201
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Calixto AR, Moreira C, Pabis A, Kötting C, Gerwert K, Rudack T, Kamerlin SCL. GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases. J Am Chem Soc 2019; 141:10684-10701. [PMID: 31199130 DOI: 10.1021/jacs.9b03193] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the Gαi subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H2PO4- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.
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Affiliation(s)
- Ana R Calixto
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Cátia Moreira
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Anna Pabis
- Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 , Uppsala , Sweden
| | - Carsten Kötting
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Klaus Gerwert
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Till Rudack
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Shina C L Kamerlin
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
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202
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Roy P, Rout AK, Maharana J, Sahoo DR, Panda SP, Pal A, Nayak KK, Behera BK, Das BK. Molecular characterization, constitutive expression and GTP binding mechanism of Cirrhinus mrigala (Hamilton, 1822) Myxovirus resistance (Mx) protein. Int J Biol Macromol 2019; 136:1258-1272. [PMID: 31242450 DOI: 10.1016/j.ijbiomac.2019.06.161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/11/2019] [Accepted: 06/21/2019] [Indexed: 12/30/2022]
Abstract
Myxovirus resistance (Mx) proteins represents the subclass of the dynamin superfamily of large Guanosine triphosphates (GTPases), play esential role in intracellular vesicle trafficking, endocytosis, organelle homeostasis and mitochondria distribution. These proteins are key players of the vertebrate immune system, induced by type-I and type-III interferons (IFN) of infected host and inhibit viral replication by sequestering its nucleoprotein. In the present study, we report the sequencing and characterization of Cirrhinus mrigala Mx protein (CmMx) for the first time and observed its constitutive expression in different tissues for a period of fourteen days. The synthetic peptide, LSGVALPRGTGI, was dissolved in PBS and injected into a rabbit and the antibody raised against CmMx was used to study the level of its expression. The full length of the CmMx cDNA is 2244 bp with a molecular mass of 70.9 kDa and a predicted isoelectric point of 8.25. The 627 amino acids polypeptide formed of three main functional domains: N-terminal GTPase domain (GD), a middle domain (MD) and GTPase effector domain (GED) with carboxy terminal leucine zipper motif. The 3D models of CmMx protein was modeled based on available close structural homologs and further validated through molecular dynamics (MD) simulations. MD study revealed the importance of G-domain responsible for recognition of GTP, which perfectly corroborate with earlier studies. MM/PBSA binding free energy analysis displayed that van der Waals and electrostatic energy were the key driving force behind molecular recognition of GTP by CmMx protein. The results from this study will illuminate more lights into the ongoing research on myxovirus resistance protein and its role in inhibition of viral replication in other eukaryotic system as well.
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Affiliation(s)
- Pragyan Roy
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751012, Odisha, India
| | - Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, West Bengal, India
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751003, Odisha, India
| | - Deepak Ranjan Sahoo
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751012, Odisha, India
| | - Soumya Prasad Panda
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751012, Odisha, India
| | - Arttatrana Pal
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751012, Odisha, India
| | | | - Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, West Bengal, India
| | - Basanta Kumar Das
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751012, Odisha, India; Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, West Bengal, India.
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203
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Qu L, Pan C, He SM, Lang B, Gao GD, Wang XL, Wang Y. The Ras Superfamily of Small GTPases in Non-neoplastic Cerebral Diseases. Front Mol Neurosci 2019; 12:121. [PMID: 31213978 PMCID: PMC6555388 DOI: 10.3389/fnmol.2019.00121] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/25/2019] [Indexed: 12/22/2022] Open
Abstract
The small GTPases from the Ras superfamily play crucial roles in basic cellular processes during practically the entire process of neurodevelopment, including neurogenesis, differentiation, gene expression, membrane and protein traffic, vesicular trafficking, and synaptic plasticity. Small GTPases are key signal transducing enzymes that link extracellular cues to the neuronal responses required for the construction of neuronal networks, as well as for synaptic function and plasticity. Different subfamilies of small GTPases have been linked to a number of non-neoplastic cerebral diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), intellectual disability, epilepsy, drug addiction, Huntington’s disease (HD), amyotrophic lateral sclerosis (ALS) and a large number of idiopathic cerebral diseases. Here, we attempted to make a clearer illustration of the relationship between Ras superfamily GTPases and non-neoplastic cerebral diseases, as well as their roles in the neural system. In future studies, potential treatments for non-neoplastic cerebral diseases which are based on small GTPase related signaling pathways should be explored further. In this paper, we review all the available literature in support of this possibility.
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Affiliation(s)
- Liang Qu
- Department of Neurosurgery, Tangdu Hospital, Air Force Military Medical University, Xi'an, China
| | - Chao Pan
- Beijing Institute of Biotechnology, Beijing, China
| | - Shi-Ming He
- Department of Neurosurgery, Tangdu Hospital, Air Force Military Medical University, Xi'an, China.,Department of Neurosurgery, Xi'an International Medical Center, Xi'an, China
| | - Bing Lang
- The School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.,Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Guo-Dong Gao
- Department of Neurosurgery, Tangdu Hospital, Air Force Military Medical University, Xi'an, China
| | - Xue-Lian Wang
- Department of Neurosurgery, Tangdu Hospital, Air Force Military Medical University, Xi'an, China
| | - Yuan Wang
- Department of Neurosurgery, Tangdu Hospital, Air Force Military Medical University, Xi'an, China
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204
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Tichauer RH, Favre G, Cabantous S, Brut M. Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21 N-ras and the Resulting GTP Electronic Density. J Phys Chem B 2019; 123:3935-3944. [PMID: 30991803 DOI: 10.1021/acs.jpcb.9b02660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
p21ras protein activity, regulated by GTP hydrolysis, constitutes an active field of research for the development of cancer targeted therapies that would concern ∼30% of human tumors to which specific mutations have been associated. Indeed, the catalyzing mechanisms provided by the protein environment during GTP hydrolysis and how they are impaired by specific mutations remain to be fully elucidated. In this article, we present results from molecular mechanics (MM) molecular dynamics (MD) simulations and density functional theory (DFT) calculations carried out for wild-type p21 N-ras and six Gln 61 mutants. In the first part, we present the water distribution within the active site of the wild-type protein according to MM MD. Significant differences are observed when comparing the results to the previous distribution assessed through quantum mechanics/molecular mechanics (QM/MM) MD. Such method-dependent results highlight the importance of accounting for the electrostatic coupling between the protein complex and the solvent molecules in identifying hydration sites. In the second part, we present the results from DFT calculations performed to determine the electronic distribution of the GTP ligand, considering the wild-type active site arrangement according to both classical and hybrid approaches. Only in the QM/MM-based configuration is the ligand electronic density similar to that of a GDP-like state observed experimentally. For this reason, in the last set of calculations carried out for p21 N-ras Gln 61 mutants, only the active site structural conformations obtained through hybrid MD are considered. Through the analysis of the GTP electronic density, we conclude that the wild-type active site arrangement according to QM/MM MD is closer to a catalytically efficient conformation of the protein than the arrangement according to MM MD. Hence, water distribution according to the hybrid approach must correspond to the optimal placement of solvent in the active site. Within all of the studied Gln 61 substituted proteins, p21ras major catalyzing effect, which consists of stabilizing a more GDP-like state, is lost.
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Affiliation(s)
- Ruth H Tichauer
- LAAS-CNRS , Université de Toulouse , CNRS, UPS, Toulouse , France
| | - Gilles Favre
- Cancer Research Center of Toulouse , INSERM U1037, Université de Toulouse , 31037 Toulouse , France
| | - Stéphanie Cabantous
- Cancer Research Center of Toulouse , INSERM U1037, Université de Toulouse , 31037 Toulouse , France
| | - Marie Brut
- LAAS-CNRS , Université de Toulouse , CNRS, UPS, Toulouse , France
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205
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The Role of p.Ser1105Ser (in NPHS1 Gene) and p.Arg548Leu (in PLCE1 Gene) with Disease Status of Vietnamese Patients with Congenital Nephrotic Syndrome: Benign or Pathogenic? ACTA ACUST UNITED AC 2019; 55:medicina55040102. [PMID: 31013750 PMCID: PMC6524047 DOI: 10.3390/medicina55040102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 11/20/2022]
Abstract
Background and Objectives: Congenital nephrotic syndrome (CNS), a genetic disease caused by mutations in genes on autosomes, usually occurs in the first three months after birth. A number of genetic mutations in genes, which encode for the components of the glomerular filtration barrier have been identified. We investigated mutations in NPHS1, NPHS2, PLCE1 (NPHS3), and WT1 genes that relate to the disease in Vietnamese patients. Materials and Methods: We performed genetic analysis of two unrelated patients, who were diagnosed with CNS in the Vietnam National Children’s Hospital with different disease status. The entire coding region and adjacent splice sites of these genes were amplified and sequenced using the Sanger method. The sequencing data were analyzed and compared with the NPHS1, NPHS2, PLCE1, and WT1 gene sequences published in Ensembl (ENSG00000161270, ENSG00000116218, ENSG00000138193, and ENSG00000184937, respectively) using BioEdit software to detect mutations. Results: We detected a new variant p.Ser607Arg and two other (p.Glu117Lys and p.Ser1105Ser) in the NPHS1 gene, as well as two variants (p.Arg548Leu, p.Pro1575Arg) in the PLCE1 gene. No mutations were detected in the NPHS2 and WT1 genes. Patient 1, who presented a heterozygous genotype of p.Ser1105Ser and p.Arg548Leu had a mild disease status but patient 2, who presented a homozygous genotype of these alleles, had a severe phenotype. Conclusions: These results suggest that variants p.Ser1105Ser (in NPHS1 gene) and p.Arg548Leu (in PLCE1 gene) in the homozygous form might play a role in the development of the disease in patients.
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206
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Slaymi C, Vignal E, Crès G, Roux P, Blangy A, Raynaud P, Fort P. The atypical RhoU/Wrch1 Rho GTPase controls cell proliferation and apoptosis in the gut epithelium. Biol Cell 2019; 111:121-141. [PMID: 30834544 DOI: 10.1111/boc.201800062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/07/2019] [Accepted: 02/07/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND The mammalian gut epithelium displays among the highest rates of self-renewal, with a turnover time of less than 5 days. Renewal involves concerted proliferation at the bottom of the crypt, migration and differentiation along the crypt-villus axis and anoïkis/shedding in the luminal epithelium. Renewal is controlled by interplay between signalling pathways, among which canonical and non-canonical Wnt signals play prominent roles. Overall 92% of colon tumours show increased canonical Wnt signalling resulting from mutations, established as major driver steps towards carcinogenesis. RESULTS Here, we examined the physiological role of RhoU/Wrch1 in gut homeostasis. RhoU is an atypical Rho GTPase related to Cdc42/Rac1 and identified as a transcriptional target of non-canonical Wnt signalling. We found that RHOU expression is reduced in human colorectal tumour samples. We show that RhoU is mainly expressed in the differentiated compartment of the gut epithelium. Rhou specific invalidation in the mouse gut elicits cell hyperplasia and is associated in the colon with a highly disorganized luminal epithelium. Hyperplasia affects all cell types in the small intestine and colon and has a higher impact on goblet cells. Hyperplasia is associated with a reduction of apoptosis and an increased proliferation. RhoU knockdown in human DLD-1 colon cancer cells also elicits a higher growth index and reduces cell apoptosis. Last, loss of RhoU function in the mouse gut epithelium or in DLD-1 cells increases RhoA activity and the level of phosphorylated Myosin Light Chain-2, which may functionally link RhoU activity to apoptosis. CONCLUSION RhoU is mostly expressed in the differentiated compartment of the gut. It plays a role in homeostasis as its specific invalidation elicits hyperplasia of all cell types. This mainly results from a reduction of apoptosis, through actomyosin-dependent mechanisms. SIGNIFICANCE RhoU negatively controls cell growth in the intestinal epithelium. Since its expression is sensitive to non-canonical Wnt signals and is reduced in colorectal tumours, downregulating RhoU may thus have an instrumental role in tumour progression.
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Affiliation(s)
- Chaker Slaymi
- CRBM, CNRS, University of Montpellier, 34293, Montpellier CEDEX 5, France
| | - Emmanuel Vignal
- CRBM, CNRS, University of Montpellier, 34293, Montpellier CEDEX 5, France
| | - Gaëlle Crès
- CRBM, CNRS, University of Montpellier, 34293, Montpellier CEDEX 5, France
| | - Pierre Roux
- CRBM, CNRS, University of Montpellier, 34293, Montpellier CEDEX 5, France
| | - Anne Blangy
- CRBM, CNRS, University of Montpellier, 34293, Montpellier CEDEX 5, France
| | - Peggy Raynaud
- CRBM, CNRS, University of Montpellier, 34293, Montpellier CEDEX 5, France
| | - Philippe Fort
- CRBM, CNRS, University of Montpellier, 34293, Montpellier CEDEX 5, France
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207
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Jerry R, Sullivan-Brown J, Yoder MD. GTP binding protein 10 is a member of the OBG family of proteins and is differentially expressed in the early Xenopus embryo. Gene Expr Patterns 2019; 32:12-17. [PMID: 30831265 DOI: 10.1016/j.gep.2019.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 02/15/2019] [Accepted: 02/21/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Razhan Jerry
- Sciences Division, Brandywine Campus, The Pennsylvania State University, Media, PA, 19063, USA
| | | | - Michael D Yoder
- Sciences Division, Brandywine Campus, The Pennsylvania State University, Media, PA, 19063, USA.
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208
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Jobst-Schwan T, Hoogstraten CA, Kolvenbach CM, Schmidt JM, Kolb A, Eddy K, Schneider R, Ashraf S, Widmeier E, Majmundar AJ, Hildebrandt F. Corticosteroid treatment exacerbates nephrotic syndrome in a zebrafish model of magi2a knockout. Kidney Int 2019; 95:1079-1090. [PMID: 31010479 DOI: 10.1016/j.kint.2018.12.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/21/2018] [Accepted: 12/13/2018] [Indexed: 01/31/2023]
Abstract
Recently, recessive mutations of MAGI2 were identified as a cause of steroid-resistant nephrotic syndrome (SRNS) in humans and mice. To further delineate the pathogenesis of MAGI2 loss of function, we generated stable knockout lines for the two zebrafish orthologues magi2a and magi2b by CRISPR/Cas9. We also developed a novel assay for the direct detection of proteinuria in zebrafish independent of transgenic background. Whereas knockout of magi2b did not yield a nephrotic syndrome phenotype, magi2a-/- larvae developed ascites, periorbital edema, and proteinuria, as indicated by increased excretion of low molecular weight protein. Electron microscopy demonstrated extensive podocyte foot process effacement. As in human SRNS, we observed genotype/phenotype correlation, with edema onset occurring earlier in zebrafish with truncating alleles (5-6 days post fertilization) versus hypomorphic alleles (19-20 days post fertilization). Paradoxically, corticosteroid treatment exacerbated the phenotype, with earlier onset of edema. In contrast, treatment with cyclosporine A or tacrolimus had no significant effect. Although RhoA signaling has been implicated as a downstream mediator of MAGI2 activity, targeting of the RhoA pathway did not modify the nephrotic syndrome phenotype. In the first CRISPR/Cas9 zebrafish knockout model of SRNS, we found that corticosteroids may have a paradoxical effect in the setting of specific genetic mutations.
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Affiliation(s)
- Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte A Hoogstraten
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Caroline M Kolvenbach
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Johanna Magdalena Schmidt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Amy Kolb
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kaitlyn Eddy
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ronen Schneider
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shazia Ashraf
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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209
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Scheffzek K, Shivalingaiah G. Ras-Specific GTPase-Activating Proteins-Structures, Mechanisms, and Interactions. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a031500. [PMID: 30104198 DOI: 10.1101/cshperspect.a031500] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ras-specific GTPase-activating proteins (RasGAPs) down-regulate the biological activity of Ras proteins by accelerating their intrinsic rate of GTP hydrolysis, basically by a transition state stabilizing mechanism. Oncogenic Ras is commonly not sensitive to RasGAPs caused by interference of mutants with the electronic or steric requirements of the transition state, resulting in up-regulation of activated Ras in respective cells. RasGAPs are modular proteins containing a helical catalytic RasGAP module surrounded by smaller domains that are frequently involved in the subcellular localization or contributing to regulatory features of their host proteins. In this review, we summarize current knowledge about RasGAP structure, mechanism, regulation, and dual-substrate specificity and discuss in some detail neurofibromin, one of the most important negative Ras regulators in cellular growth control and neuronal function.
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Affiliation(s)
- Klaus Scheffzek
- Division of Biological Chemistry (Biocenter), Medical University of Innsbruck, A-6020 Innsbruck, Austria
| | - Giridhar Shivalingaiah
- Division of Biological Chemistry (Biocenter), Medical University of Innsbruck, A-6020 Innsbruck, Austria
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210
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Balasingam N, Brandon HE, Ross JA, Wieden HJ, Thakor N. Cellular roles of the human Obg-like ATPase 1 (hOLA1) and its YchF homologs. Biochem Cell Biol 2019; 98:1-11. [PMID: 30742486 DOI: 10.1139/bcb-2018-0353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
P-loop NTPases comprise one of the major superfamilies of nucleotide binding proteins, which mediate a variety of cellular processes, such as mRNA translation, signal transduction, cell motility, and growth regulation. In this review, we discuss the structure and function of two members of the ancient Obg-related family of P-loop GTPases: human Obg-like ATPase 1 (hOLA1), and its bacterial/plant homolog, YchF. After a brief discussion of nucleotide binding proteins in general and the classification of the Obg-related family in particular, we discuss the sequence and structural features of YchF and hOLA1. We then explore the various functional roles of hOLA1 in mammalian cells during stress response and cancer progression, and of YchF in bacterial cells. Finally, we directly compare and contrast the structure and function of hOLA1 with YchF before summarizing the future perspectives of hOLA1 research. This review is timely, given the variety of recent studies aimed at understanding the roles of hOLA1 and YchF in such critical processes as cellular-stress response, oncogenesis, and protein synthesis.
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Affiliation(s)
- Nirujah Balasingam
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada
| | - Harland E Brandon
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada
| | - Joseph A Ross
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada
| | - Nehal Thakor
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.,Canadian Centre for Behavioral Neuroscience (CCBN), Department of Neuroscience, University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.,Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada
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211
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Knihtila R, Volmar AY, Meilleur F, Mattos C. Titration of ionizable groups in proteins using multiple neutron data sets from a single crystal: application to the small GTPase Ras. Acta Crystallogr F Struct Biol Commun 2019; 75:111-115. [PMID: 30713162 PMCID: PMC6360437 DOI: 10.1107/s2053230x18018125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/20/2018] [Indexed: 11/11/2022] Open
Abstract
Neutron protein crystallography (NPC) reveals the three-dimensional structures of proteins, including the positions of H atoms. The technique is particularly suited to elucidate ambiguous catalytic steps in complex biochemical reactions. While NPC uniquely complements biochemical assays and X-ray structural analyses by revealing the protonation states of ionizable groups at and around the active site of enzymes, the technique suffers from a major drawback: large single crystals must be grown to compensate for the relatively low flux of neutron beams. However, in addition to revealing the positions of hydrogens involved in enzyme catalysis, NPC has the advantage over X-ray crystallography that the crystals do not suffer radiation damage. The lack of radiation damage can be exploited to conduct in crystallo parametric studies. Here, the use of a single crystal of the small GTPase Ras to collect three neutron data sets at pD 8.4, 9.0 and 9.4 is reported, enabling an in crystallo titration study using NPC. In addition to revealing the behavior of titratable groups in the active site, the data sets will allow the analysis of allosteric water-mediated communication networks across the molecule, particularly regarding Cys118 and three tyrosine residues central to these networks, Tyr32, Tyr96 and Tyr137, with pKa values expected to be in the range sampled in our experiments.
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Affiliation(s)
- Ryan Knihtila
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Alicia Y. Volmar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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212
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Progress in targeting RAS with small molecule drugs. Biochem J 2019; 476:365-374. [PMID: 30705085 DOI: 10.1042/bcj20170441] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 01/01/2023]
Abstract
RAS proteins have traditionally been deemed undruggable, as they do not possess an active site to which small molecules could bind but small molecules that target one form of oncogenic RAS, KRAS G12C, are already in preclinical and clinical trials, and several other compounds that bind to different RAS proteins at distinct sites are in earlier stage evaluation. KRAS is the major clinical target, as it is by far the most significant form of RAS in terms of cancer incidence. Unfortunately, KRAS exists in two isoforms, each with unique biochemical properties. This complicates efforts to target KRAS specifically. KRAS is also a member of a family of closely related proteins, which share similar effector-binding regions and G-domains, further increasing the challenge of specificity. Nevertheless, progress is being made, driven by new drug discovery technologies and creative science.
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213
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Hassanzadeh G, Naing T, Graber T, Jafarnejad SM, Stojdl DF, Alain T, Holcik M. Characterizing Cellular Responses During Oncolytic Maraba Virus Infection. Int J Mol Sci 2019; 20:ijms20030580. [PMID: 30700020 PMCID: PMC6387032 DOI: 10.3390/ijms20030580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 02/07/2023] Open
Abstract
The rising demand for powerful oncolytic virotherapy agents has led to the identification of Maraba virus, one of the most potent oncolytic viruses from Rhabdoviridae family which displays high selectivity for killing malignant cells and low cytotoxicity in normal cells. Although the virus is readied to be used for clinical trials, the interactions between the virus and the host cells is still unclear. Using a newly developed interferon-sensitive mutant Maraba virus (MG1), we have identified two key regulators of global translation (4E-BP1 and eIF2α) as being involved in the regulation of protein synthesis in the infected cells. Despite the translational arrest upon viral stress, we showed an up-regulation of anti-apoptotic Bcl-xL protein that provides a survival benefit for the host cell, yet facilitates effective viral propagation. Given the fact that eIF5B canonically regulates 60S ribosome subunit end joining and is able to replace the role of eIF2 in delivering initiator tRNA to the 40S ribosome subunit upon the phosphorylation of eIF2α we have tested whether eIF5B mediates the translation of target mRNAs during MG1 infection. Our results show that the inhibition of eIF5B significantly down-regulates the level of Bcl-xL steady-state mRNA, thus indirectly attenuates viral propagation.
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Affiliation(s)
- Golnoush Hassanzadeh
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada.
| | - Thet Naing
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada.
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada.
| | - Tyson Graber
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada.
| | - Seyed Mehdi Jafarnejad
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK.
| | - David F Stojdl
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada.
| | - Tommy Alain
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada.
| | - Martin Holcik
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada.
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada.
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214
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Liang H, Xu J, Wang W. Ran1 is essential for parental macronuclear import of apoptosis-inducing factor and programmed nuclear death in Tetrahymena thermophila. FEBS J 2019; 286:913-929. [PMID: 30663224 DOI: 10.1111/febs.14761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/30/2018] [Accepted: 01/17/2019] [Indexed: 01/30/2023]
Abstract
During programmed nuclear death (PND), apoptosis-inducing factor (AIF) translocates from mitochondria to the parental macronucleus (MAC) in Tetrahymena thermophila. In the degenerating parental MAC, AIF induces chromatin condensation and large-scale DNA fragmentation in a caspase-independent manner. However, the regulation of AIF nuclear translocation and molecular mechanism of PND are less clear. In this study, we demonstrated that the asymmetric distribution of nuclear GDP-bound Ran1-mimetic mutant Ran1T25N and cytoplasmic GTP-bound Ran1-mimetic mutant Ran1Q70L exists across the parental macronuclear-cytoplasmic barrier during PND. Knockdown of RAN1 led to defects in PND progression and failure of parental macronuclear accumulation of AIF. Moreover, AIF parental macronuclear import occurred in Ran1T25N mutants, while it was inhibited in Ran1Q70L mutants. Importantly, artificial accumulation of AIF in the parental MAC rescued PND progression defects in RAN1 knockdown mutants. These data suggest that Ran1 is essential for parental macronuclear import of AIF and PND in T. thermophila.
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Affiliation(s)
- Haixia Liang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China.,MicroNano System Research Center, Key Laboratory of Advanced Transducers and Intelligent Control System of Ministry of Education and Shanxi Province, College of Information & Computer Engineering, Taiyuan University of Technology, China
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
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215
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Rahim K, Huo L, Li C, Zhang P, Basit A, Xiang B, Ting B, Hao X, Zhu X. Identification of a basidiomycete-specific Vilse-like GTPase activating proteins (GAPs) and its roles in the production of virulence factors in Cryptococcus neoformans. FEMS Yeast Res 2019; 17:4644832. [PMID: 29177429 DOI: 10.1093/femsyr/fox089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/20/2017] [Indexed: 12/25/2022] Open
Abstract
Cryptococcus neoformans is a basidiomycetous pathogenic yeast that causes fatal infections in both immunocompetent and immunocompromised patients. Regulation on the production of its virulence factors is not fully understood. Here we reported the characterization of a gene, named CVH1(CNA06260), encoding a Drosophila Vilse-like RhoGAP homolog, which is hallmarked by three conserved functional domains: WW, MyTH4 and RhoGAP. Phylogenetic analysis suggests that CVH1 is highly conserved from protists to mammals and interestingly in basidiomycetes, but absent in plants or Ascomycota and other lower fungi. This phylogenetic distribution indicates an evolutionary link among these groups of organisms. Functional analyses demonstrated that CVH1 was involved in stress tolerance and virulence factor production. By disrupting CVH1, we created a second mutant cvh1Δ with the CRISPR-Cas9 editing tool. The mutant strain exhibited hypersensitivity to osmotic stress by 2 M sorbitol and NaCl, suggesting defects in the HOG signaling pathway and an interaction of Cvh1 with the HOG pathway. Hypersensitivity of cvh1Δ to 1% Congo red and 0.01% SDS suggests that the cell wall integrity was impaired in the mutant. And cvh1Δ hardly produced the pigment melanin and capsule. Our study for the first time demonstrates that the fungal Vilse-like RhoGAP CVH1 is an important regulator of multiple biological processes in C. neoformans, and provides novel insights into the regulatory circuit of stress resistance/cell wall integrity, and laccase and capsule synthesis in C. neoformans.
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Affiliation(s)
- Kashif Rahim
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Liang Huo
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Chenxi Li
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ping Zhang
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Abdul Basit
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Biyun Xiang
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Bie Ting
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xiaoran Hao
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xudong Zhu
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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216
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Wauters L, Versées W, Kortholt A. Roco Proteins: GTPases with a Baroque Structure and Mechanism. Int J Mol Sci 2019; 20:ijms20010147. [PMID: 30609797 PMCID: PMC6337361 DOI: 10.3390/ijms20010147] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/21/2018] [Accepted: 12/25/2018] [Indexed: 01/05/2023] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are a common cause of genetically inherited Parkinson’s Disease (PD). LRRK2 is a large, multi-domain protein belonging to the Roco protein family, a family of GTPases characterized by a central RocCOR (Ras of complex proteins/C-terminal of Roc) domain tandem. Despite the progress in characterizing the GTPase function of Roco proteins, there is still an ongoing debate concerning the working mechanism of Roco proteins in general, and LRRK2 in particular. This review consists of two parts. First, an overview is given of the wide evolutionary range of Roco proteins, leading to a variety of physiological functions. The second part focusses on the GTPase function of the RocCOR domain tandem central to the action of all Roco proteins, and progress in the understanding of its structure and biochemistry is discussed and reviewed. Finally, based on the recent work of our and other labs, a new working hypothesis for the mechanism of Roco proteins is proposed.
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Affiliation(s)
- Lina Wauters
- VIB-VUB Center for Structural Biology, Pleinlaan 2, B-1050 Brussels, Belgium.
- Department of Cell Biochemistry, University of Groningen, NL-9747 AG Groningen, The Netherlands.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, B-1050 Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, NL-9747 AG Groningen, The Netherlands.
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217
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Tripathi R, Noetzel J, Marx D. Exposing catalytic versatility of GTPases: taking reaction detours in mutants of hGBP1 enzyme without additional energetic cost. Phys Chem Chem Phys 2019; 21:859-867. [DOI: 10.1039/c8cp06343e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Our study reveals that the replacement of catalytically competent residues by the inert amino acid alanine, S73A and E99A, in hGBP1 opens a plethora of molecularly different reaction pathways featuring very similar energy barriers as the wild type.
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Affiliation(s)
- Ravi Tripathi
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Jan Noetzel
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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218
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Wang Y, Li Y, Rosas-Diaz T, Caceres-Moreno C, Lozano-Duran R, Macho AP. The IMMUNE-ASSOCIATED NUCLEOTIDE-BINDING 9 Protein Is a Regulator of Basal Immunity in Arabidopsis thaliana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:65-75. [PMID: 29958083 DOI: 10.1094/mpmi-03-18-0062-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A robust regulation of plant immune responses requires a multitude of positive and negative regulators that act in concert. The immune-associated nucleotide-binding (IAN) gene family members are associated with immunity in different organisms, although no characterization of their function has been carried out to date in plants. In this work, we analyzed the expression patterns of IAN genes and found that IAN9 is repressed upon pathogen infection or treatment with immune elicitors. IAN9 encodes a plasma membrane-localized protein that genetically behaves as a negative regulator of immunity. A novel ian9 mutant generated by CRISPR/Cas9 shows increased resistance to Pseudomonas syringae, while transgenic plants overexpressing IAN9 show a slight increase in susceptibility. In vivo immunoprecipitation of IAN9-green fluorescent protein followed by mass spectrometry analysis revealed that IAN9 associates with a previously uncharacterized C3HC4-type RING-finger domain-containing protein that we named IAN9-associated protein 1 (IAP1), which also acts as a negative regulator of basal immunity. Interestingly, neither ian9 or iap1 mutant plants show any obvious developmental phenotype, suggesting that they display enhanced inducible immunity rather than constitutive immune responses. Because both IAN9 and IAP1 have orthologs in important crop species, they could be suitable targets to generate plants more resistant to diseases caused by bacterial pathogens without yield penalty.
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Affiliation(s)
- Yuanzheng Wang
- 1 Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; and
- 2 University of Chinese Academy of Sciences, Beijing, China
| | - Yansha Li
- 1 Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; and
| | - Tabata Rosas-Diaz
- 1 Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; and
| | - Carlos Caceres-Moreno
- 1 Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; and
- 2 University of Chinese Academy of Sciences, Beijing, China
| | - Rosa Lozano-Duran
- 1 Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; and
| | - Alberto P Macho
- 1 Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; and
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219
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Kulkarni Y, Kamerlin SCL. Computational physical organic chemistry using the empirical valence bond approach. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2019. [DOI: 10.1016/bs.apoc.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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220
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Mitochondrial Dynamics in Stem Cells and Differentiation. Int J Mol Sci 2018; 19:ijms19123893. [PMID: 30563106 PMCID: PMC6321186 DOI: 10.3390/ijms19123893] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 01/09/2023] Open
Abstract
Mitochondria are highly dynamic organelles that continuously change their shape. Their main function is adenosine triphosphate (ATP) production; however, they are additionally involved in a variety of cellular phenomena, such as apoptosis, cell cycle, proliferation, differentiation, reprogramming, and aging. The change in mitochondrial morphology is closely related to the functionality of mitochondria. Normal mitochondrial dynamics are critical for cellular function, embryonic development, and tissue formation. Thus, defects in proteins involved in mitochondrial dynamics that control mitochondrial fusion and fission can affect cellular differentiation, proliferation, cellular reprogramming, and aging. Here, we review the processes and proteins involved in mitochondrial dynamics and their various associated cellular phenomena.
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221
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Flis J, Holm M, Rundlet EJ, Loerke J, Hilal T, Dabrowski M, Bürger J, Mielke T, Blanchard SC, Spahn CMT, Budkevich TV. tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Cell Rep 2018; 25:2676-2688.e7. [PMID: 30517857 PMCID: PMC6314685 DOI: 10.1016/j.celrep.2018.11.040] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/14/2018] [Accepted: 11/09/2018] [Indexed: 01/04/2023] Open
Abstract
Translocation moves the tRNA2⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA2⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.
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Affiliation(s)
- Julia Flis
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Mikael Holm
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Emily J Rundlet
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, New York, NY, USA
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Tarek Hilal
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Marylena Dabrowski
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, New York, NY, USA.
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Tatyana V Budkevich
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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222
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PseudoGTPase domains in p190RhoGAP proteins: a mini-review. Biochem Soc Trans 2018; 46:1713-1720. [PMID: 30514771 DOI: 10.1042/bst20180481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/22/2018] [Accepted: 10/25/2018] [Indexed: 02/07/2023]
Abstract
Pseudoenzymes generally lack detectable catalytic activity despite adopting the overall protein fold of their catalytically competent counterparts, indeed 'pseudo' family members seem to be incorporated in all enzyme classes. The small GTPase enzymes are important signaling proteins, and recent studies have identified many new family members with noncanonical residues within the catalytic cleft, termed pseudoGTPases. To illustrate recent discoveries in the field, we use the p190RhoGAP proteins as an example. p190RhoGAP proteins (ARHGAP5 and ARHGAP35) are the most abundant GTPase activating proteins for the Rho family of small GTPases. These are key regulators of Rho signaling in processes such as cell migration, adhesion and cytokinesis. Structural biology has complemented and guided biochemical analyses for these proteins and has allowed discovery of two cryptic pseudoGTPase domains, and the re-classification of a third, previously identified, GTPase-fold domain as a pseudoGTPase. The three domains within p190RhoGAP proteins illustrate the diversity of this rapidly expanding pseudoGTPase group.
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223
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Peters DT, Kay L, Eswaran J, Lakey JH, Soundararajan M. Human Miro Proteins Act as NTP Hydrolases through a Novel, Non-Canonical Catalytic Mechanism. Int J Mol Sci 2018; 19:ijms19123839. [PMID: 30513825 PMCID: PMC6321465 DOI: 10.3390/ijms19123839] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 01/13/2023] Open
Abstract
Mitochondria are highly dynamic organelles that play a central role in multiple cellular processes, including energy metabolism, calcium homeostasis and apoptosis. Miro proteins (Miros) are “atypical” Ras superfamily GTPases that display unique domain architecture and subcellular localisation regulating mitochondrial transport, autophagy and calcium sensing. Here, we present systematic catalytic domain characterisation and structural analyses of human Miros. Despite lacking key conserved catalytic residues (equivalent to Ras Y32, T35, G60 and Q61), the Miro N-terminal GTPase domains display GTPase activity. Surprisingly, the C-terminal GTPase domains previously assumed to be “relic” domains were also active. Moreover, Miros show substrate promiscuity and function as NTPases. Molecular docking and structural analyses of Miros revealed unusual features in the Switch I and II regions, facilitating promiscuous substrate binding and suggesting the usage of a novel hydrolytic mechanism. The key substitution in position 13 in the Miros leads us to suggest the existence of an “internal arginine finger”, allowing an unusual catalytic mechanism that does not require GAP protein. Together, the data presented here indicate novel catalytic functions of human Miro atypical GTPases through altered catalytic mechanisms.
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Affiliation(s)
- Daniel T Peters
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Laura Kay
- Department of Applied Sciences Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
| | - Jeyanthy Eswaran
- Northern Institute for Cancer Research, Newcastle University, Herschel Building, Newcastle upon Tyne, NE1 7RU, UK.
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Meera Soundararajan
- Department of Applied Sciences Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
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224
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Zhou H, Guterres H, Mattos C, Makowski L. Predicting X-ray solution scattering from flexible macromolecules. Protein Sci 2018; 27:2023-2036. [PMID: 30230663 PMCID: PMC6237699 DOI: 10.1002/pro.3508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 01/08/2023]
Abstract
Wide-angle X-ray solution scattering (WAXS) patterns contain substantial information about the structure and dynamics of a protein. Solution scattering from a rigid protein can be predicted from atomic coordinate sets to within experimental error. However, structural fluctuations of proteins in solution can lead to significant changes in the observed intensities. The magnitude and form of these changes contain information about the nature and spatial extent of structural fluctuations in the protein. Molecular dynamics (MD) simulations based on a crystal structure and selected force field generate models for protein internal motions, and here we demonstrate that they can be used to predict the impact of structural fluctuations on solution scattering data. In cases where the observed and calculated intensities correspond, we can conclude that the X-ray scattering provides direct experimental validation of the structural and MD results. In cases where calculated and observed intensities are at odds, the inconsistencies can be used to determine the origins of these discrepancies. They may be because of overestimates or underestimates of structural fluctuations in MD simulations, under-sampling of the structural ensemble in the simulations, errors in the structural model, or a mismatch between the experimental conditions and the parameters used in carrying out the MD simulation.
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Affiliation(s)
- Hao Zhou
- Department of Electrical and Computer EngineeringNortheastern UniversityBostonMassachusetts
| | - Hugo Guterres
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusetts
| | - Carla Mattos
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusetts
| | - Lee Makowski
- Department of BioengineeringNortheastern UniversityBostonMassachusetts
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225
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Mela A, Momany M. Septin mutations and phenotypes in S. cerevisiae. Cytoskeleton (Hoboken) 2018; 76:33-44. [PMID: 30171672 DOI: 10.1002/cm.21492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/09/2018] [Accepted: 08/22/2018] [Indexed: 11/07/2022]
Abstract
Septins are highly conserved guanosine triphosphate (GTP)-binding proteins that are a component of the cytoskeletal systems of virtually all eukaryotes (except higher plants). Septins play important roles in a multitude of cellular processes, including cytokinesis, establishment of cell polarity, and cellular partitioning. The ease of genetic screens and a fully sequenced genome have made Saccharomyces cerevisiae one of the most extensively studied and well-annotated model organisms in eukaryotic biology. Here, we present a synopsis of the known point mutations in the seven S. cerevisiae septin genes: CDC3, CDC10, CDC11, CDC12, SHS1, SPR3, and SPR28. We map these mutations onto septin protein structures, highlighting important conserved motifs, and relating the functional consequences of mutations in each domain.
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Affiliation(s)
- Alexander Mela
- Department of Plant Biology, University of Georgia, Athens, GA 30602
| | - Michelle Momany
- Department of Plant Biology, University of Georgia, Athens, GA 30602
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226
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Li H, Yao XQ, Grant BJ. Comparative structural dynamic analysis of GTPases. PLoS Comput Biol 2018; 14:e1006364. [PMID: 30412578 PMCID: PMC6249014 DOI: 10.1371/journal.pcbi.1006364] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/21/2018] [Accepted: 10/11/2018] [Indexed: 12/30/2022] Open
Abstract
GTPases regulate a multitude of essential cellular processes ranging from movement and division to differentiation and neuronal activity. These ubiquitous enzymes operate by hydrolyzing GTP to GDP with associated conformational changes that modulate affinity for family-specific binding partners. There are three major GTPase superfamilies: Ras-like GTPases, heterotrimeric G proteins and protein-synthesizing GTPases. Although they contain similar nucleotide-binding sites, the detailed mechanisms by which these structurally and functionally diverse superfamilies operate remain unclear. Here we compare and contrast the structural dynamic mechanisms of each superfamily using extensive molecular dynamics (MD) simulations and subsequent network analysis approaches. In particular, dissection of the cross-correlations of atomic displacements in both the GTP and GDP-bound states of Ras, transducin and elongation factor EF-Tu reveals analogous dynamic features. This includes similar dynamic communities and subdomain structures (termed lobes). For all three proteins the GTP-bound state has stronger couplings between equivalent lobes. Network analysis further identifies common and family-specific residues mediating the state-specific coupling of distal functional sites. Mutational simulations demonstrate how disrupting these couplings leads to distal dynamic effects at the nucleotide-binding site of each family. Collectively our studies extend current understanding of GTPase allosteric mechanisms and highlight previously unappreciated similarities across functionally diverse families. GTPases are a large superfamily of essential enzymes that regulate a variety of cellular processes. They share a common core structure supporting nucleotide binding and hydrolysis, and are potentially descended from the same ancestor. Yet their biological functions diverge dramatically, ranging from cell division and movement to signal transduction and translation. It has been shown that conformational changes through binding to different substrates underlie the regulation of their activities. Here we investigate the conformational dynamics of three typical GTPases by in silico simulation. We find that these three GTPases possess overall similar substrate-associated dynamic features, beyond their distinct functions. Further identification of key common and family-specific elements in these three families helps us understand how enzymes are adapted to acquire distinct functions from a common core structure. Our results provide unprecedented insights into the functional mechanism of GTPases in general, which potentially facilitates novel protein design in the future.
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Affiliation(s)
- Hongyang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States of America
| | - Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, GA, United States of America
| | - Barry J. Grant
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA, United States of America
- * E-mail:
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227
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G protein subunit phosphorylation as a regulatory mechanism in heterotrimeric G protein signaling in mammals, yeast, and plants. Biochem J 2018; 475:3331-3357. [PMID: 30413679 DOI: 10.1042/bcj20160819] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/28/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022]
Abstract
Heterotrimeric G proteins composed of Gα, Gβ, and Gγ subunits are vital eukaryotic signaling elements that convey information from ligand-regulated G protein-coupled receptors (GPCRs) to cellular effectors. Heterotrimeric G protein-based signaling pathways are fundamental to human health [Biochimica et Biophysica Acta (2007) 1768, 994-1005] and are the target of >30% of pharmaceuticals in clinical use [Biotechnology Advances (2013) 31, 1676-1694; Nature Reviews Drug Discovery (2017) 16, 829-842]. This review focuses on phosphorylation of G protein subunits as a regulatory mechanism in mammals, budding yeast, and plants. This is a re-emerging field, as evidence for phosphoregulation of mammalian G protein subunits from biochemical studies in the early 1990s can now be complemented with contemporary phosphoproteomics and genetic approaches applied to a diversity of model systems. In addition, new evidence implicates a family of plant kinases, the receptor-like kinases, which are monophyletic with the interleukin-1 receptor-associated kinase/Pelle kinases of metazoans, as possible GPCRs that signal via subunit phosphorylation. We describe early and modern observations on G protein subunit phosphorylation and its functional consequences in these three classes of organisms, and suggest future research directions.
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228
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Stiegler AL, Boggon TJ. The N-Terminal GTPase Domain of p190RhoGAP Proteins Is a PseudoGTPase. Structure 2018; 26:1451-1461.e4. [PMID: 30174148 PMCID: PMC6249675 DOI: 10.1016/j.str.2018.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/28/2018] [Accepted: 07/25/2018] [Indexed: 12/29/2022]
Abstract
The pseudoGTPases are a rapidly growing and important group of pseudoenzymes. p190RhoGAP proteins are critical regulators of Rho signaling and contain two previously identified pseudoGTPase domains. Here we report that p190RhoGAP proteins contain a third pseudoGTPase domain, termed N-GTPase. We find that GTP constitutively purifies with the N-GTPase domain, and a 2.8-Å crystal structure of p190RhoGAP-A co-purified with GTP reveals an unusual GTP-Mg2+ binding pocket. Six inserts in N-GTPase indicate perturbed catalytic activity and inability to bind to canonical GTPase activating proteins, guanine nucleotide exchange factors, and effector proteins. Biochemical analysis shows that N-GTPase does not detectably hydrolyze GTP, and exchanges nucleotide only under harsh Mg2+ chelation. Furthermore, mutational analysis shows that GTP and Mg2+ binding stabilizes the domain. Therefore, our results support that N-GTPase is a nucleotide binding, non-hydrolyzing, pseudoGTPase domain that may act as a protein-protein interaction domain. Thus, unique among known proteins, p190RhoGAPs contain three pseudoGTPase domains.
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Affiliation(s)
- Amy L Stiegler
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Yale Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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229
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Novelli ET, First JT, Webb LJ. Quantitative Measurement of Intrinsic GTP Hydrolysis for Carcinogenic Glutamine 61 Mutants in H-Ras. Biochemistry 2018; 57:6356-6366. [PMID: 30339365 DOI: 10.1021/acs.biochem.8b00878] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mutations of human oncoprotein p21H-Ras (hereafter "Ras") at glutamine 61 are known to slow the rate of guanosine triphosphate (GTP) hydrolysis and transform healthy cells into malignant cells. It has been hypothesized that this glutamine plays a role in the intrinsic mechanism of GTP hydrolysis by interacting with an active site water molecule that stabilizes the formation of the charged transition state at the γ-phosphate during hydrolysis. However, there is no comprehensive data set of the effects of mutations to Q61 on the protein's intrinsic catalytic rate, structure, or interactions with water at the active site. Here, we present the first comprehensive and quantitative set of initial rates of intrinsic hydrolysis for all stable variants of RasQ61X. We further conducted enhanced molecular dynamics (MD) simulations of each construct to determine the solvent accessible surface area (SASA) of the side chain at position 61 and compared these results to previously measured changes in electric fields caused by RasQ61X mutations. For polar and negatively charged residues, we found that the rates are normally distributed about an optimal electrostatic contribution, close to that of the native Q61 residue, and the rates are strongly correlated to the number of waters in the active site. Together, these results support a mechanism of GTP hydrolysis in which Q61 stabilizes a transient hydronium ion, which then stabilizes the transition state while the γ-phosphate is undergoing nucleophilic attack by a second, catalytically active water molecule. We discuss the implications of such a mechanism on future strategies for combating Ras-based cancers.
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Affiliation(s)
- Elisa T Novelli
- Department of Chemistry, Texas Materials Institute, Institute for Cell and Molecular Biology , The University of Texas at Austin , 105 E 24th Street STOP A5300 , Austin , Texas 78712-1224 , United States
| | - Jeremy T First
- Department of Chemistry, Texas Materials Institute, Institute for Cell and Molecular Biology , The University of Texas at Austin , 105 E 24th Street STOP A5300 , Austin , Texas 78712-1224 , United States
| | - Lauren J Webb
- Department of Chemistry, Texas Materials Institute, Institute for Cell and Molecular Biology , The University of Texas at Austin , 105 E 24th Street STOP A5300 , Austin , Texas 78712-1224 , United States
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230
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Bortolus M, Costantini P, Doni D, Carbonera D. Overview of the Maturation Machinery of the H-Cluster of [FeFe]-Hydrogenases with a Focus on HydF. Int J Mol Sci 2018; 19:E3118. [PMID: 30314343 PMCID: PMC6212873 DOI: 10.3390/ijms19103118] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/04/2018] [Accepted: 10/06/2018] [Indexed: 01/01/2023] Open
Abstract
Hydrogen production in nature is performed by hydrogenases. Among them, [FeFe]-hydrogenases have a peculiar active site, named H-cluster, that is made of two parts, synthesized in different pathways. The cubane sub-cluster requires the normal iron-sulfur cluster maturation machinery. The [2Fe] sub-cluster instead requires a dedicated set of maturase proteins, HydE, HydF, and HydG that work to assemble the cluster and deliver it to the apo-hydrogenase. In particular, the delivery is performed by HydF. In this review, we will perform an overview of the latest knowledge on the maturation machinery of the H-cluster, focusing in particular on HydF.
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Affiliation(s)
- Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy.
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.
| | - Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy.
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231
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Choi E, Hwang J. The GTPase BipA expressed at low temperature in Escherichia coli assists ribosome assembly and has chaperone-like activity. J Biol Chem 2018; 293:18404-18419. [PMID: 30305394 DOI: 10.1074/jbc.ra118.002295] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 09/27/2018] [Indexed: 12/29/2022] Open
Abstract
BPI-inducible protein A (BipA) is a conserved ribosome-associated GTPase in bacteria that is structurally similar to other GTPases associated with protein translation, including IF2, EF-Tu, and EF-G. Its binding site on the ribosome appears to overlap those of these translational GTPases. Mutations in the bipA gene cause a variety of phenotypes, including cold and antibiotics sensitivities and decreased pathogenicity, implying that BipA may participate in diverse cellular processes by regulating translation. According to recent studies, a bipA-deletion strain of Escherichia coli displays a ribosome assembly defect at low temperature, suggesting that BipA might be involved in ribosome assembly. To further investigate BipA's role in ribosome biogenesis, here, we compared and analyzed the ribosomal protein compositions of MG1655 WT and bipA-deletion strains at 20 °C. Aberrant 50S ribosomal subunits (i.e. 44S particles) accumulated in the bipA-deletion strain at 20 °C, and the ribosomal protein L6 was absent in these 44S particles. Furthermore, bipA expression was significantly stimulated at 20 °C, suggesting that it encodes a cold shock-inducible GTPase. Moreover, the transcriptional regulator cAMP receptor protein (CRP) positively promoted bipA expression only at 20 °C. Importantly, GFP and α-glucosidase refolding assays revealed that BipA has chaperone activity. Our findings indicate that BipA is a cold shock-inducible GTPase that participates in 50S ribosomal subunit assembly by incorporating the L6 ribosomal protein into the 44S particle during the assembly.
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Affiliation(s)
- Eunsil Choi
- From the Department of Microbiology, Pusan National University, Busan 46241, Korea
| | - Jihwan Hwang
- From the Department of Microbiology, Pusan National University, Busan 46241, Korea.
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232
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Zhu C, Cheng C, Wang Y, Muhammad W, Liu S, Zhu W, Shao B, Zhang Z, Yan X, He Q, Xu Z, Yu C, Qian X, Lu L, Zhang S, Zhang Y, Xiong W, Gao X, Xu Z, Chai R. Loss of ARHGEF6 Causes Hair Cell Stereocilia Deficits and Hearing Loss in Mice. Front Mol Neurosci 2018; 11:362. [PMID: 30333726 PMCID: PMC6176010 DOI: 10.3389/fnmol.2018.00362] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/13/2018] [Indexed: 11/13/2022] Open
Abstract
ARHGEF6 belongs to the family of guanine nucleotide exchange factors (GEFs) for Rho GTPases, and it specifically activates Rho GTPases CDC42 and RAC1. Arhgef6 is the X-linked intellectual disability gene also known as XLID46, and clinical features of patients carrying Arhgef6 mutations include intellectual disability and, in some cases, sensorineural hearing loss. Rho GTPases act as molecular switches in many cellular processes. Their activities are regulated by binding or hydrolysis of GTP, which is facilitated by GEFs and GTPase-activating proteins, respectively. RAC1 and CDC42 have been shown to play important roles in hair cell (HC) stereocilia development. However, the role of ARHGEF6 in inner ear development and hearing function has not yet been investigated. Here, we found that ARHGEF6 is expressed in mouse cochlear HCs, including the HC stereocilia. We established Arhgef6 knockdown mice using the clustered regularly interspaced short palindromic repeat-associated Cas9 nuclease (CRISPR-Cas9) genome editing technique. We showed that ARHGEF6 was indispensable for the maintenance of outer hair cell (OHC) stereocilia, and loss of ARHGEF6 in mice caused HC stereocilia deficits that eventually led to progressive HC loss and hearing loss. However, the loss of ARHGEF6 did not affect the synapse density and did not affect the mechanoelectrical transduction currents in OHCs at postnatal day 3. At the molecular level, the levels of active CDC42 and RAC1 were dramatically decreased in the Arhgef6 knockdown mice, suggesting that ARHGEF6 regulates stereocilia maintenance through RAC1/CDC42.
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Affiliation(s)
- Chengwen Zhu
- Department of Otolaryngology Head and Neck Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China.,Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, China.,Research Institute of Otolaryngology, Nanjing, China
| | - Cheng Cheng
- Department of Otolaryngology Head and Neck Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China.,Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, China.,Research Institute of Otolaryngology, Nanjing, China.,Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yanfei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, China.,Shandong Provincial Collaborative Innovation Center of Cell Biology, Shandong Normal University, Jinan, China
| | - Waqas Muhammad
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, China.,Department of Biotechnology, Federal Urdu University of Arts, Science and Technology, Karachi, Pakistan
| | - Shuang Liu
- School of Life Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Weijie Zhu
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Buwei Shao
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Zhong Zhang
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Xiaoqian Yan
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Qingqing He
- Department of Otolaryngology Head and Neck Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Zhengrong Xu
- Department of Otolaryngology Head and Neck Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Chenjie Yu
- Department of Otolaryngology Head and Neck Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Xiaoyun Qian
- Department of Otolaryngology Head and Neck Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Ling Lu
- Department of Otolaryngology Head and Neck Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Shasha Zhang
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, China.,Research Institute of Otolaryngology, Nanjing, China.,Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China.,Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, China
| | - Yuan Zhang
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Wei Xiong
- School of Life Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Xia Gao
- Department of Otolaryngology Head and Neck Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China.,Research Institute of Otolaryngology, Nanjing, China
| | - Zhigang Xu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, China.,Shandong Provincial Collaborative Innovation Center of Cell Biology, Shandong Normal University, Jinan, China
| | - Renjie Chai
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, China.,Research Institute of Otolaryngology, Nanjing, China.,Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China.,Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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233
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Jamilloux Y, Magnotti F, Belot A, Henry T. The pyrin inflammasome: from sensing RhoA GTPases-inhibiting toxins to triggering autoinflammatory syndromes. Pathog Dis 2018; 76:4956042. [PMID: 29718184 DOI: 10.1093/femspd/fty020] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/02/2018] [Indexed: 02/07/2023] Open
Abstract
Numerous pathogens including Clostridium difficile and Yersinia pestis have evolved toxins or effectors targeting GTPases from the RhoA subfamily (RhoA/B/C) to inhibit or hijack the host cytoskeleton dynamics. The resulting impairment of RhoA GTPases activity is sensed by the host via an innate immune complex termed the pyrin inflammasome in which caspase-1 is activated. The cascade leading to activation of the pyrin inflammasome has been recently uncovered. In this review, following a brief presentation of RhoA GTPases-modulating toxins, we present the pyrin inflammasome and its regulatory mechanisms. Furthermore, we discuss how some pathogens have developed strategies to escape detection by the pyrin inflammasome. Finally, we present five monogenic autoinflammatory diseases associated with pyrin inflammasome deregulation. The molecular insights provided by the study of these diseases and the corresponding mutations on pyrin inflammasome regulation and activation are presented.
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Affiliation(s)
- Yvan Jamilloux
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France.,Departement de Médecine Interne, Hopital de la Croix-Rousse, Université Claude Bernard Lyon 1, F-69004 Lyon, France
| | - Flora Magnotti
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Alexandre Belot
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France.,Service de Néphrologie, Rhumatologie, Dermatologie pédiatrique, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, F-69677 Lyon, France
| | - Thomas Henry
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
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234
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Tichauer RH, Favre G, Cabantous S, Landa G, Hemeryck A, Brut M. Water Distribution within Wild-Type NRas Protein and Q61 Mutants during Unrestrained QM/MM Dynamics. Biophys J 2018; 115:1417-1430. [PMID: 30224050 DOI: 10.1016/j.bpj.2018.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022] Open
Abstract
Point mutations in p21ras are associated with ∼30% of human tumors by disrupting its GTP hydrolysis cycle, which is critical to its molecular switch function in cellular signaling pathways. In this work, we investigate the impact of Gln 61 substitutions in the structure of the p21N-ras active site and particularly focus on water reorganization around GTP, which appears to be crucial to evaluate favorable and unfavorable hydration sites for hydrolysis. The NRas-GTP complex is analyzed using a hybrid quantum mechanics/molecular mechanics approach, treating for the first time to our knowledge transient water molecules at the ab initio level and leading to results that account for the electrostatic coupling between the protein complex and the solvent. We show that for the wild-type protein, water molecules are found around the GTP γ-phosphate group, forming an arch extended from residues 12 to 35. Two density peaks are observed, supporting previous results that suggest the presence of two water molecules in the active site, one in the vicinity of residue 35 and a second one stabilized by hydrogen bonds formed with nitrogen backbone atoms of residues 12 and 60. The structural changes observed in NRas Gln 61 mutants result in the drastic delocalization of water molecules that we discuss. In mutants Q61H and Q61K, for which water distribution is overlocalized next to residue 60, the second density peak supports the hypothesis of a second water molecule. We also conclude that Gly 60 indirectly participates in GTP hydrolysis by correctly positioning transient water molecules in the protein complex and that Gln 61 has an indirect steric effect in stabilizing the preorganized catalytic site.
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Affiliation(s)
- Ruth H Tichauer
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse, INSERM U1037, Toulouse, France; Université de Toulouse, Toulouse, France
| | - Stéphanie Cabantous
- Cancer Research Center of Toulouse, INSERM U1037, Toulouse, France; Université de Toulouse, Toulouse, France
| | - Georges Landa
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anne Hemeryck
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie Brut
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France.
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235
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Huang N, Ling H, Su Y, Liu F, Xu L, Su W, Wu Q, Guo J, Gao S, Que Y. Transcriptional analysis identifies major pathways as response components to Sporisorium scitamineum stress in sugarcane. Gene 2018; 678:207-218. [PMID: 30099025 DOI: 10.1016/j.gene.2018.08.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Sugarcane smut, which is caused by Sporisorium scitamineum, is a severe fungal disease affecting sugarcane. However, the major pathways involved in the interaction between sugarcane and S. scitamineum remains unclear. RESULTS In the present study, suppression subtractive hybridization (SSH) library construction, together with reverse northern blotting, was conducted on the most prevalent sugarcane genotype ROC22 challenged with S. scitamineum. After alignment and homologous expressed sequence tag (EST) assembly, a total of 155 differentially expressed unigenes were identified from SSH libraries. Totally, 26 of 155 differentially expressed unigenes were analyzed by qRT-PCR in sugarcane smut-resistant genotype YC05-179 and susceptible genotype ROC22. Genes encoded two unknown protein (Q1 and Q11), serine/threonine kinase (Q2), fiber protein (Q3), eukaryotic translation initiation factor 5A (Q23), and Sc14-3-3-like protein (Q24) were induced in sugarcane smut-resistant genotype YC05-179 but inhibited in susceptible genotype ROC22. Based on the differential expression data achieved from SSH libraries and qRT-PCR, we found that, serine/threonine kinases, Ca2+ sensors, mitogen-activated protein genes and some NBS-LRR genes may involve in the signal recognition and transduction of smut fungus infection in sugarcane. While in the plant hormone signaling pathways, the genes related to auxin, abscisic acid, salicylic acid and ethylene were more apparently in response to smut fungus invasion. The hypersensitive response, protein metabolism, polyamine synthesis, and cell wall formation may play an important role in sugarcane defense against smut fungus colonization. Additionally, the Sc14-3-3 might serve as a molecular modulator in sugarcane being immune to smut disease by interacting with proteins like ScGAPN (Q10), which have been further verified by BiFC assay. CONCLUSIONS The findings of the present study could provide a general view about gene pathways involving in sugarcane defense against smut disease and facilitate a better understanding of the molecular mechanism underlying sugarcane-S. scitamineum interaction.
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Affiliation(s)
- Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Shiwu Gao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
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236
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Chakraborti S, Sarkar J, Bhuyan R, Chakraborti T. Role of catechins on ET-1-induced stimulation of PLD and NADPH oxidase activities in pulmonary smooth muscle cells: determination of the probable mechanism by molecular docking studies. Biochem Cell Biol 2018; 96:417-432. [PMID: 29206487 DOI: 10.1139/bcb-2017-0179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The treatment of human pulmonary artery smooth muscle cells with ET-1 stimulates the activity of PLD and NADPH oxidase, but this stimulation is inhibited by pretreatment with bosentan (ET-1 receptor antagonist), FIPI (PLD inhibitor), apocynin (NADPH oxidase inhibitor), and EGCG and ECG (catechins having a galloyl group), but not EGC and EC (catechins devoid of a galloyl group). Herein, using molecular docking analyses based on our biochemical studies, we determined the probable mechanism by which the catechins containing a galloyl group inhibit the stimulation of PLD activity induced by ET-1. The ET-1-induced stimulation of PLD activity was inhibited by SecinH3 (inhibitor of cytohesin). Arf6 and cytohesin-1 are associated in the cell membrane, which is not inhibited by the catechins during ET-1 treatment of the cells. However, EGCG and ECG inhibited the binding of GTPγS with Arf6, even in the presence of cytohesin-1. The molecular docking analyses revealed that the catechins containing a galloyl group (EGCG and ECG) with cytohesin-1–Arf6GDP, but not the catechins without a galloyl group (EGC and EC), prevent GDP–GTP exchange in Arf6, which seems to be an important mechanism for inhibiting the activation of PLD induced by ET-1, and subsequently increases the activity of NADPH oxidase.
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Affiliation(s)
- Sajal Chakraborti
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Jaganmay Sarkar
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Rajabrata Bhuyan
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Tapati Chakraborti
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
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237
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Chakraborty PK, Murphy B, Mustafi SB, Dey A, Xiong X, Rao G, Naz S, Zhang M, Yang D, Dhanasekaran DN, Bhattacharya R, Mukherjee P. Cystathionine β-synthase regulates mitochondrial morphogenesis in ovarian cancer. FASEB J 2018; 32:4145-4157. [PMID: 29494264 PMCID: PMC6044063 DOI: 10.1096/fj.201701095r] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/20/2018] [Indexed: 12/12/2022]
Abstract
Deregulation of mitochondrial morphogenesis, a dynamic equilibrium between mitochondrial fusion and fission processes, is now evolving as a key metabolic event that fuels tumor growth and therapy resistance. However, fundamental knowledge underpinning how cancer cells reprogram mitochondrial morphogenesis remains incomplete. Here, we report that cystathionine β-synthase (CBS) reprograms mitochondrial morphogenesis in ovarian cancer (OvCa) cells by selectively regulating the stability of mitofusin 2 (MFN2). Clinically, high expression of both CBS and MFN2 implicates poor overall survival of OvCa patients, and a significant association between CBS and MFN2 expression exists in individual patients in the same data set. The silencing of CBS by small interfering RNA or inhibition of its catalytic activity by a small molecule inhibitor creates oxidative stress that activates JNK. Activated JNK phosphorylates MFN2 to recruit homologous to the E6-AP carboxyl terminus' domain-containing ubiquitin E3 ligase for its degradation via the ubiquitin-proteasome system. Supplementation with hydrogen sulfide or glutathione (the catalytic products of CBS enzymatic activity), anti-oxidants, or a JNK inhibitor restores MFN2 expression. In CBS-silenced orthotopic xenograft tumor tissues, MFN2 but not MFN1 is selectively downregulated. In summary, this report reveals a role for deregulated mitochondrial morphogenesis in OvCa, suggests one of the mechanisms for this deregulation, and provides a way to correct it through modulation of the metabolic enzyme CBS.-Chakraborty, P. K., Murphy, B., Mustafi, S. B., Dey, A., Xiong, X., Rao, G., Naz, S., Zhang, M., Yang, D., Dhanasekaran, D. N., Bhattacharya, R., Mukherjee, P. Cystathionine β-synthase regulates mitochondrial morphogenesis in ovarian cancer.
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Affiliation(s)
- Prabir Kumar Chakraborty
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Peggy and Charles Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Brennah Murphy
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Soumyajit Banerjee Mustafi
- Department of Obstetrics and Gynecology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; and
| | - Anindya Dey
- Department of Obstetrics and Gynecology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; and
| | - Xunhao Xiong
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Peggy and Charles Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Geeta Rao
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Sarwat Naz
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Min Zhang
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Da Yang
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Danny N. Dhanasekaran
- Peggy and Charles Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Resham Bhattacharya
- Peggy and Charles Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Department of Obstetrics and Gynecology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; and
| | - Priyabrata Mukherjee
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Peggy and Charles Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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238
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Parker JA, Mattos C. The K-Ras, N-Ras, and H-Ras Isoforms: Unique Conformational Preferences and Implications for Targeting Oncogenic Mutants. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031427. [PMID: 29038336 DOI: 10.1101/cshperspect.a031427] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ras controls a multitude of cellular signaling processes, including cell proliferation, differentiation, and apoptosis. Deregulation of Ras cycling often promotes tumorigenesis and various other developmental disorders, termed RASopothies. Although the structure of Ras has been known for many decades, it is still one of the most highly sought-after drug targets today, and is often referred to as "undruggable." At the center of this paradoxical protein is a lack of understanding of fundamental differences in the G domains between the highly similar Ras isoforms and common oncogenic mutations, despite the immense wealth of knowledge accumulated about this protein to date. A shift in the field during the past few years toward a high-resolution understanding of the structure confirms the hypothesis that each isoform and oncogenic mutation must be considered individually, and that not all Ras mutations are created equal. For the first time in Ras history, we have the ability to directly compare the structures of each wild-type isoform to construct a "base-line" understanding, which can then be used as a springboard for analyzing the effects of oncogenic mutations on the structure-function relationship in Ras. This is a fundamental and large step toward the goal of developing personalized therapies for patients with Ras-driven cancers and diseases.
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Affiliation(s)
- Jillian A Parker
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
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239
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Huang J, Liu H, Berberich T, Liu Y, Tao LZ, Liu T. Guanine Nucleotide Exchange Factor 7B (RopGEF7B) is involved in floral organ development in Oryza sativa. RICE (NEW YORK, N.Y.) 2018; 11:42. [PMID: 30062598 PMCID: PMC6066601 DOI: 10.1186/s12284-018-0235-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/10/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND RAC/ROP GTPase are versatile signaling molecules controlling diverse biological processes including cell polarity establishment, cell growth, morphogenesis, hormone responses and many other cellular processes in plants. The activities of ROPs are positively regulated by guanine nucleotide exchange factors (GEFs). Evidence suggests that RopGEFs regulate polar auxin transport and polar growth in pollen tube in Arabidopsis thaliana. However, the biological functions of rice RopGEFs during plant development remain largely unknown. RESULTS We investigated a member of the OsRopGEF family, namely OsRopGEF7B. OsRopGEF7Bpro:GUS analysis indicates that OsRopGEF7B is expressed in various tissues, especially in the floral meristem and floral organ primordia. Knock-out and -down of OsRopGEF7B by T-DNA insertion and RNA interference, respectively, predominantly caused an increase in the number of floral organs in the inner whorls (stamen and ovary), as well as abnormal paleae/lemmas and ectopic growth of lodicules, resulting in decline of rice seed setting. Bimolecular fluorescence complement (BiFC) assays as well as yeast two-hybrid assays indicate that OsRopGEF7B interacts with OsRACs. CONCLUSIONS OsRopGEF7B plays roles in floral organ development in rice, affecting rice seed setting rate. Manipulation of OsRopGEF7B has potential for application in genetically modified crops.
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Affiliation(s)
- Jiaqing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huili Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Thomas Berberich
- Senckenberg Biodiversity and Climate Research Center, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
| | - Yuting Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Li-Zhen Tao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Taibo Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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240
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Lou F, Yang T, Han Z, Gao T. Transcriptome analysis for identification of candidate genes related to sex determination and growth in Charybdis japonica. Gene 2018; 677:10-16. [PMID: 30036655 DOI: 10.1016/j.gene.2018.07.044] [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: 03/23/2018] [Revised: 07/07/2018] [Accepted: 07/13/2018] [Indexed: 11/27/2022]
Abstract
Charybdis japonica is an important cultured crab in China and it exhibits sex differences in their growth. Growth is an important economic trait that is controlled by many genes. In order to discover the growth-related regulatory mechanisms, whole-body transcriptomic sequencing and comparative analyses in different genders of C. japonica were conducted based on Illumina RNA-seq technology. In the present study, we obtained 62,879,204 and 60,226,334 clean reads in female and male libraries, respectively. 25,000,000 clean reads of every library were randomly selected and compared with Nt database to examine the possible contamination. Results showed that all clean reads were distributed among C. japonica or other species that were closely relative to this species, indicating no-pollution. De novo assembly was performed and a total of 32,543 and 44,174 unigenes were produced in female and male of C. japonica, respectively. Among all the unigenes, 12,591 and 14,455 unigenes of female and male crabs were annotated based on protein databases. Moreover, a total of 33,926 unigenes were found to contain ORFs and 52,839 SSRs were detected. The contrast between male and female C. japonica identifying 1939 unigenes were significantly differentially expressed. In addition, we specifically discussed some gene functions and pathways potentially associated with sex determination and growth. This is the first systematic report of whole transcriptome in C. japonica. The transcriptome information provides a basic resource for further studies on understanding the molecular basis of biological processes in C. japonica and other crustaceans.
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Affiliation(s)
- Fangrui Lou
- Fishery College, Ocean University of China, Qingdao, China
| | - Tianyan Yang
- Fishery College, Zhejiang Ocean University, Zhoushan, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, China.
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, China
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241
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Tysarowski A, Nasierowska-Guttmejer A. Quality and practical aspects of pathological and molecular diagnostics in metastatic colorectal cancer (mCRC). Contemp Oncol (Pozn) 2018; 22:75-85. [PMID: 30150883 PMCID: PMC6103235 DOI: 10.5114/wo.2018.77047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/27/2018] [Indexed: 01/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies worldwide. In recent years novel therapies targeted at EGFR receptor have been developed. However, this treatment can only be beneficial if no mutation in specific loci of KRAS/NRAS and BRAF genes is found in tumour specimen. Therefore, clinically useful pathological diagnosis of CRC in the era of personalised medicine is a multistep procedure, requiring good cooperation between the clinician/surgeon, pathomorphologist, and molecular biologist. Herein we propose the guidelines of colorectal cancer operating material proceedings for clinicians and pathomorphologists, which determines the correct pathomorphological diagnosis, and we discuss the colorectal cancer molecular biology issues useful in the selection of individual molecular targeted therapy. We discuss and stress the importance of each diagnostic phase: from tumour resection and sample collection at preanalytical stage, through proper pathological preparation, evaluation and selection of material for molecular testing, to molecular analysis and finally preparation of a pathological molecular report.
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Affiliation(s)
- Andrzej Tysarowski
- Department of Pathology and Laboratory Medicine, Maria Skłodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
- Department of Molecular and Translational Oncology, Maria Skłodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Anna Nasierowska-Guttmejer
- Pathology Department, The Jan Kochanowski University in Kielce, Poland
- Pathology Department, Central Clinical Hospital of the MSWiA in Warsaw, Poland
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242
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Sasine JP, Himburg HA, Termini CM, Roos M, Tran E, Zhao L, Kan J, Li M, Zhang Y, de Barros SC, Rao DS, Counter CM, Chute JP. Wild-type Kras expands and exhausts hematopoietic stem cells. JCI Insight 2018; 3:98197. [PMID: 29875320 DOI: 10.1172/jci.insight.98197] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/19/2018] [Indexed: 12/14/2022] Open
Abstract
Oncogenic Kras expression specifically in hematopoietic stem cells (HSCs) induces a rapidly fatal myeloproliferative neoplasm in mice, suggesting that Kras signaling plays a dominant role in normal hematopoiesis. However, such a conclusion is based on expression of an oncogenic version of Kras. Hence, we sought to determine the effect of simply increasing the amount of endogenous wild-type Kras on HSC fate. To this end, we utilized a codon-optimized version of the murine Kras gene (Krasex3op) that we developed, in which silent mutations in exon 3 render the encoded mRNA more efficiently translated, leading to increased protein expression without disruption to the normal gene architecture. We found that Kras protein levels were significantly increased in bone marrow (BM) HSCs in Krasex3op/ex3op mice, demonstrating that the translation of Kras in HSCs is normally constrained by rare codons. Krasex3op/ex3op mice displayed expansion of BM HSCs, progenitor cells, and B lymphocytes, but no evidence of myeloproliferative disease or leukemia in mice followed for 12 months. BM HSCs from Krasex3op/ex3op mice demonstrated increased multilineage repopulating capacity in primary competitive transplantation assays, but secondary competitive transplants revealed exhaustion of long-term HSCs. Following total body irradiation, Krasex3op/ex3op mice displayed accelerated hematologic recovery and increased survival. Mechanistically, HSCs from Krasex3op/ex3op mice demonstrated increased proliferation at baseline, with a corresponding increase in Erk1/2 phosphorylation and cyclin-dependent kinase 4 and 6 (Cdk4/6) activation. Furthermore, both the enhanced colony-forming capacity and in vivo repopulating capacity of HSCs from Krasex3op/ex3op mice were dependent on Cdk4/6 activation. Finally, BM transplantation studies revealed that augmented Kras expression produced expansion of HSCs, progenitor cells, and B cells in a hematopoietic cell-autonomous manner, independent from effects on the BM microenvironment. This study provides fundamental demonstration of codon usage in a mammal having a biological consequence, which may speak to the importance of codon usage in mammalian biology.
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Affiliation(s)
- Joshua P Sasine
- Division of Hematology/Oncology, Department of Medicine.,Molecular, Cellular and Integrative Physiology.,Jonsson Comprehensive Cancer Center.,Eli and Edythe Broad Center for Stem Cell Research, and
| | | | | | - Martina Roos
- Division of Hematology/Oncology, Department of Medicine.,Jonsson Comprehensive Cancer Center.,Eli and Edythe Broad Center for Stem Cell Research, and
| | - Evelyn Tran
- Division of Hematology/Oncology, Department of Medicine
| | - Liman Zhao
- Division of Hematology/Oncology, Department of Medicine
| | - Jenny Kan
- Division of Hematology/Oncology, Department of Medicine
| | - Michelle Li
- Division of Hematology/Oncology, Department of Medicine
| | - Yurun Zhang
- Division of Hematology/Oncology, Department of Medicine
| | | | - Dinesh S Rao
- Division of Hematology/Oncology, Department of Medicine.,Jonsson Comprehensive Cancer Center.,Eli and Edythe Broad Center for Stem Cell Research, and.,Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, USA
| | - Christopher M Counter
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North California, USA
| | - John P Chute
- Division of Hematology/Oncology, Department of Medicine.,Jonsson Comprehensive Cancer Center.,Eli and Edythe Broad Center for Stem Cell Research, and
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243
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Napolitano F, D'Angelo L, de Girolamo P, Avallone L, de Lange P, Usiello A. The Thyroid Hormone-target Gene Rhes a Novel Crossroad for Neurological and Psychiatric Disorders: New Insights from Animal Models. Neuroscience 2018; 384:419-428. [PMID: 29857029 DOI: 10.1016/j.neuroscience.2018.05.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 02/08/2023]
Abstract
Ras homolog enriched in striatum (Rhes) is predominantly expressed in the corpus striatum. Rhes mRNA is localized in virtually all dopamine D1 and D2 receptor-bearing medium-sized spiny neurons (MSNs), and cholinergic interneurons of striatum. Early studies in rodents showed that Rhes is developmentally regulated by thyroid hormone, as well as by dopamine innervation in adult rat, monkey and human brains. At cellular level, Rhes interferes with adenosine A2A- and dopamine D1 receptor-dependent cAMP/PKA pathway, upstream of the activation of the heterotrimeric G protein complex. Besides its involvement in GPCR-mediated signaling, Rhes modulates Akt pathway activation, acts as E3-ligase of mutant huntingtin, whose sumoylation accounts for neurotoxicity in Huntington's disease, and physically interacts with Beclin-1, suggesting its potential involvement in autophagy-related cellular events. In addition, this protein can also bind to and activate striatal mTORC1, one of the key players in l-DOPA-induced dyskinesia in rodent models of Parkinson's disease. Accordingly, lack of Rhes attenuated such motor disturbances in 6-OHDA-lesioned Rhes knockout mice. In support of its role in MSN-dependent functions, several studies documented that mutant animals displayed alterations in striatum-related phenotypes reminiscent of psychiatric illness in humans, including deficits in prepulse inhibition of startle reflex and, most interestingly, a striking enhancement of behavioral responses elicited by caffeine, phencyclidine or amphetamine. Overall, these data suggest that Rhes modulates molecular and biochemical events underlying striatal functioning, both in physiological and pathological conditions.
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Affiliation(s)
- Francesco Napolitano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Ceinge Biotecnologie Avanzate, Naples, Italy.
| | - Livia D'Angelo
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy; Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Paolo de Girolamo
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Luigi Avallone
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Pieter de Lange
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Alessandro Usiello
- Ceinge Biotecnologie Avanzate, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy.
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244
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The Effect of Overexpressed DdRabS on Development, Cell Death, Vesicular Trafficking, and the Secretion of Lysosomal Glycosidase Enzymes. BIOLOGY 2018; 7:biology7020033. [PMID: 29843387 PMCID: PMC6023087 DOI: 10.3390/biology7020033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 11/21/2022]
Abstract
Rab GTPases are essential regulators of many cellular processes and play an important role in downstream signaling vital to proper cell function. We sought to elucidate the role of novel D. discoideum GTPase RabS. Cell lines over-expressing DdRabS and expressing DdRabS N137I (dominant negative (DN)) proteins were generated, and it was determined that DdRabS localized to endosomes, ER-Golgi membranes, and the contractile vacuole system. It appeared to function in vesicular trafficking, and the secretion of lysosomal enzymes. Interestingly, microscopic analysis of GFP-tagged DdRabS (DN) cells showed differential localization to lysosomes and endosomes compared to GFP-tagged DdRabS overexpressing cells. Both cell lines over-secreted lysosomal glycosidase enzymes, especially β-glucosidase. Furthermore, DdRabS overexpressing cells were defective in aggregation due to decreased cell–cell cohesion and sensitivity to cAMP, leading to abnormal chemotactic migration, the inability to complete development, and increased induced cell death. These data support a role for DdRabS in trafficking along the vesicular and biosynthetic pathways. We hypothesize that overexpression of DdRabS may interfere with GTP activation of related proteins essential for normal development resulting in a cascade of defects throughout these processes.
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245
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Fu X, Liang C, Li F, Wang L, Wu X, Lu A, Xiao G, Zhang G. The Rules and Functions of Nucleocytoplasmic Shuttling Proteins. Int J Mol Sci 2018; 19:ijms19051445. [PMID: 29757215 PMCID: PMC5983729 DOI: 10.3390/ijms19051445] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 12/14/2022] Open
Abstract
Biological macromolecules are the basis of life activities. There is a separation of spatial dimension between DNA replication and RNA biogenesis, and protein synthesis, which is an interesting phenomenon. The former occurs in the cell nucleus, while the latter in the cytoplasm. The separation requires protein to transport across the nuclear envelope to realize a variety of biological functions. Nucleocytoplasmic transport of protein including import to the nucleus and export to the cytoplasm is a complicated process that requires involvement and interaction of many proteins. In recent years, many studies have found that proteins constantly shuttle between the cytoplasm and the nucleus. These shuttling proteins play a crucial role as transport carriers and signal transduction regulators within cells. In this review, we describe the mechanism of nucleocytoplasmic transport of shuttling proteins and summarize some important diseases related shuttling proteins.
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Affiliation(s)
- Xuekun Fu
- Department of Biology and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China.
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
| | - Chao Liang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518057, China.
| | - Fangfei Li
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518057, China.
| | - Luyao Wang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518057, China.
| | - Xiaoqiu Wu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518057, China.
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518057, China.
| | - Guozhi Xiao
- Department of Biology and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China.
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA.
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518057, China.
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246
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Parker JA, Volmar AY, Pavlopoulos S, Mattos C. K-Ras Populates Conformational States Differently from Its Isoform H-Ras and Oncogenic Mutant K-RasG12D. Structure 2018; 26:810-820.e4. [PMID: 29706533 DOI: 10.1016/j.str.2018.03.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 02/04/2018] [Accepted: 03/28/2018] [Indexed: 10/17/2022]
Abstract
Structures of wild-type K-Ras from crystals obtained in the presence of guanosine triphosphate (GTP) or its analogs have remained elusive. Of the K-Ras mutants, only K-RasG12D and K-RasQ61H are available in the PDB representing the activated form of the GTPase not in complex with other proteins. We present the crystal structure of wild-type K-Ras bound to the GTP analog GppCH2p, with K-Ras in the state 1 conformation. Signatures of conformational states obtained by one-dimensional proton NMR confirm that K-Ras has a more substantial population of state 1 in solution than H-Ras, which predominantly favors state 2. The oncogenic mutant K-RasG12D favors state 2, changing the balance of conformational states in favor of interactions with effector proteins. Differences in the population of conformational states between K-Ras and H-Ras, as well as between K-Ras and its mutants, can provide a structural basis for focused targeting of the K-Ras isoform in cancer-specific strategies.
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Affiliation(s)
- Jillian A Parker
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Alicia Y Volmar
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Spiro Pavlopoulos
- Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
| | - Carla Mattos
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA.
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247
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Ntai I, Fornelli L, DeHart CJ, Hutton JE, Doubleday PF, LeDuc RD, van Nispen AJ, Fellers RT, Whiteley G, Boja ES, Rodriguez H, Kelleher NL. Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk. Proc Natl Acad Sci U S A 2018; 115:4140-4145. [PMID: 29610327 PMCID: PMC5910823 DOI: 10.1073/pnas.1716122115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mutations of the KRAS gene are found in human cancers with high frequency and result in the constitutive activation of its protein products. This leads to aberrant regulation of downstream pathways, promoting cell survival, proliferation, and tumorigenesis that drive cancer progression and negatively affect treatment outcomes. Here, we describe a workflow that can detect and quantify mutation-specific consequences of KRAS biochemistry, namely linked changes in posttranslational modifications (PTMs). We combined immunoaffinity enrichment with detection by top-down mass spectrometry to discover and quantify proteoforms with or without the Gly13Asp mutation (G13D) specifically in the KRAS4b isoform. The workflow was applied first to isogenic KRAS colorectal cancer (CRC) cell lines and then to patient CRC tumors with matching KRAS genotypes. In two cellular models, a direct link between the knockout of the mutant G13D allele and the complete nitrosylation of cysteine 118 of the remaining WT KRAS4b was observed. Analysis of tumor samples quantified the percentage of mutant KRAS4b actually present in cancer tissue and identified major differences in the levels of C-terminal carboxymethylation, a modification critical for membrane association. These data from CRC cells and human tumors suggest mechanisms of posttranslational regulation that are highly context-dependent and which lead to preferential production of specific KRAS4b proteoforms.
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Affiliation(s)
- Ioanna Ntai
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Luca Fornelli
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Caroline J DeHart
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Josiah E Hutton
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Peter F Doubleday
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Richard D LeDuc
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Alexandra J van Nispen
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Ryan T Fellers
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Gordon Whiteley
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892
| | - Neil L Kelleher
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208;
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
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248
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Shahid MA, Marenda MS, Markham PF, Noormohammadi AH. Complementation of the Mycoplasma synoviae MS-H vaccine strain with wild-type obg influencing its growth characteristics. PLoS One 2018; 13:e0194528. [PMID: 29590172 PMCID: PMC5874028 DOI: 10.1371/journal.pone.0194528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 03/05/2018] [Indexed: 11/19/2022] Open
Abstract
The temperature-sensitive (ts+) Mycoplasma synoviae vaccine strain MS-H harbors a non-synonymous mutation which results in Glycine to Arginine substitution at position 123 in the highly conserved glycine-rich motif of Obg-fold in the GTP-binding protein Obg. In-silico analysis of the wild-type and mutant Obgs of M. synoviae has indicated that this amino acid substitution affects structure of the protein, potentially leading to abrogation of Obg function in vivo. Present study was conducted to develop the first expression vector for M. synoviae and to investigate the potential effect(s) of complementation of MS-H vaccine with the wild-type obg from 86079/7NS, the parent strain of MS-H. An oriC vector, pKS-VOTL, harboring the 86079/7NS obg gene, downstream of the variable lipoprotein haemagglutinin (vlhA) gene promoter, also cloned from 86079/7NS, was used to transform MS-H. The plasmid was localised at the chromosomal oriC locus of MS-H without any detectable integration at the chromosomal obg locus. Analysis of the MS-H transformants revealed abundant obg transcripts as well as Obg protein, when compared to the MS-H transformed with a similar vector, pMAS-LoriC, lacking obg coding sequence. The MS-H transformants complemented with wild-type Obg maintained their original temperature-sensitivity phenotype (consistent with MS-H vaccine) but, when compared to the MS-H transformed with pMAS-LoriC, had significantly higher (p < 0.05) growth rate and viability at the permissive (33°C) and non-permissive temperature (39.5°C), respectively. Analysis of Obg expression in MS-H and its wild-type parent strain revealed comparatively lower levels of Obg in MS-H. These results indicate that not only the mutation in Obg, but also the level of Obg expression, can confer functional abnormalities in the bacterial host. Furthermore, with the construction of first expression vector for M. synoviae, this study has set foundation for the development of recombinant vaccine(s) based on MS-H.
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Affiliation(s)
- Muhammad A. Shahid
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Marc S. Marenda
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Philip F. Markham
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Amir H. Noormohammadi
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
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249
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Casy W, Prater AR, Cornish PV. Operative Binding of Class I Release Factors and YaeJ Stabilizes the Ribosome in the Nonrotated State. Biochemistry 2018; 57:1954-1966. [PMID: 29499110 DOI: 10.1021/acs.biochem.7b00824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During translation, the small subunit of the ribosome rotates with respect to the large subunit primarily between two states as mRNA is being translated into a protein. At the termination of bacterial translation, class I release factors (RFs) bind to a stop codon in the A-site and catalyze the release of the peptide chain from the ribosome. Periodically, mRNA is truncated prematurely, and the translating ribosome stalls at the end of the mRNA forming a nonstop complex requiring one of several ribosome rescue factors to intervene. One factor, YaeJ, is structurally homologous with the catalytic region of RFs but differs by binding to the ribosome directly through its C-terminal tail. Structures of the ribosome show that the ribosome adopts the nonrotated state conformation when these factors are bound. However, these studies do not elucidate the influence of binding to cognate or noncognate codons on the dynamics of intersubunit rotation. Here, we investigate the effects of wild-type and mutant forms of RF1, RF2, and YaeJ binding on ribosome intersubunit rotation using single-molecule Förster resonance energy transfer. We show that both RF1 binding and RF2 binding are sufficient to shift the population of posthydrolysis ribosome complexes from primarily the rotated to the nonrotated state only when a cognate stop codon is present in the A-site. Similarly, YaeJ binding stabilizes nonstop ribosomal complexes in the nonrotated state. Along with previous studies, these results are consistent with the idea that directed conformational changes and binding of subsequent factors to the ribosome are requisite for efficient termination and ribosome recycling.
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Affiliation(s)
- Widler Casy
- Department of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
| | - Austin R Prater
- Department of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
| | - Peter V Cornish
- Department of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
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250
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Affiliation(s)
- Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94143, USA
- Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
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