl polarity control system - that comprises the Ras-like MglA GTPase protein and its regulators. Here, we discuss how variations in the GTPase interactome landscape underlie single-cell decisions and consequently, multicellular patterns.
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Affiliation(s)
- Céline Dinet
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille University, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille University, France
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8
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Szadkowski D, Carreira LAM, Søgaard-Andersen L. A bipartite, low-affinity roadblock domain-containing GAP complex regulates bacterial front-rear polarity. PLoS Genet 2022; 18:e1010384. [PMID: 36067225 PMCID: PMC9481161 DOI: 10.1371/journal.pgen.1010384] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/16/2022] [Accepted: 08/17/2022] [Indexed: 11/29/2022] Open
Abstract
The Ras-like GTPase MglA is a key regulator of front-rear polarity in the rod-shaped Myxococcus xanthus cells. MglA-GTP localizes to the leading cell pole and stimulates assembly of the two machineries for type IV pili-dependent motility and gliding motility. MglA-GTP localization is spatially constrained by its cognate GEF, the RomR/RomX complex, and GAP, the MglB Roadblock-domain protein. Paradoxically, RomR/RomX and MglB localize similarly with low and high concentrations at the leading and lagging poles, respectively. Yet, GEF activity dominates at the leading and GAP activity at the lagging pole by unknown mechanisms. Here, we identify RomY and show that it stimulates MglB GAP activity. The MglB/RomY interaction is low affinity, restricting formation of the bipartite MglB/RomY GAP complex almost exclusively to the lagging pole with the high MglB concentration. Our data support a model wherein RomY, by forming a low-affinity complex with MglB, ensures that the high MglB/RomY GAP activity is confined to the lagging pole where it dominates and outcompetes the GEF activity of the RomR/RomX complex. Thereby, MglA-GTP localization is constrained to the leading pole establishing front-rear polarity. Bacterial cells are spatially highly organized with proteins localizing to distinct subcellular locations. This spatial organization, or cell polarity, is important for many cellular processes including motility. The rod-shaped M. xanthus cells move with defined leading and lagging cell poles. This front-rear polarity is brought about by the polarity module, which consists of the small Ras-like GTPase MglA, its GEF (the RomR/RomX complex) and its GAP (MglB). Specifically, MglA-GTP localizes to the leading pole and stimulates assembly of the motility machineries. MglA-GTP localization, in turn, is spatially constrained by its GEF and GAP. Paradoxically, the RomR/RomX GEF and MglB GAP localize similarly with low and high concentrations at the leading and lagging poles, respectively. Yet, GEF activity dominates at the leading and GAP activity at the lagging pole. Here, we identify RomY and show that it stimulates MglB GAP activity. Interestingly, the MglB/RomY interaction is low affinity. Consequently, MglB/RomY complex formation almost exclusively occurs at the lagging cell pole with the high MglB concentration. Thus, the key to precisely stimulating MglB GAP activity only at the lagging pole is that the MglB/RomY interaction is low-affinity, ultimately restricting MglA-GTP to the leading pole.
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Affiliation(s)
- Dobromir Szadkowski
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
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9
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Carreira LAM, Szadkowski D, Müller F, Søgaard-Andersen L. Spatiotemporal regulation of switching front–rear cell polarity. Curr Opin Cell Biol 2022; 76:102076. [DOI: 10.1016/j.ceb.2022.102076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 11/30/2022]
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10
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Structure of the Mon1-Ccz1 complex reveals molecular basis of membrane binding for Rab7 activation. Proc Natl Acad Sci U S A 2022; 119:2121494119. [PMID: 35105815 PMCID: PMC8833172 DOI: 10.1073/pnas.2121494119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2021] [Indexed: 01/02/2023] Open
Abstract
Activation of the GTPase Rab7/Ypt7 by its cognate guanine nucleotide exchange factor (GEF) Mon1-Ccz1 marks organelles such as endosomes and autophagosomes for fusion with lysosomes/vacuoles and degradation of their content. Here, we present a high-resolution cryogenic electron microscopy structure of the Mon1-Ccz1 complex that reveals its architecture in atomic detail. Mon1 and Ccz1 are arranged side by side in a pseudo-twofold symmetrical heterodimer. The three Longin domains of each Mon1 and Ccz1 are triangularly arranged, providing a strong scaffold for the catalytic center of the GEF. At the opposite side of the Ypt7-binding site, a positively charged and relatively flat patch stretches the Longin domains 2/3 of Mon1 and functions as a phosphatidylinositol phosphate-binding site, explaining how the GEF is targeted to membranes. Our work provides molecular insight into the mechanisms of endosomal Rab activation and serves as a blueprint for understanding the function of members of the Tri Longin domain Rab-GEF family.
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11
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Jiang L, Zhang T, Lu K, Qi S. The progress in C9orf72 research: ALS/FTD pathogenesis, functions and structure. Small GTPases 2022; 13:56-76. [PMID: 33663328 PMCID: PMC9707547 DOI: 10.1080/21541248.2021.1892443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The hexanucleotide repeat (GGGGCC) expansion in C9orf72 is accounted for a large proportion of the genetic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The hypotheses of how the massive G4C2 repeats in C9orf72 destroy the neurons and lead to ALS/FTD are raised and improving. As a multirole player, C9orf72 exerts critical roles in many cellular processes, including autophagy, membrane trafficking, immune response, and so on. Notably, the partners of C9orf72, through which C9orf72 participates in the cell activities, have been identified. Notably, the structures of the C9orf72-SMCR8-WDR41 complex shed light on its activity as GTPase activating proteins (GAP). In this manuscript, we reviewed the latest research progress in the C9orf72-mediated ALS/FTD, the physiological functions of C9orf72, and the putative function models of C9orf72/C9orf72-containing complex.
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Affiliation(s)
- Lan Jiang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tizhong Zhang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kefeng Lu
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shiqian Qi
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China,CONTACT Shiqian Qi Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China.
These authors contributed equally to this work.
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12
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Loissell-Baltazar YA, Dokudovskaya S. SEA and GATOR 10 Years Later. Cells 2021; 10:cells10102689. [PMID: 34685669 PMCID: PMC8534245 DOI: 10.3390/cells10102689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/30/2021] [Accepted: 10/03/2021] [Indexed: 12/17/2022] Open
Abstract
The SEA complex was described for the first time in yeast Saccharomyces cerevisiae ten years ago, and its human homologue GATOR complex two years later. During the past decade, many advances on the SEA/GATOR biology in different organisms have been made that allowed its role as an essential upstream regulator of the mTORC1 pathway to be defined. In this review, we describe these advances in relation to the identification of multiple functions of the SEA/GATOR complex in nutrient response and beyond and highlight the consequence of GATOR mutations in cancer and neurodegenerative diseases.
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13
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Galindo A, Planelles-Herrero VJ, Degliesposti G, Munro S. Cryo-EM structure of metazoan TRAPPIII, the multi-subunit complex that activates the GTPase Rab1. EMBO J 2021; 40:e107608. [PMID: 34018214 PMCID: PMC8204870 DOI: 10.15252/embj.2020107608] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/30/2021] [Accepted: 04/11/2021] [Indexed: 12/19/2022] Open
Abstract
The TRAPP complexes are nucleotide exchange factors that play essential roles in membrane traffic and autophagy. TRAPPII activates Rab11, and TRAPPIII activates Rab1, with the two complexes sharing a core of small subunits that affect nucleotide exchange but being distinguished by specific large subunits that are essential for activity in vivo. Crystal structures of core subunits have revealed the mechanism of Rab activation, but how the core and the large subunits assemble to form the complexes is unknown. We report a cryo‐EM structure of the entire Drosophila TRAPPIII complex. The TRAPPIII‐specific subunits TRAPPC8 and TRAPPC11 hold the catalytic core like a pair of tongs, with TRAPPC12 and TRAPPC13 positioned at the joint between them. TRAPPC2 and TRAPPC2L link the core to the two large arms, with the interfaces containing residues affected by disease‐causing mutations. The TRAPPC8 arm is positioned such that it would contact Rab1 that is bound to the core, indicating how the arm could determine the specificity of the complex. A lower resolution structure of TRAPPII shows a similar architecture and suggests that the TRAPP complexes evolved from a single ur‐TRAPP.
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Affiliation(s)
| | | | | | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK
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14
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Ye Z, Wang D, Lu Y, He Y, Yu J, Wei W, Chen C, Wang R, Zhang L, Zhang L, Le MTN, Cho WC, Yang M, Zhang H, Yue J. Vacuolin-1 inhibits endosomal trafficking and metastasis via CapZβ. Oncogene 2021; 40:1775-1791. [PMID: 33564074 PMCID: PMC7946642 DOI: 10.1038/s41388-021-01662-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/14/2020] [Accepted: 01/15/2021] [Indexed: 01/31/2023]
Abstract
Metastasis is the fundamental cause of cancer mortality, but there are still very few anti-metastatic drugs available. Endosomal trafficking has been implicated in tumor metastasis, and we have previously found that small chemical vacuolin-1 (V1) potently inhibits autophagosome-lysosome fusion and general endosomal-lysosomal degradation. Here, we assessed the anti-metastatic activity of V1 both in vitro and in vivo. V1 significantly inhibits colony formation, migration, and invasion of various cancer cells in vitro. It also compromises the assembly-disassembly dynamics of focal adhesions (FAs) by inhibiting the recycling and degradation of integrins. In various experimental or transgenic mouse models, V1 significantly suppresses the metastasis and/or tumor growth of breast cancer or melanoma. We further identified capping protein Zβ (CapZβ) as a V1 binding protein and showed that it is required for the V1-mediated inhibition of migration and metastasis of cancer cells. Collectively, our results indicate that V1 targets CapZβ to inhibit endosomal trafficking and metastasis.
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Affiliation(s)
- Zuodong Ye
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Dawei Wang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Yingying Lu
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Yunjiao He
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research and Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jingting Yu
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Wenjie Wei
- Research Core Facilities, South University of Science and Technology of China, Shenzhen, 518052, China
| | - Chang Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191, Beijing, China
| | - Rui Wang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Liang Zhang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191, Beijing, China
| | - Minh T N Le
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, 30 Gascoigne Road, Kowloon, Hong Kong, China
| | - Mengsu Yang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Hongmin Zhang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research and Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jianbo Yue
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.
- City University of Hong Kong Chengdu Research Institute, Chengdu, China.
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15
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Kapoor S, Kodesia A, Kalidas N, Ashish, Thakur KG. Structural characterization of Myxococcus xanthus MglC, a component of the polarity control system, and its interactions with its paralog MglB. J Biol Chem 2021; 296:100308. [PMID: 33493516 PMCID: PMC7949163 DOI: 10.1016/j.jbc.2021.100308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/28/2022] Open
Abstract
The δ-proteobacteria Myxococcus xanthus displays social (S) and adventurous (A) motilities, which require pole-to-pole reversal of the motility regulator proteins. Mutual gliding motility protein C (MglC), a paralog of GTPase-activating protein Mutual gliding motility protein B (MglB), is a member of the polarity module involved in regulating motility. However, little is known about the structure and function of MglC. Here, we determined ∼1.85 Å resolution crystal structure of MglC using Selenomethionine Single-wavelength anomalous diffraction. The crystal structure revealed that, despite sharing <9% sequence identity, both MglB and MglC adopt a Regulatory Light Chain 7 family fold. However, MglC has a distinct ∼30° to 40° shift in the orientation of the functionally important α2 helix compared with other structural homologs. Using isothermal titration calorimetry and size-exclusion chromatography, we show that MglC binds MglB in 2:4 stoichiometry with submicromolar range dissociation constant. Using small-angle X-ray scattering and molecular docking studies, we show that the MglBC complex consists of a MglC homodimer sandwiched between two homodimers of MglB. A combination of size-exclusion chromatography and site-directed mutagenesis studies confirmed the MglBC interacting interface obtained by molecular docking studies. Finally, we show that the C-terminal region of MglB, crucial for binding its established partner MglA, is not required for binding MglC. These studies suggest that the MglB uses distinct interfaces to bind MglA and MglC. Based on these data, we propose a model suggesting a new role for MglC in polarity reversal in M. xanthus.
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Affiliation(s)
- Srajan Kapoor
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Akriti Kodesia
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Nidhi Kalidas
- Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Ashish
- Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India.
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16
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Jenkins ML, Harris NJ, Dalwadi U, Fleming KD, Ziemianowicz DS, Rafiei A, Martin EM, Schriemer DC, Yip CK, Burke JE. The substrate specificity of the human TRAPPII complex's Rab-guanine nucleotide exchange factor activity. Commun Biol 2020; 3:735. [PMID: 33277614 PMCID: PMC7719173 DOI: 10.1038/s42003-020-01459-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
The TRAnsport Protein Particle (TRAPP) complexes act as Guanine nucleotide exchange factors (GEFs) for Rab GTPases, which are master regulators of membrane trafficking in eukaryotic cells. In metazoans, there are two large multi-protein TRAPP complexes: TRAPPII and TRAPPIII, with the TRAPPII complex able to activate both Rab1 and Rab11. Here we present detailed biochemical characterisation of Rab-GEF specificity of the human TRAPPII complex, and molecular insight into Rab binding. GEF assays of the TRAPPII complex against a panel of 20 different Rab GTPases revealed GEF activity on Rab43 and Rab19. Electron microscopy and chemical cross-linking revealed the architecture of mammalian TRAPPII. Hydrogen deuterium exchange MS showed that Rab1, Rab11 and Rab43 share a conserved binding interface. Clinical mutations in Rab11, and phosphomimics of Rab43, showed decreased TRAPPII GEF mediated exchange. Finally, we designed a Rab11 mutation that maintained TRAPPII-mediated GEF activity while decreasing activity of the Rab11-GEF SH3BP5, providing a tool to dissect Rab11 signalling. Overall, our results provide insight into the GTPase specificity of TRAPPII, and how clinical mutations disrupt this regulation. Here the authors reveal unique structural organization of the mammalian TRAPPII complex, which is critical in regulating membrane trafficking. They find that TRAPPII serves as a guanine nucleotide exchange factor for unexpected Rab GTPases such as Rab43 and Rab19.
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Affiliation(s)
- Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Udit Dalwadi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Daniel S Ziemianowicz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Emily M Martin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada. .,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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17
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Factors affecting yeast ethanol tolerance and fermentation efficiency. World J Microbiol Biotechnol 2020; 36:114. [DOI: 10.1007/s11274-020-02881-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/27/2020] [Indexed: 01/01/2023]
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18
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Cryo-EM structure of C9ORF72-SMCR8-WDR41 reveals the role as a GAP for Rab8a and Rab11a. Proc Natl Acad Sci U S A 2020; 117:9876-9883. [PMID: 32303654 DOI: 10.1073/pnas.2002110117] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A massive intronic hexanucleotide repeat (GGGGCC) expansion in C9ORF72 is a genetic origin of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recently, C9ORF72, together with SMCR8 and WDR41, has been shown to regulate autophagy and function as Rab GEF. However, the precise function of C9ORF72 remains unclear. Here, we report the cryogenic electron microscopy (cryo-EM) structure of the human C9ORF72-SMCR8-WDR41 complex at a resolution of 3.2 Å. The structure reveals the dimeric assembly of a heterotrimer of C9ORF72-SMCR8-WDR41. Notably, the C-terminal tail of C9ORF72 and the DENN domain of SMCR8 play critical roles in the dimerization of the two protomers of the C9ORF72-SMCR8-WDR41 complex. In the protomer, C9ORF72 and WDR41 are joined by SMCR8 without direct interaction. WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix. Interestingly, the prominent structural feature of C9ORF72-SMCR8 resembles that of the FLNC-FNIP2 complex, the GTPase activating protein (GAP) of RagC/D. Structural comparison and sequence alignment revealed that Arg147 of SMCR8 is conserved and corresponds to the arginine finger of FLCN, and biochemical analysis indicated that the Arg147 of SMCR8 is critical to the stimulatory effect of the C9ORF72-SMCR8 complex on Rab8a and Rab11a. Our study not only illustrates the basis of C9ORF72-SMCR8-WDR41 complex assembly but also reveals the GAP activity of the C9ORF72-SMCR8 complex.
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19
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González A, Hall MN, Lin SC, Hardie DG. AMPK and TOR: The Yin and Yang of Cellular Nutrient Sensing and Growth Control. Cell Metab 2020; 31:472-492. [PMID: 32130880 DOI: 10.1016/j.cmet.2020.01.015] [Citation(s) in RCA: 369] [Impact Index Per Article: 92.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The AMPK (AMP-activated protein kinase) and TOR (target-of-rapamycin) pathways are interlinked, opposing signaling pathways involved in sensing availability of nutrients and energy and regulation of cell growth. AMPK (Yin, or the "dark side") is switched on by lack of energy or nutrients and inhibits cell growth, while TOR (Yang, or the "bright side") is switched on by nutrient availability and promotes cell growth. Genes encoding the AMPK and TOR complexes are found in almost all eukaryotes, suggesting that these pathways arose very early during eukaryotic evolution. During the development of multicellularity, an additional tier of cell-extrinsic growth control arose that is mediated by growth factors, but these often act by modulating nutrient uptake so that AMPK and TOR remain the underlying regulators of cellular growth control. In this review, we discuss the evolution, structure, and regulation of the AMPK and TOR pathways and the complex mechanisms by which they interact.
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Affiliation(s)
- Asier González
- Biozentrum, University of Basel, CH4056 Basel, Switzerland
| | - Michael N Hall
- Biozentrum, University of Basel, CH4056 Basel, Switzerland
| | - Sheng-Cai Lin
- School of Life Sciences, Xiamen University, Xiamen, 361102 Fujian, China
| | - D Grahame Hardie
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK.
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20
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de Martín Garrido N, Aylett CHS. Nutrient Signaling and Lysosome Positioning Crosstalk Through a Multifunctional Protein, Folliculin. Front Cell Dev Biol 2020; 8:108. [PMID: 32195250 PMCID: PMC7063858 DOI: 10.3389/fcell.2020.00108] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
FLCN was identified as the gene responsible for Birt-Hogg-Dubé (BHD) syndrome, a hereditary syndrome associated with the appearance of familiar renal oncocytomas. Most mutations affecting FLCN result in the truncation of the protein, and therefore loss of its associated functions, as typical for a tumor suppressor. FLCN encodes the protein folliculin (FLCN), which is involved in numerous biological processes; mutations affecting this protein thus lead to different phenotypes depending on the cellular context. FLCN forms complexes with two large interacting proteins, FNIP1 and FNIP2. Structural studies have shown that both FLCN and FNIPs contain longin and differentially expressed in normal versus neoplastic cells (DENN) domains, typically involved in the regulation of small GTPases. Accordingly, functional studies show that FLCN regulates both the Rag and the Rab GTPases depending on nutrient availability, which are respectively involved in the mTORC1 pathway and lysosomal positioning. Although recent structural studies shed light on the precise mechanism by which FLCN regulates the Rag GTPases, which in turn regulate mTORC1, how FLCN regulates membrane trafficking through the Rab GTPases or the significance of the intriguing FLCN-FNIP-AMPK complex formation are questions that still remain unanswered. We discuss the recent progress in our understanding of FLCN regulation of both growth signaling and lysosomal positioning, as well as future approaches to establish detailed mechanisms to explain the disparate phenotypes caused by the loss of FLCN function and the development of BHD-associated and other tumors.
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Affiliation(s)
| | - Christopher H. S. Aylett
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
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21
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Sanchez-Pulido L, Ponting CP. Hexa-Longin domain scaffolds for inter-Rab signalling. Bioinformatics 2020; 36:990-993. [PMID: 31562761 PMCID: PMC7703760 DOI: 10.1093/bioinformatics/btz739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/26/2019] [Accepted: 09/25/2019] [Indexed: 11/13/2022] Open
Abstract
Summary CPLANE is a protein complex required for assembly and maintenance of primary cilia. It contains several proteins, such as INTU, FUZ, WDPCP, JBTS17 and RSG1 (REM2- and RAB-like small GTPase 1), whose genes are mutated in ciliopathies. Using two contrasting evolutionary analyses, coevolution-based contact prediction and sequence conservation, we first identified the INTU/FUZ heterodimer as a novel member of homologous HerMon (Hermansky-Pudlak syndrome and MON1-CCZ1) complexes. Subsequently, we identified homologous Longin domains that are triplicated in each of these six proteins (MON1A, CCZ1, HPS1, HPS4, INTU and FUZ). HerMon complexes are known to be Rab effectors and Rab GEFs (Guanine nucleotide Exchange Factors) that regulate vesicular trafficking. Consequently, INTU/FUZ, their homologous complex, is likely to act as a GEF during activation of Rab GTPases involved in ciliogenesis. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Chris P Ponting
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
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22
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Bertuzzi M, Tang D, Calligaris R, Vlachouli C, Finaurini S, Sanges R, Goldwurm S, Catalan M, Antonutti L, Manganotti P, Pizzolato G, Pezzoli G, Persichetti F, Carninci P, Gustincich S. A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number-dependent manner. Hum Mutat 2020; 41:807-824. [PMID: 31898848 DOI: 10.1002/humu.23974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 11/16/2019] [Accepted: 12/24/2019] [Indexed: 12/21/2022]
Abstract
Minisatellites, also called variable number of tandem repeats (VNTRs), are a class of repetitive elements that may affect gene expression at multiple levels and have been correlated to disease. Their identification and role as expression quantitative trait loci (eQTL) have been limited by their absence in comparative genomic hybridization and single nucleotide polymorphisms arrays. By taking advantage of cap analysis of gene expression (CAGE), we describe a new example of a minisatellite hosting a transcription start site (TSS) which expression is dependent on the repeat number. It is located in the third intron of the gene nitrogen permease regulator like protein 3 (NPRL3). NPRL3 is a component of the GAP activity toward rags 1 protein complex that inhibits mammalian target of rapamycin complex 1 (mTORC1) activity and it is found mutated in familial focal cortical dysplasia and familial focal epilepsy. CAGE tags represent an alternative TSS identifying TAGNPRL3 messenger RNAs (mRNAs). TAGNPRL3 is expressed in red blood cells both at mRNA and protein levels, it interacts with its protein partner NPRL2 and its overexpression inhibits cell proliferation. This study provides an example of a minisatellite that is both a TSS and an eQTL as well as identifies a new VNTR that may modify mTORC1 activity.
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Affiliation(s)
| | - Dave Tang
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Raffaella Calligaris
- Area of Neuroscience, SISSA, Trieste, Italy.,Department of Medical Sciences, Neurology Unit, University of Trieste, Trieste, Italy
| | | | - Sara Finaurini
- Area of Neuroscience, SISSA, Trieste, Italy.,Department of Health Sciences, Università del Piemonte Orientale and IRCAD, Novara, Italy
| | - Remo Sanges
- Area of Neuroscience, SISSA, Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | | | - Mauro Catalan
- Department of Medical Sciences, Neurology Unit, University of Trieste, Trieste, Italy
| | - Lucia Antonutti
- Department of Medical Sciences, Neurology Unit, University of Trieste, Trieste, Italy
| | - Paolo Manganotti
- Department of Medical Sciences, Neurology Unit, University of Trieste, Trieste, Italy
| | - Gilberto Pizzolato
- Department of Medical Sciences, Neurology Unit, University of Trieste, Trieste, Italy
| | - Gianni Pezzoli
- Parkinson Institute, ASST G. Pini-CTO, ex ICP, Milan, Italy
| | - Francesca Persichetti
- Department of Health Sciences, Università del Piemonte Orientale and IRCAD, Novara, Italy
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.,Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
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23
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Raza A, Pandey MS, Jin Q, Mulder KM. km23-1/DYNLRB1 regulation of MEK/ERK signaling and R-Ras in invasive human colorectal cancer cells. Cell Biol Int 2020; 44:155-165. [PMID: 31393067 PMCID: PMC7007335 DOI: 10.1002/cbin.11215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/03/2019] [Indexed: 01/25/2023]
Abstract
We previously found that km23-1/DYNLRB1 is required for transforming growth factor-β (TGFβ) production through Ras/ERK pathways in TGFβ-sensitive epithelial cells and in human colorectal cancer (CRC) cells. Here we demonstrate that km23-1/DYNLRB1 is required for mitogen-activated protein kinase kinase (MEK) activation in human CRC cells, detected by km23-1/DYNLRB1-siRNA inhibition of phospho-(p)-MEK immunostaining in RKO cells. Furthermore, we show that CRISPR-Cas9 knock-out (KO) of km23-1/DYNLRB1 reduced cell migration in two additional CRC models, HCT116 and DLD-1. Of interest, in contrast to our previous work showing that dynein motor activity was required for TGFβ-mediated nuclear translocation of Smad2, in the current report, we demonstrate for the first time that disruption of dynein motor activity did not reduce TGFβ-mediated activation of MEK1/2 or c-Jun N-terminal kinase (JNK). Moreover, size exclusion chromatography of RKO cell lysates revealed that B-Raf, extracellular signal-regulated kinase (ERK), and p-ERK were not present in the large molecular weight fractions containing dynein holocomplex components. Furthermore, sucrose gradient fractionation of cell lysates from both HCT116 and CBS CRC cells demonstrated that km23-1/DYNLRB1 co-sedimented with Ras, p-ERK, and ERK in fractions that did not contain components of holo-dynein. Thus, km23-1/DYNLRB1 may be associated with activated Ras/ERK signaling complexes in cell compartments that do not contain the dynein holoprotein complex, suggesting dynein-independent km23-1/DYNLRB1 functions in Ras/ERK signaling. Finally, of the Ras isoforms, R-Ras is most often associated with cell migration, adhesion, and protrusive activity. Here, we show that a significant fraction of km23-1/DYNLRB1 and RRas wase co-localized at the protruding edges of migrating HCT116 cells, suggesting an important role for the km23-1/DYNLRB1-R-Ras complex in CRC invasion.
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Affiliation(s)
| | | | | | - Kathleen M. Mulder
- To whom correspondence should be addressed: Dr. Kathleen M. Mulder, Professor, Department of Biochemistry and Molecular Biology-MC H171, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, Telephone: 1-717-531-6789; FAX: 1-717-531-0939
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24
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Anandapadamanaban M, Masson GR, Perisic O, Berndt A, Kaufman J, Johnson CM, Santhanam B, Rogala KB, Sabatini DM, Williams RL. Architecture of human Rag GTPase heterodimers and their complex with mTORC1. Science 2019; 366:203-210. [PMID: 31601764 PMCID: PMC6795536 DOI: 10.1126/science.aax3939] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/03/2019] [Indexed: 12/11/2022]
Abstract
The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag heterodimers is critical for their association with mTORC1. Our cryo-electron microscopy structure of RagA/RagC in complex with mTORC1 shows the details of RagA/RagC binding to the RAPTOR subunit of mTORC1 and explains why only the RagAGTP/RagCGDP nucleotide state binds mTORC1. Previous kinetic studies suggested that GTP binding to one Rag locks the heterodimer to prevent GTP binding to the other. Our crystal structures and dynamics of RagA/RagC show the mechanism for this locking and explain how oncogenic hotspot mutations disrupt this process. In contrast to allosteric activation by RHEB, Rag heterodimer binding does not change mTORC1 conformation and activates mTORC1 by targeting it to lysosomes.
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Affiliation(s)
| | - Glenn R Masson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Olga Perisic
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Alex Berndt
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | | | - Kacper B Rogala
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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25
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Gerondopoulos A, Strutt H, Stevenson NL, Sobajima T, Levine TP, Stephens DJ, Strutt D, Barr FA. Planar Cell Polarity Effector Proteins Inturned and Fuzzy Form a Rab23 GEF Complex. Curr Biol 2019; 29:3323-3330.e8. [PMID: 31564489 PMCID: PMC6864590 DOI: 10.1016/j.cub.2019.07.090] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 01/12/2023]
Abstract
A subset of Rab GTPases have been implicated in cilium formation in cultured mammalian cells [1-6]. Rab11 and Rab8, together with their GDP-GTP exchange factors (GEFs), TRAPP-II and Rabin8, promote recruitment of the ciliary vesicle to the mother centriole and its subsequent maturation, docking, and fusion with the cell surface [2-5]. Rab23 has been linked to cilium formation and membrane trafficking at mature cilia [1, 7, 8]; however, the identity of the GEF pathway activating Rab23, a member of the Rab7 subfamily of Rabs, remains unclear. Longin-domain-containing complexes have been shown to act as GEFs for Rab7 subfamily GTPases [9-12]. Here, we show that Inturned and Fuzzy, proteins previously implicated as planar cell polarity (PCP) effectors and in developmentally regulated cilium formation [13, 14], contain multiple longin domains characteristic of the Mon1-Ccz1 family of Rab7 GEFs and form a specific Rab23 GEF complex. In flies, loss of Rab23 function gave rise to defects in planar-polarized trichome formation consistent with this biochemical relationship. In cultured human and mouse cells, Inturned and Fuzzy localized to the basal body and proximal region of cilia, and cilium formation was compromised by depletion of either Inturned or Fuzzy. Cilium formation arrested after docking of the ciliary vesicle to the mother centriole but prior to axoneme elongation and fusion of the ciliary vesicle and plasma membrane. These findings extend the family of longin domain GEFs and define a molecular activity linking Rab23-regulated membrane traffic to cilia and planar cell polarity.
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Affiliation(s)
- Andreas Gerondopoulos
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Helen Strutt
- Department of Biomedical Science, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Nicola L Stevenson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Tomoaki Sobajima
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Tim P Levine
- Institute of Ophthalmology, University College London, 11-43 Bath St., London EC1V 9EL, UK
| | - David J Stephens
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - David Strutt
- Department of Biomedical Science, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Francis A Barr
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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26
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Allosteric regulation of a prokaryotic small Ras-like GTPase contributes to cell polarity oscillations in bacterial motility. PLoS Biol 2019; 17:e3000459. [PMID: 31560685 PMCID: PMC6785124 DOI: 10.1371/journal.pbio.3000459] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/09/2019] [Accepted: 09/04/2019] [Indexed: 11/25/2022] Open
Abstract
Mutual gliding motility A (MglA), a small Ras-like GTPase; Mutual gliding motility B (MglB), its GTPase activating protein (GAP); and Required for Motility Response Regulator (RomR), a protein that contains a response regulator receiver domain, are major components of a GTPase-dependent biochemical oscillator that drives cell polarity reversals in the bacterium Myxococcus xanthus. We report the crystal structure of a complex of M. xanthus MglA and MglB, which reveals that the C-terminal helix (Ct-helix) from one protomer of the dimeric MglB binds to a pocket distal to the active site of MglA. MglB increases the GTPase activity of MglA by reorientation of key catalytic residues of MglA (a GAP function) combined with allosteric regulation of nucleotide exchange by the Ct-helix (a guanine nucleotide exchange factor [GEF] function). The dual GAP-GEF activities of MglB accelerate the rate of GTP hydrolysis over multiple enzymatic cycles. Consistent with its GAP and GEF activities, MglB interacts with MglA bound to either GTP or GDP. The regulation is essential for cell polarity, because deletion of the Ct-helix causes bipolar localization of MglA, MglB, and RomR, thereby causing reversal defects in M. xanthus. A bioinformatics analysis reveals the presence of Ct-helix in homologues of MglB in other bacterial phyla, suggestive of the prevalence of the allosteric mechanism among other prokaryotic small Ras-like GTPases. A study on the mechanism of cell polarity oscillations in Myxococcus xanthus reveals a novel allosteric regulatory mechanism for a small Ras-like GTPase. The motility protein MglB is the first example of both GTPase activating protein (GAP) and guanosine nucleotide exchange factor (GEF) activities being integrated into a single regulator of the small Ras-like GTPase MglA.
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Rasheed N, Lima TB, Mercaldi GF, Nascimento AFZ, Silva ALS, Righetto GL, Bar-Peled L, Shen K, Sabatini DM, Gozzo FC, Aparicio R, Smetana JHC. C7orf59/LAMTOR4 phosphorylation and structural flexibility modulate Ragulator assembly. FEBS Open Bio 2019; 9:1589-1602. [PMID: 31314152 PMCID: PMC6722880 DOI: 10.1002/2211-5463.12700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/28/2019] [Accepted: 07/15/2019] [Indexed: 01/09/2023] Open
Abstract
Ragulator is a pentamer composed of p18, MP1, p14, C7orf59, and hepatitis B virus X‐interacting protein (HBXIP; LAMTOR 1—5) which acts as a lysosomal scaffold of the Rag GTPases in the amino acid sensitive branch of TORC1 signaling. Here, we present the crystal structure of human HBXIP‐C7orf59 dimer (LAMTOR 4/5) at 2.9 Å and identify a phosphorylation site on C7orf59 which modulates its interaction with p18. Additionally, we demonstrate the requirement of HBXIP‐C7orf59 to stabilize p18 and allow further binding of MP1‐p14. The structure of the dimer revealed an unfolded N terminus in C7orf59 (residues 1–15) which was shown to be essential for p18 binding. Full‐length p18 does not interact stably with MP1‐p14 in the absence of HBXIP‐C7orf59, but deletion of p18 residues 108–161 rescues MP1‐p14 binding. C7orf59 was phosphorylated by protein kinase A (PKA) in vitro and mutation of the conserved Ser67 residue to aspartate prevented phosphorylation and negatively affected the C7orf59 interaction with p18 both in cell culture and in vitro. C7orf59 Ser67 was phosphorylated in human embryonic kidney 293T cells. PKA activation with forskolin induced dissociation of p18 from C7orf59, which was prevented by the PKA inhibitor H‐89. Our results highlight the essential role of HBXIP‐C7orf59 dimer as a nucleator of pentameric Ragulator and support a sequential model of Ragulator assembly in which HBXIP‐C7orf59 binds and stabilizes p18 which allows subsequent binding of MP1‐p14.
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Affiliation(s)
- Nadia Rasheed
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Institute of Biology, University of Campinas, Brazil
| | - Tatiani B Lima
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Institute of Chemistry, University of Campinas, Brazil
| | - Gustavo F Mercaldi
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Andrey F Z Nascimento
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Ana L S Silva
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Germanna L Righetto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Liron Bar-Peled
- The Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Kuang Shen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David M Sabatini
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fabio C Gozzo
- Institute of Chemistry, University of Campinas, Brazil
| | | | - Juliana H C Smetana
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
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28
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Cherfils J. Encoding Allostery in mTOR Signaling: The Structure of the Rag GTPase/Ragulator Complex. Mol Cell 2019; 68:823-824. [PMID: 29220648 DOI: 10.1016/j.molcel.2017.11.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this issue of Molecular Cell, Su et al. (2017) describe the structure of the Rag/Ragulator complex, a key relay in nutrient sensing by mTOR. The structure sheds new light on how signals are conveyed from the lysosome to mTOR.
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Affiliation(s)
- Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS and Ecole Normale Supérieure Paris-Saclay, Cachan, France.
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29
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Deretic D, Lorentzen E, Fresquez T. The ins and outs of the Arf4-based ciliary membrane-targeting complex. Small GTPases 2019; 12:1-12. [PMID: 31068062 DOI: 10.1080/21541248.2019.1616355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The small GTPase Arf4-based ciliary membrane-targeting complex recognizes specific targeting signals within sensory receptors and regulates their directed movement to primary cilia. Activated Arf4 directly binds the VxPx ciliary-targeting signal (CTS) of the light-sensing receptor rhodopsin. Recent findings revealed that at the trans-Golgi, marked by the small GTPase Rab6, activated Arf4 forms a functional complex with rhodopsin and the Arf guanine nucleotide exchange factor (GEF) GBF1, providing positive feedback that drives further Arf4 activation in ciliary trafficking. Arf4 function is conserved across diverse cell types; however, it appears that not all its aspects are conserved across species, as mouse Arf4 is a natural mutant in the conserved α3 helix, which is essential for its interaction with rhodopsin. Generally, activated Arf4 regulates the assembly of the targeting nexus containing the Arf GAP ASAP1 and the Rab11a-FIP3-Rabin8 dual effector complex, which controls the assembly of the highly conserved Rab11a-Rabin8-Rab8 ciliary-targeting module. It was recently found that this module interacts with the R-SNARE VAMP7, likely in its activated, c-Src-phosphorylated form. Rab11 and Rab8 bind VAMP7 regulatory longin domain (LD), whereas Rabin8 interacts with the SNARE domain, capturing VAMP7 for delivery to the ciliary base and subsequent pairing with the cognate SNAREs syntaxin 3 and SNAP-25. This review will focus on the implications of these novel findings that further illuminate the role of well-ordered Arf and Rab interaction networks in targeting of sensory receptors to primary cilia. Abbreviations: CTS: Ciliary-Targeting Signal; GAP: GTPase Activating Protein; GEF: Guanine Nucleotide Exchange Factor; RTC(s), Rhodopsin Transport Carrier(s); SNARE: Soluble N-ethylmaleimide-sensitive Factor Attachment Protein Receptor; TGN: Trans-Golgi Network.
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Affiliation(s)
- Dusanka Deretic
- Departments of Surgery, Division of Ophthalmology, University of New Mexico , Albuquerque, NM, USA.,Cell Biology and Physiology, University of New Mexico , Albuquerque, NM, USA
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Theresa Fresquez
- Departments of Surgery, Division of Ophthalmology, University of New Mexico , Albuquerque, NM, USA
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Lamber EP, Siedenburg AC, Barr FA. Rab regulation by GEFs and GAPs during membrane traffic. Curr Opin Cell Biol 2019; 59:34-39. [PMID: 30981180 DOI: 10.1016/j.ceb.2019.03.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/06/2019] [Indexed: 01/05/2023]
Abstract
Rab GTPases and their regulatory proteins play a crucial role in vesicle-mediated membrane trafficking. During vesicle membrane tethering Rab GTPases are activated by GEFs (guanine nucleotide exchange factors) and then inactivated by GAPs (GTPase activating proteins). Recent evidence shows that in addition to activating and inactivating Rab GTPases, both Rab GEFs and GAPs directly contribute to membrane tethering events during vesicle traffic. Other studies have extended the range of processes, in which Rabs function, and revealed roles for Rabs and their GAPs in the regulation of autophagy. Here, we will discuss these advances and the emerging relationship between the domain architectures of Rab GEFs and vesicle coat protein complexes linked with GTPases of the Sar, ARF and Arl families in animal cells.
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Affiliation(s)
- Ekaterina P Lamber
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Francis A Barr
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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31
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Kandachar V, Tam BM, Moritz OL, Deretic D. An interaction network between the SNARE VAMP7 and Rab GTPases within a ciliary membrane-targeting complex. J Cell Sci 2018; 131:jcs.222034. [PMID: 30404838 DOI: 10.1242/jcs.222034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
The Arf4-rhodopsin complex (mediated by the VxPx motif in rhodopsin) initiates expansion of vertebrate rod photoreceptor cilia-derived light-sensing organelles through stepwise assembly of a conserved trafficking network. Here, we examine its role in the sorting of VAMP7 (also known as TI-VAMP) - an R-SNARE possessing a regulatory longin domain (LD) - into rhodopsin transport carriers (RTCs). During RTC formation and trafficking, VAMP7 colocalizes with the ciliary cargo rhodopsin and interacts with the Rab11-Rabin8-Rab8 trafficking module. Rab11 and Rab8 bind the VAMP7 LD, whereas Rabin8 (also known as RAB3IP) interacts with the SNARE domain. The Arf/Rab11 effector FIP3 (also known as RAB11FIP3) regulates VAMP7 access to Rab11. At the ciliary base, VAMP7 forms a complex with the cognate SNAREs syntaxin 3 and SNAP-25. When expressed in transgenic animals, a GFP-VAMP7ΔLD fusion protein and a Y45E phosphomimetic mutant colocalize with endogenous VAMP7. The GFP-VAMP7-R150E mutant displays considerable localization defects that imply an important role of the R-SNARE motif in intracellular trafficking, rather than cognate SNARE pairing. Our study defines the link between VAMP7 and the ciliary targeting nexus that is conserved across diverse cell types, and contributes to general understanding of how functional Arf and Rab networks assemble SNAREs in membrane trafficking.
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Affiliation(s)
- Vasundhara Kandachar
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Beatrice M Tam
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC V5Z 3N9, Canada
| | - Orson L Moritz
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC V5Z 3N9, Canada
| | - Dusanka Deretic
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM 87131, USA .,Cell Biology and Physiology, University of New Mexico, Albuquerque, NM 87131, USA
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Amino acids stimulate the endosome-to-Golgi trafficking through Ragulator and small GTPase Arl5. Nat Commun 2018; 9:4987. [PMID: 30478271 PMCID: PMC6255761 DOI: 10.1038/s41467-018-07444-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/31/2018] [Indexed: 11/22/2022] Open
Abstract
The endosome-to-Golgi or endocytic retrograde trafficking pathway is an important post-Golgi recycling route. Here we show that amino acids (AAs) can stimulate the retrograde trafficking and regulate the cell surface localization of certain Golgi membrane proteins. By testing components of the AA-stimulated mTORC1 signaling pathway, we demonstrate that SLC38A9, v-ATPase and Ragulator, but not Rag GTPases and mTORC1, are essential for the AA-stimulated trafficking. Arl5, an ARF-like family small GTPase, interacts with Ragulator in an AA-regulated manner and both Arl5 and its effector, the Golgi-associated retrograde protein complex (GARP), are required for the AA-stimulated trafficking. We have therefore identified a mechanistic connection between the nutrient signaling and the retrograde trafficking pathway, whereby SLC38A9 and v-ATPase sense AA-sufficiency and Ragulator might function as a guanine nucleotide exchange factor to activate Arl5, which, together with GARP, a tethering factor, probably facilitates the endosome-to-Golgi trafficking. Amino acid levels are known to regulate anabolic and catabolic pathways. Here, the authors report that amino acids also affect membrane trafficking by stimulating endosome-to-Golgi retrograde trafficking and regulating cell surface localization of certain Golgi proteins through Ragulator and Arl5.
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33
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Morris C, Foster OK, Handa S, Peloza K, Voss L, Somhegyi H, Jian Y, Vo MV, Harp M, Rambo FM, Yang C, Hermann GJ. Function and regulation of the Caenorhabditis elegans Rab32 family member GLO-1 in lysosome-related organelle biogenesis. PLoS Genet 2018; 14:e1007772. [PMID: 30419011 PMCID: PMC6268011 DOI: 10.1371/journal.pgen.1007772] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 11/30/2018] [Accepted: 10/17/2018] [Indexed: 02/07/2023] Open
Abstract
Cell type-specific modifications of conventional endosomal trafficking pathways lead to the formation of lysosome-related organelles (LROs). C. elegans gut granules are intestinally restricted LROs that coexist with conventional degradative lysosomes. The formation of gut granules requires the Rab32 family member GLO-1. We show that the loss of glo-1 leads to the mistrafficking of gut granule proteins but does not significantly alter conventional endolysosome biogenesis. GLO-3 directly binds to CCZ-1 and they both function to promote the gut granule association of GLO-1, strongly suggesting that together, GLO-3 and CCZ-1 activate GLO-1. We found that a point mutation in GLO-1 predicted to spontaneously activate, and function independently of it guanine nucleotide exchange factor (GEF), localizes to gut granules and partially restores gut granule protein localization in ccz-1(-) and glo-3(-) mutants. CCZ-1 forms a heterodimeric complex with SAND-1(MON1), which does not function in gut granule formation, to activate RAB-7 in trafficking pathways to conventional lysosomes. Therefore, our data suggest a model whereby the function of a Rab GEF can be altered by subunit exchange. glo-3(-) mutants, which retain low levels of GLO-3 activity, generate gut granules that lack GLO-1 and improperly accumulate RAB-7 in a SAND-1 dependent process. We show that GLO-1 and GLO-3 restrict the distribution of RAB-7 to conventional endolysosomes, providing insights into the segregation of pathways leading to conventional lysosomes and LROs.
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Affiliation(s)
- Caitlin Morris
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Olivia K. Foster
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Simran Handa
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Kimberly Peloza
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Laura Voss
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Hannah Somhegyi
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Youli Jian
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - My Van Vo
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Marie Harp
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Fiona M. Rambo
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Chonglin Yang
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Greg J. Hermann
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
- * E-mail:
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34
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Abstract
Background The protein kinase Target Of Rapamycin (TOR) is a nexus for the regulation of eukaryotic cell growth. TOR assembles into one of two distinct signalling complexes, TOR complex 1 (TORC1) and TORC2 (mTORC1/2 in mammals), with a set of largely non-overlapping protein partners. (m)TORC1 activation occurs in response to a series of stimuli relevant to cell growth, including nutrient availability, growth factor signals and stress, and regulates much of the cell's biosynthetic activity, from proteins to lipids, and recycling through autophagy. mTORC1 regulation is of great therapeutic significance, since in humans many of these signalling complexes, alongside subunits of mTORC1 itself, are implicated in a wide variety of pathophysiologies, including multiple types of cancer, neurological disorders, neurodegenerative diseases and metabolic disorders including diabetes. Methodology Recent years have seen numerous structures determined of (m)TOR, which have provided mechanistic insight into (m)TORC1 activation in particular, however the integration of cellular signals occurs upstream of the kinase and remains incompletely understood. Here we have collected and analysed in detail as many as possible of the molecular and structural studies which have shed light on (m)TORC1 repression, activation and signal integration. Conclusions A molecular understanding of this signal integration pathway is required to understand how (m)TORC1 activation is reconciled with the many diverse and contradictory stimuli affecting cell growth. We discuss the current level of molecular understanding of the upstream components of the (m)TORC1 signalling pathway, recent progress on this key biochemical frontier, and the future studies necessary to establish a mechanistic understanding of this master-switch for eukaryotic cell growth.
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Affiliation(s)
- Kailash Ramlaul
- Section of Structural Biology, Department of Medicine, Imperial College London, SW7 2AZ, UK
| | - Christopher H S Aylett
- Section of Structural Biology, Department of Medicine, Imperial College London, SW7 2AZ, UK
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35
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Shen K, Huang RK, Brignole EJ, Condon KJ, Valenstein ML, Chantranupong L, Bomaliyamu A, Choe A, Hong C, Yu Z, Sabatini DM. Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes. Nature 2018; 556:64-69. [PMID: 29590090 PMCID: PMC5975964 DOI: 10.1038/nature26158] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 02/16/2018] [Indexed: 12/22/2022]
Abstract
Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase-activating protein (GAP) for RAGA; loss of GATOR1 desensitizes mTORC1 signalling to nutrient starvation. GATOR1 components have no sequence homology to other proteins, so the function of GATOR1 at the molecular level is currently unknown. Here we used cryo-electron microscopy to solve structures of GATOR1 and GATOR1-Rag GTPases complexes. GATOR1 adopts an extended architecture with a cavity in the middle; NPRL2 links DEPDC5 and NPRL3, and DEPDC5 contacts the Rag GTPase heterodimer. Biochemical analyses reveal that our GATOR1-Rag GTPases structure is inhibitory, and that at least two binding modes must exist between the Rag GTPases and GATOR1. Direct interaction of DEPDC5 with RAGA inhibits GATOR1-mediated stimulation of GTP hydrolysis by RAGA, whereas weaker interactions between the NPRL2-NPRL3 heterodimer and RAGA execute GAP activity. These data reveal the structure of a component of the nutrient-sensing mTORC1 pathway and a non-canonical interaction between a GAP and its substrate GTPase.
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Affiliation(s)
- Kuang Shen
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Rick K. Huang
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Edward J. Brignole
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kendall J. Condon
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Max L. Valenstein
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Lynne Chantranupong
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Aimaiti Bomaliyamu
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Abigail Choe
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Chuan Hong
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zhiheng Yu
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - David M. Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
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Abstract
All organisms must adapt to ever-changing environmental conditions and accordingly have evolved diverse signal transduction systems. In bacteria, the most abundant networks are built around the two-component signal transduction systems that include histidine kinases and receiver domains. In contrast, eukaryotic signal transduction is dominated by serine/threonine/tyrosine protein kinases. Both of these systems are also found in archaea, but they are not as common and diversified as their bacterial and eukaryotic counterparts, suggesting the possibility that archaea have evolved other, still uncharacterized signal transduction networks. Here we propose a role for KaiC family ATPases, known to be key components of the circadian clock in cyanobacteria, in archaeal signal transduction. The KaiC family is notably expanded in most archaeal genomes, and although most of these ATPases remain poorly characterized, members of the KaiC family have been shown to control archaellum assembly and have been found to be a stable component of the gas vesicle system in Halobacteria Computational analyses described here suggest that KaiC-like ATPases and their homologues with inactivated ATPase domains are involved in many other archaeal signal transduction pathways and comprise major hubs of complex regulatory networks. We predict numerous input and output domains that are linked to KaiC-like proteins, including putative homologues of eukaryotic DEATH domains that could function as adapters in archaeal signaling networks. We further address the relationships of the archaeal family of KaiC homologues to the bona fide KaiC of cyanobacteria and implications for the existence of a KaiC-based circadian clock apparatus in archaea.IMPORTANCE Little is currently known about signal transduction pathways in Archaea Recent studies indicate that KaiC-like ATPases, known as key components of the circadian clock apparatus in cyanobacteria, are involved in the regulation of archaellum assembly and, likely, type IV pili and the gas vesicle system in Archaea We performed comprehensive comparative genomic analyses of the KaiC family. A vast protein interaction network was revealed, with KaiC family proteins as hubs for numerous input and output components, many of which are shared with two-component signal transduction systems. Putative KaiC-based signal transduction systems are predicted to regulate the activities of membrane-associated complexes and individual proteins, such as signal recognition particle and membrane transporters, and also could be important for oxidative stress response regulation. KaiC-centered signal transduction networks are predicted to play major roles in archaeal physiology, and this work is expected to stimulate their experimental characterization.
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Yonehara R, Nada S, Nakai T, Nakai M, Kitamura A, Ogawa A, Nakatsumi H, Nakayama KI, Li S, Standley DM, Yamashita E, Nakagawa A, Okada M. Structural basis for the assembly of the Ragulator-Rag GTPase complex. Nat Commun 2017; 8:1625. [PMID: 29158492 PMCID: PMC5696360 DOI: 10.1038/s41467-017-01762-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/13/2017] [Indexed: 12/31/2022] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) plays a central role in regulating cell growth and metabolism by responding to cellular nutrient conditions. The activity of mTORC1 is controlled by Rag GTPases, which are anchored to lysosomes via Ragulator, a pentameric protein complex consisting of membrane-anchored p18/LAMTOR1 and two roadblock heterodimers. Here we report the crystal structure of Ragulator in complex with the roadblock domains of RagA-C, which helps to elucidate the molecular basis for the regulation of Rag GTPases. In the structure, p18 wraps around the three pairs of roadblock heterodimers to tandemly assemble them onto lysosomes. Cellular and in vitro analyses further demonstrate that p18 is required for Ragulator-Rag GTPase assembly and amino acid-dependent activation of mTORC1. These results establish p18 as a critical organizing scaffold for the Ragulator-Rag GTPase complex, which may provide a platform for nutrient sensing on lysosomes. mTORC1 activity is controlled through Rag GTPases, which are anchored to the lysosome through the Ragulator. Here, the authors give molecular insights into Ragulator-Rag GTPase assembly and present the crystal structures of the Ragulator alone and in complex with the RagA-C roadblock domains.
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Affiliation(s)
- Ryo Yonehara
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shigeyuki Nada
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomokazu Nakai
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masahiro Nakai
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ayaka Kitamura
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Akira Ogawa
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hirokazu Nakatsumi
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Keiichi I Nakayama
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Songling Li
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Daron M Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eiki Yamashita
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Atsushi Nakagawa
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Masato Okada
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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38
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Ma Y, Silveri L, LaCava J, Dokudovskaya S. Tumor suppressor NPRL2 induces ROS production and DNA damage response. Sci Rep 2017; 7:15311. [PMID: 29127423 PMCID: PMC5681675 DOI: 10.1038/s41598-017-15497-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/23/2017] [Indexed: 02/07/2023] Open
Abstract
The SEA/GATOR complex is an essential regulator of the mTORC1 pathway. In mammals the GATOR1 complex is composed of the proteins DEPDC5, NPRL2 and NPRL3. GATOR1 serves as an mTORC1 inhibitor and activates the mTORC1-modulating RagA GTPase. However, several GATOR members have mTORC1 independent functions. Here we characterize mammalian cells overexpressing the GATOR1 component NPRL2. We demonstrate that, in the cells with active p53, ectopic expression of NPRL2 induces NOX2-dependent production of reactive oxygen species and DNA damage. Overexpressed NPRL2 accumulates in the nucleus, together with apoptosis-inducing factor (AIF). These events are accompanied by phosphorylation of p53, activation of a DNA-damage response and cell cycle arrest in G1 phase, followed by apoptosis. In the cells negative for active p53, NPRL2 ectopic expression leads to activation of CHK1 or CHK2 kinases and cell cycle arrest in S or G2/M phases. Combined, these results demonstrate a new role for the NPRL2, distinct from its function in mTORC1 regulation.
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Affiliation(s)
- Yinxing Ma
- CNRS UMR 8126, Université Paris-Sud 11, Institut Gustave Roussy, 114, rue Edouard Vaillant, 94805, Villejuif, France
| | - Licia Silveri
- CNRS UMR 8126, Université Paris-Sud 11, Institut Gustave Roussy, 114, rue Edouard Vaillant, 94805, Villejuif, France
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA.,Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, 10016, USA
| | - Svetlana Dokudovskaya
- CNRS UMR 8126, Université Paris-Sud 11, Institut Gustave Roussy, 114, rue Edouard Vaillant, 94805, Villejuif, France.
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39
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Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1. Nat Commun 2017; 8:1394. [PMID: 29123114 PMCID: PMC5680233 DOI: 10.1038/s41467-017-01567-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/29/2017] [Indexed: 01/26/2023] Open
Abstract
Amino acid-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) is mediated by Rag GTPases, which are recruited to the lysosome by the Ragulator complex consisting of p18, MP1, p14, HBXIP and C7orf59; however, the molecular mechanism is elusive. Here, we report the crystal structure of Ragulator, in which p18 wraps around the MP1-p14 and C7orf59-HBXIP heterodimers and the interactions of p18 with MP1, C7orf59, and HBXIP are essential for the assembly of Ragulator. There are two binding sites for the Roadblock domains of Rag GTPases: helix α1 of p18 and the two helices side of MP1-p14. The interaction of Ragulator with Rag GTPases is required for their cellular co-localization and can be competitively inhibited by C17orf59. Collectively, our data indicate that Ragulator functions as a scaffold to recruit Rag GTPases to lysosomal membrane in mTORC1 signaling. Activated Rag GTPases recruit mTORC1 to lysosomes. Here the authors present the crystal structure of the Ragulator complex and identify the binding sites for the Roadblock domains of Rag GTPases, which gives insights how Rag GTPases are tethered to the lysosomal membrane.
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40
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Shen K, Choe A, Sabatini DM. Intersubunit Crosstalk in the Rag GTPase Heterodimer Enables mTORC1 to Respond Rapidly to Amino Acid Availability. Mol Cell 2017; 68:552-565.e8. [PMID: 29056322 PMCID: PMC5674802 DOI: 10.1016/j.molcel.2017.09.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/14/2017] [Accepted: 09/19/2017] [Indexed: 01/03/2023]
Abstract
mTOR complex I (mTORC1) is a central growth regulator that senses amino acids through a pathway that converges on the Rag GTPases, an obligate heterodimer of two related GTPases. Despite their central role in amino acid sensing, it is unknown why the Rag GTPases are heterodimeric and whether their subunits communicate with each other. Here, we find that the binding of guanosine triphosphate (GTP) to one subunit inhibits the binding and induces the hydrolysis of GTP by the other. This intersubunit communication pushes the Rag GTPases into either of two stable configurations, which represent active "on" or "off" states that interconvert via transient intermediates. Subunit coupling confers on the mTORC1 pathway its capacity to respond rapidly to the amino acid level. Thus, the dynamic response of mTORC1 requires intersubunit communication by the Rag GTPases, providing a rationale for why they exist as a dimer and revealing a distinct mode of control for a GTP-binding protein.
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Affiliation(s)
- Kuang Shen
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Abigail Choe
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA.
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41
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Nguyen TP, Frank AR, Jewell JL. Amino acid and small GTPase regulation of mTORC1. CELLULAR LOGISTICS 2017; 7:e1378794. [PMID: 29296509 PMCID: PMC5739091 DOI: 10.1080/21592799.2017.1378794] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 11/03/2022]
Abstract
The mammalian target of rapamycin (mTOR) is an evolutionarily conserved serine/threonine kinase that belongs to the phosphatidylinositol 3-kinase-related kinase (PIKK) family. mTOR is the catalytic subunit of mTOR complex 1 (mTORC1), which integrates multiple environmental signals to control cell growth and metabolism. Nutrients, specifically amino acids, are the most potent stimuli for mTORC1 activation. Multiple studies have focused on how leucine and arginine activate mTORC1 through the Rag GTPases, with mechanistic details slowly emerging. Recently, a Rag GTPase-independent glutamine signaling pathway to mTORC1 has been identified, suggesting that mTORC1 is differentially regulated through distinct pathways by specific amino acids. In this review, we summarize our current understanding of how amino acids modulate mTORC1, and the role of other small GTPases in the regulation of mTORC1 activity.
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Affiliation(s)
- Thu P Nguyen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Anderson R Frank
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Jenna L Jewell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX USA
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42
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Abstract
Rab proteins are the major regulators of vesicular trafficking in eukaryotic cells. Their activity can be tightly controlled within cells: Regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), they switch between an active GTP-bound state and an inactive GDP-bound state, interacting with downstream effector proteins only in the active state. Additionally, they can bind to membranes via C-terminal prenylated cysteine residues and they can be solubilized and shuttled between membranes by chaperone-like molecules called GDP dissociation inhibitors (GDIs). In this review we give an overview of Rab proteins with a focus on the current understanding of their regulation by GEFs, GAPs and GDI.
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Affiliation(s)
- Matthias P Müller
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Roger S Goody
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
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43
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González A, Hall MN. Nutrient sensing and TOR signaling in yeast and mammals. EMBO J 2017; 36:397-408. [PMID: 28096180 DOI: 10.15252/embj.201696010] [Citation(s) in RCA: 477] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/12/2016] [Accepted: 12/15/2016] [Indexed: 01/13/2023] Open
Abstract
Coordinating cell growth with nutrient availability is critical for cell survival. The evolutionarily conserved TOR (target of rapamycin) controls cell growth in response to nutrients, in particular amino acids. As a central controller of cell growth, mTOR (mammalian TOR) is implicated in several disorders, including cancer, obesity, and diabetes. Here, we review how nutrient availability is sensed and transduced to TOR in budding yeast and mammals. A better understanding of how nutrient availability is transduced to TOR may allow novel strategies in the treatment for mTOR-related diseases.
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44
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Architecture and mechanism of the late endosomal Rab7-like Ypt7 guanine nucleotide exchange factor complex Mon1-Ccz1. Nat Commun 2017; 8:14034. [PMID: 28051187 PMCID: PMC5216073 DOI: 10.1038/ncomms14034] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/23/2016] [Indexed: 01/21/2023] Open
Abstract
The Mon1–Ccz1 complex (MC1) is the guanine nucleotide exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 and is required for endosomal maturation and fusion at the vacuole/lysosome. Here we present the overall architecture of MC1 from Chaetomium thermophilum, and in combining biochemical studies and mutational analysis in yeast, we identify the domains required for catalytic activity, complex assembly and localization of MC1. The crystal structure of a catalytic MC1 core complex bound to Ypt7 provides mechanistic insight into its function. We pinpoint the determinants that allow for a discrimination of the Rab7-like Ypt7 over the Rab5-like Vps21, which are both located on the same membrane. MC1 shares structural similarities with the TRAPP complex, but employs a novel mechanism to promote nucleotide exchange that utilizes a conserved lysine residue of Ypt7, which is inserted upon MC1 binding into the nucleotide-binding pocket of Ypt7 and contributes to specificity. The Mon1-Ccz1 (MC1) complex is a Rab guanine nucleotide exchange factor (RabGEF) for Ypt7/Rab7 important for endosomal maturation. Here the authors present the biochemical and structural characterization of MC1, elucidating its catalytic mechanism and showing that MC1 represents novel class of RabGEFs.
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45
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Overexpression of smORF YNR034W-A/EGO4 in Saccharomyces cerevisiae increases the fermentative efficiency of Agave tequilana Weber must. ACTA ACUST UNITED AC 2017; 44:63-74. [DOI: 10.1007/s10295-016-1871-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/09/2016] [Indexed: 10/20/2022]
Abstract
Abstract
Fermentative processes are widely used to produce food, beverages and biofuels. Saccharomyces cerevisiae is an efficient ethanol-producing microorganism. However, a concentration of high ethanol and other metabolites can affect yeast viability and decrease the ethanol yield. Many studies have focused on improving the fermentative efficiency, mostly through the genetic engineering of genes that have a direct impact on specific metabolic pathways. In the present study, we characterized a small open reading frame encoding a protein with an unknown function and biological role termed YNR034W-A. We analyzed the expression profile of the YNR034W-A gene during growth and glucose treatment, finding that it is expressed during the diauxic shift and stationary phase and is negatively regulated by glucose. We overexpressed the YNR034W-A gene in the BY4741 laboratory strain and a wild-type yeast strain (AR5) isolated during the Tequila fermentation process. Transformant derivatives of the AR5 strain showed an improved fermentative efficiency during fermentation of Agave tequilana Weber juice. We suggest that the improved fermentative efficiency is the result of a higher stress tolerance response in the YNR034W-A overexpressing transformant.
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46
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Wei Y, Reveal B, Cai W, Lilly MA. The GATOR1 Complex Regulates Metabolic Homeostasis and the Response to Nutrient Stress in Drosophila melanogaster. G3 (BETHESDA, MD.) 2016; 6:3859-3867. [PMID: 27672113 PMCID: PMC5144957 DOI: 10.1534/g3.116.035337] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/15/2016] [Indexed: 02/06/2023]
Abstract
TORC1 regulates metabolism and growth in response to a large array of upstream inputs. The evolutionarily conserved trimeric GATOR1 complex inhibits TORC1 activity in response to amino acid limitation. In humans, the GATOR1 complex has been implicated in a wide array of pathologies including cancer and hereditary forms of epilepsy. However, the precise role of GATOR1 in animal physiology remains largely undefined. Here, we characterize null mutants of the GATOR1 components nprl2, nprl3, and iml1 in Drosophila melanogaster We demonstrate that all three mutants have inappropriately high baseline levels of TORC1 activity and decreased adult viability. Consistent with increased TORC1 activity, GATOR1 mutants exhibit a cell autonomous increase in cell growth. Notably, escaper nprl2 and nprl3 mutant adults have a profound locomotion defect. In line with a nonautonomous role in the regulation of systemic metabolism, expressing the Nprl3 protein in the fat body, a nutrient storage organ, and hemocytes but not muscles and neurons rescues the motility of nprl3 mutants. Finally, we show that nprl2 and nprl3 mutants fail to activate autophagy in response to amino acid limitation and are extremely sensitive to both amino acid and complete starvation. Thus, in Drosophila, in addition to maintaining baseline levels of TORC1 activity, the GATOR1 complex has retained a critical role in the response to nutrient stress. In summary, the TORC1 inhibitor GATOR1 contributes to multiple aspects of the development and physiology of Drosophila.
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Affiliation(s)
- Youheng Wei
- Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Brad Reveal
- Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Weili Cai
- Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Mary A Lilly
- Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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47
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Fidler DR, Murphy SE, Courtis K, Antonoudiou P, El-Tohamy R, Ient J, Levine TP. Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains. Traffic 2016; 17:1214-1226. [PMID: 27601190 PMCID: PMC5091641 DOI: 10.1111/tra.12432] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 01/08/2023]
Abstract
Advances in membrane cell biology are hampered by the relatively high proportion of proteins with no known function. Such proteins are largely or entirely devoid of structurally significant domain annotations. Structural bioinformaticians have developed profile‐profile tools such as HHsearch (online version called HHpred), which can detect remote homologies that are missed by tools used to annotate databases. Here we have applied HHsearch to study a single structural fold in a single model organism as proof of principle. In the entire clan of protein domains sharing the pleckstrin homology domain fold in yeast, systematic application of HHsearch accurately identified known PH‐like domains. It also predicted 16 new domains in 13 yeast proteins many of which are implicated in intracellular traffic. One of these was Vps13p, where we confirmed the functional importance of the predicted PH‐like domain. Even though such predictions require considerable work to be corroborated, they are useful first steps. HHsearch should be applied more widely, particularly across entire proteomes of model organisms, to significantly improve database annotations.
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Affiliation(s)
- David R Fidler
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | - Sarah E Murphy
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | - Katherine Courtis
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | | | - Rana El-Tohamy
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | - Jonathan Ient
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | - Timothy P Levine
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK.
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48
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Tang BL. C9orf72's Interaction with Rab GTPases-Modulation of Membrane Traffic and Autophagy. Front Cell Neurosci 2016; 10:228. [PMID: 27774051 PMCID: PMC5053994 DOI: 10.3389/fncel.2016.00228] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/21/2016] [Indexed: 12/12/2022] Open
Abstract
Hexanucleotide repeat expansion in an intron of Chromosome 9 open reading frame 72 (C9orf72) is the most common genetic cause of Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD). While functional haploinsufficiency of C9orf72 resulting from the mutation may play a role in ALS/FTD, the actual cellular role of the protein has been unclear. Recent findings have now shown that C9orf72 physically and functionally interacts with multiple members of the Rab small GTPases family, consequently exerting important influences on cellular membrane traffic and the process of autophagy. Loss of C9orf72 impairs endocytosis in neuronal cell lines, and attenuated autophagosome formation. Interestingly, C9orf72 could influence autophagy both as part of a Guanine nucleotide exchange factor (GEF) complex, or as a Rab effector that facilitates transport of the Unc-51-like Autophagy Activating Kinase 1 (Ulk1) autophagy initiation complex. The cellular function of C9orf72 is discussed in the light of these recent findings.
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Affiliation(s)
- Bor L Tang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of SingaporeSingapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of SingaporeSingapore, Singapore
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49
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Pacitto A, Ascher DB, Wong LH, Blaszczyk BK, Nookala RK, Zhang N, Dokudovskaya S, Levine TP, Blundell TL. Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein. Open Biol 2016; 5:150174. [PMID: 26631379 PMCID: PMC4703059 DOI: 10.1098/rsob.150174] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The folliculin/Fnip complex has been demonstrated to play a crucial role in the mechanisms underlying Birt–Hogg–Dubé (BHD) syndrome, a rare inherited cancer syndrome. Lst4 has been previously proposed to be the Fnip1/2 orthologue in yeast and therefore a member of the DENN family. In order to confirm this, we solved the crystal structure of the N-terminal region of Lst4 from Kluyveromyces lactis and show it contains a longin domain, the first domain of the full DENN module. Furthermore, we demonstrate that Lst4 through its DENN domain interacts with Lst7, the yeast folliculin orthologue. Like its human counterpart, the Lst7/Lst4 complex relocates to the vacuolar membrane in response to nutrient starvation, most notably in carbon starvation. Finally, we express and purify the recombinant Lst7/Lst4 complex and show that it exists as a 1 : 1 heterodimer in solution. This work confirms the membership of Lst4 and the Fnip proteins in the DENN family, and provides a basis for using the Lst7/Lst4 complex to understand the molecular function of folliculin and its role in the pathogenesis of BHD syndrome.
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Affiliation(s)
- Angela Pacitto
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - David B Ascher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Louise H Wong
- Department of Cell Biology, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Beata K Blaszczyk
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Ravi K Nookala
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Nianshu Zhang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Svetlana Dokudovskaya
- CNRS UMR 8126, Université Paris-Sud 11, Institut Gustave Roussy, 114, rue Edouard Vaillant, Villejuif 94805, France
| | - Tim P Levine
- Department of Cell Biology, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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50
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Ishida M, E Oguchi M, Fukuda M. Multiple Types of Guanine Nucleotide Exchange Factors (GEFs) for Rab Small GTPases. Cell Struct Funct 2016; 41:61-79. [PMID: 27246931 DOI: 10.1247/csf.16008] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Rab small GTPases are highly conserved master regulators of membrane traffic in all eukaryotes. The same as the activation and inactivation of other small GTPases, the activation and inactivation of Rabs are tightly controlled by specific GEFs (guanine nucleotide exchange factors) and GAPs (GTPase-activating proteins), respectively. Although almost all Rab-GAPs reported thus far have a TBC (Tre-2/Bub2/Cdc16)/Rab-GAP domain in common, recent accumulating evidence has indicated the existence of a number of structurally unrelated types of Rab-GEFs, including DENN proteins, VPS9 proteins, Sec2 proteins, TRAPP complexes, heterodimer GEFs (Mon1-Ccz1, HPS1-HPS4 (BLOC-3 complex), Ric1-Rgp1 and Rab3GAP1/2), and other GEFs (e.g., REI-1 and RPGR). In this review article we provide an up-to-date overview of the structures and functions of all putative Rab-GEFs in mammals, with a special focus on their substrate Rabs, interacting proteins, associations with genetic diseases, and intracellular localizations.
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Affiliation(s)
- Morié Ishida
- Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University
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