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Frank PH, Hong M, Higgins B, Perkins S, Taylor T, Wall VE, Drew M, Waybright T, Gillette W, Esposito D, Messing S. Adapting recombinant bacterial alkaline phosphatase for nucleotide exchange of small GTPases. Protein Expr Purif 2024; 218:106446. [PMID: 38395209 PMCID: PMC11000209 DOI: 10.1016/j.pep.2024.106446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/05/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
The small GTPase Rat sarcoma virus proteins (RAS) are key regulators of cell growth and involved in 20-30% of cancers. RAS switches between its active state and inactive state via exchange of GTP (active) and GDP (inactive). Therefore, to study active protein, it needs to undergo nucleotide exchange to a non-hydrolysable GTP analog. Calf intestine alkaline phosphatase bound to agarose beads (CIP-agarose) is regularly used in a nucleotide exchange protocol to replace GDP with a non-hydrolysable analog. Due to pandemic supply problems and product shortages, we found the need for an alternative to this commercially available product. Here we describe how we generated a bacterial alkaline phosphatase (BAP) with an affinity tag bound to an agarose bead. This BAP completely exchanges the nucleotide in our samples, thereby demonstrating an alternative to the commercially available product using generally available laboratory equipment.
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Affiliation(s)
- Peter H Frank
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Min Hong
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Brianna Higgins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Shelley Perkins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Vanessa E Wall
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Matthew Drew
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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2
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Li X, Dan X, Liu J, Lv Q, Li X. Translation elongation factor-1α is pivotal for plant heat tolerance despite its pronounced heat-induced aggregation. Plant Physiol Biochem 2024; 210:108649. [PMID: 38653099 DOI: 10.1016/j.plaphy.2024.108649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
The translation elongation factor 1α (EF1α) protein is a highly conserved G protein that is crucial for protein translation in all eukaryotic organisms. EF1α quickly became insoluble at temperatures 42 °C treatment for 2h in vitro, but generally remained soluble in vivo even after being exposed to temperatures as high as 45 °C for an extended period, which suggests that protective mechanisms exist for keeping EF1α soluble in plant cells under heat stress. EF1α had fast in vivo insolubilization when exposed to 45 °C, resulting in about 40% of the protein aggregating after 9 h. Given its established role in protein translation, heat-induced aggregation is most likely to impact the function of the elongation factor. Overexpression of constitutive mutants in both GTP-bound and GDP-bound forms of EF1α resulted in significantly decreased heat tolerance. These findings provide evidence to support the critical role of EF1α, a thermosensitive protein, in the heat tolerance of plants.
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Affiliation(s)
- Xifeng Li
- College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China; College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
| | - Xinya Dan
- College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Jia Liu
- College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Qiaoqiao Lv
- College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Xie Li
- College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
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3
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Ayano T, Yokosawa T, Oki M. GTP-dependent regulation of heterochromatin fluctuations at subtelomeric regions in Saccharomyces cerevisiae. Genes Cells 2024; 29:217-230. [PMID: 38229233 DOI: 10.1111/gtc.13094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024]
Abstract
In eukaryotes, single cells in a population display different transcriptional profiles. One of the factors regulating this heterogeneity is the chromatin state in each cell. However, the mechanisms of epigenetic chromatin regulation of specific chromosomal regions remain unclear. Therefore, we used single-cell tracking system to analyze IMD2. IMD2 is located at the subtelomeric region of budding yeast, and its expression is epigenetically regulated by heterochromatin fluctuations. Treatment with mycophenolic acid, an inhibitor of de novo GTP biosynthesis, triggered a decrease in GTP, which caused heterochromatin fluctuations at the IMD2 locus. Interestingly, within individually tracked cells, IMD2 expression state underwent repeated switches even though IMD2 is positioned within the heterochromatin region. We also found that 30% of the cells in a population always expressed IMD2. Furthermore, the addition of nicotinamide, a histone deacetylase inhibitor, or guanine, the GTP biosynthesis factor in salvage pathway of GTP biosynthesis, regulated heterogeneity, resulting in IMD2 expression being uniformly induced or suppressed in the population. These results suggest that gene expression heterogeneity in the IMD2 region is regulated by changes in chromatin structure triggered by slight decreases in GTP.
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Affiliation(s)
- Takahito Ayano
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
- Research Fellowships of Japan Society for the Promotion of Science for Young Scientists (JSPS), Tokyo, Japan
| | - Takuma Yokosawa
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
| | - Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
- Life Science Innovation Center, University of Fukui, Fukui, Japan
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Shivangi, Khan Y, Ekka MK, Meena LS. Structural and functional characterization of mycobacterial PhoH2 and identification of potential inhibitor of its enzymatic activity. Braz J Microbiol 2024:10.1007/s42770-024-01267-4. [PMID: 38386260 DOI: 10.1007/s42770-024-01267-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Mycobacterium tuberculosis is composed of a cumbersome signaling and protein network which partakes in bacterial survival and augments its pathogenesis. Mycobacterial PhoH2 (Mt-PhoH2) is a signaling element and a predictive phosphate starvation protein that works in an ATP-dependent manner. Here, we elaborated the characterization of Mt-PhoH2 through biophysical, biochemical, and computational methods. In addition to its intrinsic ATPase activity, the biochemical experiments revealed its GTPase activity and both activities are metal ion dependent. Magnesium, manganese, copper, iron, nickel, zinc, cesium, calcium, and lithium were examined for their effect on activity, and the optimum activity was found with 10 mM of Mg2+ ions. The kinetic parameters of 3 µM Mt-PhoH2 were observed as Km 4.873 ± 0.44 µM, Vmax 12.3817 ± 0.084 µM/min/mg, Kcat 0.0075 ± 0.00005 s-1, and Kcat/Km 0.0015 ± 0.000001 µM-1 s-1 with GTP. In the case of GTP as a substrate, a 20% decrease in enzymatic activity and a 50% increase in binding affinity of Mt-PhoH2 were observed. The substrates ADP and GDP inhibit the ATPase and GTPase activity of Mt-PhoH2. CD spectroscopy showed the dominance of alpha helix in the secondary structure of Mt-PhoH2, and this structural pattern was altered upon addition of ATP and GTP. In silico inhibitor screening revealed ML141 and NAV_2729 as two potential inhibitors of the catalytic activity of Mt-PhoH2. Mt-PhoH2 is essential for mycobacterial growth as its knockdown strain showed a decreased growth effect. Overall, the present article emphasizes the factors essential for the proper functioning of Mt-PhoH2 which is a participant in the toxin-antitoxin machinery and may also play an important role in phosphate starvation.
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Affiliation(s)
- Shivangi
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Yasmeen Khan
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Mary Krishna Ekka
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, 201 002, India.
- CSIR-Central Drug Research Institute, Lucknow, 226031, India.
- CSIR-Institute of Genomics and Integrative Biology, Academy of Scientific & Innovative Research (AcSIR), Mall Road, Delhi, 110007, India.
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Van Loon JC, Whitfield GB, Wong N, O'Neal L, Henrickson A, Demeler B, O'Toole GA, Parsek MR, Howell PL. Binding of GTP to BifA is required for the production of Pel-dependent biofilms in Pseudomonas aeruginosa. J Bacteriol 2024; 206:e0033123. [PMID: 38197635 PMCID: PMC10882990 DOI: 10.1128/jb.00331-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024] Open
Abstract
The Pel exopolysaccharide is one of the most mechanistically conserved and phylogenetically diverse bacterial biofilm matrix determinants. Pel is a major contributor to the structural integrity of Pseudomonas aeruginosa biofilms, and its biosynthesis is regulated by the binding of cyclic-3',5'-dimeric guanosine monophosphate (c-di-GMP) to the PelD receptor. c-di-GMP is synthesized from two molecules of guanosine triphosphate (GTP) by diguanylate cyclases with GGDEF domains and degraded by phosphodiesterases with EAL or HD-GYP domains. As the P. aeruginosa genome encodes 43 c-di-GMP metabolic enzymes, one way signaling specificity can be achieved is through direct interaction between specific enzyme-receptor pairs. Here, we show that the inner membrane hybrid GGDEF-EAL enzyme, BifA, directly interacts with PelD via its cytoplasmic HAMP, GGDEF, and EAL domains. Despite having no catalytic function, the degenerate active site motif of the BifA GGDEF domain (GGDQF) has retained the ability to bind GTP with micromolar affinity. Mutations that abolish GTP binding result in increased biofilm formation but stable global c-di-GMP levels. Our data suggest that BifA forms a dimer in solution and that GTP binding induces conformational changes in dimeric BifA that enhance the BifA-PelD interaction and stimulate its phosphodiesterase activity, thus reducing c-di-GMP levels and downregulating Pel biosynthesis. Structural comparisons between the dimeric AlphaFold2 model of BifA and the structures of other hybrid GGDEF-EAL proteins suggest that the regulation of BifA by GTP may occur through a novel mechanism.IMPORTANCEc-di-GMP is the most common cyclic dinucleotide used by bacteria to regulate phenotypes such as motility, biofilm formation, virulence factor production, cell cycle progression, and cell differentiation. While the identification and initial characterization of c-di-GMP metabolic enzymes are well established, our understanding of how these enzymes are regulated to provide signaling specificity remains understudied. Here we demonstrate that the inactive GGDEF domain of BifA binds GTP and regulates the adjacent phosphodiesterase EAL domain, ultimately downregulating Pel-dependent P. aeruginosa biofilm formation through an interaction with PelD. This discovery adds to the growing body of literature regarding how hybrid GGDEF-EAL enzymes are regulated and provides additional precedence for studying how direct interactions between c-di-GMP metabolic enzymes and effectors result in signaling specificity.
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Affiliation(s)
- Jaime C. Van Loon
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Gregory B. Whitfield
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Wong
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Lindsey O'Neal
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - G. A. O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Matthew R. Parsek
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - P. Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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Agarwal P, Kumar A, Meena LS. Decoding the structural integrity and multifunctional role of Era protein in the survival of Mycobacterium tuberculosis H 37Rv. J Biomol Struct Dyn 2024:1-16. [PMID: 38319024 DOI: 10.1080/07391102.2024.2309332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/15/2024] [Indexed: 02/07/2024]
Abstract
Era, a widely known GTP binding protein found in many organisms including prokaryotes and eukaryotes and plays a significant role in many fundamental cellular processes like cell growth, differentiation and signaling. In Mycobacterium tuberculosis (Mtb) H37Rv, Era protein had been proved as a GTPase protein but its structural and functional insights are still lacking. Through comparative analysis, structural modeling, docking and using various bioinformatic tools, a detailed investigation of Era was carried out to deduce the structure, function and residues involved in the activity of the protein. Intriguingly, docking results revealed high binding affinity of Era not only with GTP but also with ATP. Myristoylation modifications and phosphorylations on Era were predicted to possibly aid in regulating Era activity and localization; and also the role of Era in translation regulation was foreseen by showing its association with 16s rRNA. Moreover, point mutation of Era residues revealed the effect of W288G and K19G in highly destabilizing the protein structure and activity. Additionally, Era protein was docked with 25 GTPase/ATPase inhibitors, where, Dynasore inhibitor showed the highest affinity for the protein's GTP binding sites and can be used for further drug trials to inhibit growth of mycobacteria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Preeti Agarwal
- AID, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG, Ghaziabad, India
| | - Ajit Kumar
- AID, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG, Ghaziabad, India
| | - Laxman S Meena
- AID, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG, Ghaziabad, India
- CSIR-Central Drug Research Institute, Lucknow, India
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7
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Sharma AK, Pei J, Yang Y, Dyba M, Smith B, Rabara D, Larsen EK, Lightstone FC, Esposito D, Stephen AG, Wang B, Beltran PJ, Wallace E, Nissley DV, McCormick F, Maciag AE. Revealing the mechanism of action of a first-in-class covalent inhibitor of KRASG12C (ON) and other functional properties of oncogenic KRAS by 31P NMR. J Biol Chem 2024; 300:105650. [PMID: 38237681 PMCID: PMC10877953 DOI: 10.1016/j.jbc.2024.105650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 02/17/2024] Open
Abstract
Individual oncogenic KRAS mutants confer distinct differences in biochemical properties and signaling for reasons that are not well understood. KRAS activity is closely coupled to protein dynamics and is regulated through two interconverting conformations: state 1 (inactive, effector binding deficient) and state 2 (active, effector binding enabled). Here, we use 31P NMR to delineate the differences in state 1 and state 2 populations present in WT and common KRAS oncogenic mutants (G12C, G12D, G12V, G13D, and Q61L) bound to its natural substrate GTP or a commonly used nonhydrolyzable analog GppNHp (guanosine-5'-[(β,γ)-imido] triphosphate). Our results show that GppNHp-bound proteins exhibit significant state 1 population, whereas GTP-bound KRAS is primarily (90% or more) in state 2 conformation. This observation suggests that the predominance of state 1 shown here and in other studies is related to GppNHp and is most likely nonexistent in cells. We characterize the impact of this differential conformational equilibrium of oncogenic KRAS on RAF1 kinase effector RAS-binding domain and intrinsic hydrolysis. Through a KRAS G12C drug discovery, we have identified a novel small-molecule inhibitor, BBO-8956, which is effective against both GDP- and GTP-bound KRAS G12C. We show that binding of this inhibitor significantly perturbs state 1-state 2 equilibrium and induces an inactive state 1 conformation in GTP-bound KRAS G12C. In the presence of BBO-8956, RAF1-RAS-binding domain is unable to induce a signaling competent state 2 conformation within the ternary complex, demonstrating the mechanism of action for this novel and active-conformation inhibitor.
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Affiliation(s)
- Alok K Sharma
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA.
| | - Jun Pei
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Yue Yang
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Marcin Dyba
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Brian Smith
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Dana Rabara
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Erik K Larsen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Felice C Lightstone
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Bin Wang
- BridgeBio Oncology Therapeutics, BridgeBio Pharma, Inc, Palo Alto, California, USA
| | - Pedro J Beltran
- BridgeBio Oncology Therapeutics, BridgeBio Pharma, Inc, Palo Alto, California, USA
| | - Eli Wallace
- BridgeBio Oncology Therapeutics, BridgeBio Pharma, Inc, Palo Alto, California, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA; BridgeBio Oncology Therapeutics, BridgeBio Pharma, Inc, Palo Alto, California, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Anna E Maciag
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA.
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8
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Lin P, Qian J, Huang CC, Xu WM, Wang YY, Gao ZR, Zheng SQ, Wang P, Jia DQ, Feng Q, Yang JL. RGD-p21Ras-scFv expressed prokaryotically on a pilot scale inhibits ras-driven colorectal cancer growth by blocking p21Ras- GTP. BMC Cancer 2024; 24:71. [PMID: 38216883 PMCID: PMC10787443 DOI: 10.1186/s12885-023-11686-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/28/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Ras gene mutation and/or overexpression are drivers in the progression of cancers, including colorectal cancer. Blocking the Ras signaling has become a significant strategy for cancer therapy. Previously, we constructed a recombinant scFv, RGD-p21Ras-scFv by linking RGD membrane-penetrating peptide gene with the anti-p21Ras scFv gene. Here, we expressed prokaryotically RGD-p21Ras-scFv on a pilot scale, then investigated the anti-tumor effect and the mechanism of blocking Ras signaling. METHODS The E. coli bacteria which could highly express RGD-p21Ras-scFv was screened and grown in 100 L fermentation tank to produce RGD-p21Ras-scFv on optimized induced expression conditions. The scFv was purified from E. coli bacteria using His Ni-NTA column. ELISA was adopted to test the immunoreactivity of RGD-p21Ras-scFv against p21Ras proteins, and the IC50 of RGD-p21Ras-scFv was analyzed by CCK-8. Immunofluorescence colocalization and pull-down assays were used to determine the localization and binding between RGD-p21Ras-scFv and p21Ras. The interaction forces between RGD-p21Ras-scFv and p21Ras after binding were analyzed by molecular docking, and the stability after binding was determined by molecular dynamics simulations. p21Ras-GTP interaction was detected by Ras pull-down. Changes in the MEK-ERK /PI3K-AKT signaling paths downstream of Ras were detected by WB assays. The anti-tumor activity of RGD-p21Ras-scFv was investigated by nude mouse xenograft models. RESULTS The technique of RGD-p21Ras-scFv expression on a pilot scale was established. The wet weight of the harvested bacteria was 31.064 g/L, and 31.6 mg RGD-p21Ras-scFv was obtained from 1 L of bacterial medium. The purity of the recombinant antibody was above 85%, we found that the prepared on a pilot scale RGD-p21Ras-scFv could penetrate the cell membrane of colon cancer cells and bind to p21Ras, then led to reduce of p21Ras-GTP (active p21Ras). The phosphorylation of downstream effectors MEK-ERK /PI3K-AKT was downregulated. In vivo antitumor activity assays showed that the RGD-p21Ras-scFv inhibited the proliferation of colorectal cancer cell lines. CONCLUSION RGD-p21Ras-scFv prokaryotic expressed on pilot-scale could inhibited Ras-driven colorectal cancer growth by partially blocking p21Ras-GTP and might be able to be a hidden therapeutic antibody for treating RAS-driven tumors.
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Affiliation(s)
- Peng Lin
- Medical school, Kunming University of Science and Technology, Kunming, 650500, P.R. China
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Jing Qian
- Medical school, Kunming University of Science and Technology, Kunming, 650500, P.R. China
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
- Faculty of Life science and Technology, Kunming University of Science and Technology, Kunming, 650500, P.R. China
| | - Cheng-Cheng Huang
- Medical school, Kunming University of Science and Technology, Kunming, 650500, P.R. China
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Wen-Mang Xu
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Yuan-Yuan Wang
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Zi-Ran Gao
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Shi-Qi Zheng
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
- The Graduate School, Kunming Medical University, Kunming, 650500, P.R. China
| | - Peng Wang
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Da-Qi Jia
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
- The Graduate School, Kunming Medical University, Kunming, 650500, P.R. China
| | - Qiang Feng
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China.
| | - Ju-Lun Yang
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China.
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9
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Scott KL, Halfmann CT, Hoefakker AD, Purkayastha P, Wang TC, Lele TP, Roux KJ. Nucleocytoplasmic transport rates are regulated by cellular processes that modulate GTP availability. bioRxiv 2023:2023.12.29.573651. [PMID: 38234722 PMCID: PMC10793428 DOI: 10.1101/2023.12.29.573651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Nucleocytoplasmic transport (NCT), the facilitated diffusion of cargo molecules between the nucleus and cytoplasm through nuclear pore complexes (NPCs), enables numerous fundamental eukaryotic cellular processes. Ran GTPase uses cellular energy in the direct form of GTP to create a gradient across the nuclear envelope (NE) that drives the majority of NCT. We report here that changes in GTP availability resulting from altered cellular physiology modulate the rate of NCT, as monitored using synthetic and natural cargo, and the dynamics of Ran itself. Cell migration, cell spreading and/or modulation of the cytoskeleton or its connection to the nucleus alter GTP availability and thus rates of NCT, regulating RNA export and protein synthesis. These findings support a model in which changes in cellular physiology that alter GTP availability can regulate the rate of NCT, impacting fundamental cellular processes that extensively utilize NCT.
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Affiliation(s)
- Kelsey L. Scott
- Enabling Technologies Group, Sanford Research, Sioux Falls SD
| | | | - Allison D. Hoefakker
- Enabling Technologies Group, Sanford Research, Sioux Falls SD
- Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD
| | - Purboja Purkayastha
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Ting Ching Wang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Tanmay P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas
- Department of Translational Medical Sciences, Texas A&M University, Houston, Texas
| | - Kyle J. Roux
- Enabling Technologies Group, Sanford Research, Sioux Falls SD
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD
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10
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Niu M, Liang X, Zhao H, Li H, Fu X, Liu C. Bipolar hemicyanine cationic probe for simultaneous sensing of ATP and GTP. Spectrochim Acta A Mol Biomol Spectrosc 2023; 303:123249. [PMID: 37579665 DOI: 10.1016/j.saa.2023.123249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/19/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023]
Abstract
Adenosine 5'-triphosphate (ATP) and guanosine 5'-triphosphate (GTP) are the most essential energy source in enormous biological processes. Various probes for ATP or GTP sensing, have been widely established, but the probe that could simultaneously monitor ATP and GTP is still rarely reported. Herein, we report a bipolar hemicyanine cationic probe for simultaneous sensing of ATP and GTP via a one-step monitoring process. This probe exhibited strong affinity to ATP and GTP through intramolecular electrostatic and π-π stacking interactions, which the binding constant on each step were determined as 6.15 × 107 M-1 and 1.57 × 106 M-1 for ATP, 3.19 × 107 M-1 and 3.81 × 106 M-1 for GTP. The sensitivity and specificity of this probe toward ATP or GTP over other twelve biological analogues (adenosine 5'-diphosphate (ADP), adenosine 5'-monophosphate (AMP), guanosine 5'-diphosphate (GDP), guanosine 5'-monophosphate (GMP), Etc.) have also been successfully demonstrated. Furthermore, due to the rapid response rate (within 10 s), we also proved that this probe could be employed as a monitor tool during the ATP or GTP-related enzymatic reaction process.
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Affiliation(s)
- Mengxing Niu
- School of Applied Engineering, Henan University of Science and Technology, Sanmenxia 472000, PR China
| | - Xiaofei Liang
- School of Music, Henan University, Kaifeng 475001, PR China
| | - Haotian Zhao
- Department of Physical Education, Jiangnan University, Wuxi 214122, PR China
| | - Huixin Li
- School of Sport Science, Beijing Sport University, Beijing 100084, PR China
| | - Xuancheng Fu
- Department of Chemistry, Syracuse University, Syracuse 13244, United States.
| | - Chang Liu
- School of Sport Science, Beijing Sport University, Beijing 100084, PR China.
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11
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Abstract
Metastatic progression is regulated by metastasis promoter and suppressor genes. NME1, the prototypic and first described metastasis suppressor gene, encodes a nucleoside diphosphate kinase (NDPK) involved in nucleotide metabolism; two related family members, NME2 and NME4, are also reported as metastasis suppressors. These proteins physically interact with members of the GTPase dynamin family, which have key functions in membrane fission and fusion reactions necessary for endocytosis and mitochondrial dynamics. Evidence supports a model in which NDPKs provide GTP to dynamins to maintain a high local GTP concentration for optimal dynamin function. NME1 and NME2 are cytosolic enzymes that provide GTP to dynamins at the plasma membrane, which drive endocytosis, suggesting that these NMEs are necessary to attenuate signaling by receptors on the cell surface. Disruption of NDPK activity in NME-deficient tumors may thus drive metastasis by prolonging signaling. NME4 is a mitochondrial enzyme that interacts with the dynamin OPA1 at the mitochondria inner membrane to drive inner membrane fusion and maintain a fused mitochondrial network. This function is consistent with the current view that mitochondrial fusion inhibits the metastatic potential of tumor cells whereas mitochondrial fission promotes metastasis progression. The roles of NME family members in dynamin-mediated endocytosis and mitochondrial dynamics and the intimate link between these processes and metastasis provide a new framework to understand the metastasis suppressor functions of NME proteins.
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Affiliation(s)
- Céline Prunier
- Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Philippe Chavrier
- Actin and Membrane Dynamics Laboratory, Institut Curie - Research Center, CNRS UMR144, PSL Research University, Paris, France
| | - Mathieu Boissan
- Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France.
- Laboratoire de Biochimie Endocrinienne Et Oncologique, Oncobiologie Cellulaire Et Moléculaire, APHP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Paris, France.
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12
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Muthukumar VC. The dynamics of Escherichia coli FtsZ dimer. J Biomol Struct Dyn 2023:1-14. [PMID: 38014448 DOI: 10.1080/07391102.2023.2287486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Abstract
The E. coli FtsZ dimer was studied to gain insights into FtsZ protofilament formation. In the simulation study of the M. janaschii dimer it was found that the monomer-monomer contacts in the GDP bound dimer is lower which results in the high curvature of the GDP bound protofilaments. In this study, the E. coli FtsZ dimer was simulated. The initial structure was obtained from our previous study in which we had simulated the E. coli FtsZ monomer with its C-terminal IDR (Intrinsically Disordered Region). The M. janaschii FtsZ dimer subunit contacts were used as the starting configuration. Simulations of the dimer were performed with GTP and with GDP. It is found that the central helix H5 closes by about 15 degrees in the simulation with GTP than in the simulation with GDP. The C-terminal IDR and the C-terminal domain region between SC2 and HC2 are found to have much high flexibility and hence exhibit domain motion.Communicated by Ramaswamy H. Sarma.
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13
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Gookin TE, Chakravorty D, Assmann SM. Influence of expression and purification protocols on Gα biochemical activity: kinetics of plant and mammalian G protein cycles. bioRxiv 2023:2023.05.10.540258. [PMID: 37214830 PMCID: PMC10197700 DOI: 10.1101/2023.05.10.540258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Heterotrimeric G proteins, composed of Gα, Gβ, and Gγ subunits, are a class of signal transduction complexes with broad roles in human health and agriculturally relevant plant physiological and developmental traits. In the classic paradigm, guanine nucleotide binding to the Gα subunit regulates the activation status of the complex. We sought to develop improved methods for heterologous expression and rapid purification of Gα subunits. Using GPA1, the sole canonical Gα subunit of the model plant species, Arabidopsis thaliana, we observed that, compared to conventional purification methods, rapid StrepII-tag mediated purification facilitates isolation of protein with increased GTP binding and hydrolysis activities. Human GNAI1 purified using our approach also displayed the expected binding and hydrolysis activities, indicating our protocol is applicable to mammalian Gα subunits, potentially including those for which purification of enzymatically active protein has been historically problematic. We subsequently utilized domain swaps of GPA1 and human GNAO1 to demonstrate that the inherent instability of GPA1 is a function of the interaction between the Ras and helical domains. Additionally, we found that GPA1-GNAO1 domain swaps partially uncouple the instability from the rapid nucleotide binding kinetics displayed by GPA1.
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Affiliation(s)
- Timothy E. Gookin
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - David Chakravorty
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sarah M. Assmann
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
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14
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Takeuchi K, Senda M, Ikeda Y, Okuwaki K, Fukuzawa K, Nakagawa S, Sasaki M, Sasaki AT, Senda T. Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ. FEBS J 2023; 290:4419-4428. [PMID: 36856076 PMCID: PMC10471773 DOI: 10.1111/febs.16763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/02/2023]
Abstract
Over 4 billion years of evolution, multiple mutations, including nucleotide substitutions, gene and genome duplications and recombination, have established de novo genes that translate into proteins with novel properties essential for high-order cellular functions. However, molecular processes through which a protein evolutionarily acquires a novel function are mostly speculative. Recently, we have provided evidence for a potential evolutionary mechanism underlying how, in mammalian cells, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) evolved into a GTP sensor from ATP-utilizing kinase. Mechanistically, PI5P4Kβ has acquired the guanine efficient association (GEA) motif by mutating its nucleotide base recognition sequence, enabling the evolutionary transition from an ATP-dependent kinase to a distinct GTP/ATP dual kinase with its KM for GTP falling into physiological GTP concentrations-the genesis of GTP sensing activity. Importantly, the GTP sensing activity of PI5P4Kβ is critical for the manifestation of cellular metabolism and tumourigenic activity in the multicellular organism. The combination of structural, biochemical and biophysical analyses used in our study provides a novel framework for analysing how a protein can evolutionarily acquire a novel activity, which potentially introduces a critical function to the cell.
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Affiliation(s)
- Koh Takeuchi
- Graduate School of Pharmacological Sciences, The University of Tokyo, Japan
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Ibaraki, Japan
| | - Yoshiki Ikeda
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, Hirakata, Japan
| | - Koji Okuwaki
- Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - Kaori Fukuzawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Mika Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
- Department of Cancer Biology, University of Cincinnati College of Medicine, OH, USA
- Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, Cincinnati, OH, USA
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Department of Clinical and Molecular Genetics, Hiroshima University Hospital, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Ibaraki, Japan
- Department of Accelerator Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), Ibaraki, Japan
- Faculty of Pure and Applied Sciences, University of Tsukuba, Ibaraki, Japan
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15
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Bartas M, Slychko K, Červeň J, Pečinka P, Arndt-Jovin DJ, Jovin TM. Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions. Int J Mol Sci 2023; 24:10740. [PMID: 37445918 DOI: 10.3390/ijms241310740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
The dynamic processes operating on genomic DNA, such as gene expression and cellular division, lead inexorably to topological challenges in the form of entanglements, catenanes, knots, "bubbles", R-loops, and other outcomes of supercoiling and helical disruption. The resolution of toxic topological stress is the function attributed to DNA topoisomerases. A prominent example is the negative supercoiling (nsc) trailing processive enzymes such as DNA and RNA polymerases. The multiple equilibrium states that nscDNA can adopt by redistribution of helical twist and writhe include the left-handed double-helical conformation known as Z-DNA. Thirty years ago, one of our labs isolated a protein from Drosophila cells and embryos with a 100-fold greater affinity for Z-DNA than for B-DNA, and identified it as topoisomerase II (gene Top2, orthologous to the human UniProt proteins TOP2A and TOP2B). GTP increased the affinity and selectivity for Z-DNA even further and also led to inhibition of the isomerase enzymatic activity. An allosteric mechanism was proposed, in which topoII acts as a Z-DNA-binding protein (ZBP) to stabilize given states of topological (sub)domains and associated multiprotein complexes. We have now explored this possibility by comprehensive bioinformatic analyses of the available protein sequences of topoII representing organisms covering the whole tree of life. Multiple alignment of these sequences revealed an extremely high level of evolutionary conservation, including a winged-helix protein segment, here denoted as Zτ, constituting the putative structural homolog of Zα, the canonical Z-DNA/Z-RNA binding domain previously identified in the interferon-inducible RNA Adenosine-to-Inosine-editing deaminase, ADAR1p150. In contrast to Zα, which is separate from the protein segment responsible for catalysis, Zτ encompasses the active site tyrosine of topoII; a GTP-binding site and a GxxG sequence motif are in close proximity. Quantitative Zτ-Zα similarity comparisons and molecular docking with interaction scoring further supported the "B-Z-topoII hypothesis" and has led to an expanded mechanism for topoII function incorporating the recognition of Z-DNA segments ("Z-flipons") as an inherent and essential element. We further propose that the two Zτ domains of the topoII homodimer exhibit a single-turnover "conformase" activity on given G(ate) B-DNA segments ("Z-flipins"), inducing their transition to the left-handed Z-conformation. Inasmuch as the topoII-Z-DNA complexes are isomerase inactive, we infer that they fulfill important structural roles in key processes such as mitosis. Topoisomerases are preeminent targets of anti-cancer drug discovery, and we anticipate that detailed elucidation of their structural-functional interactions with Z-DNA and GTP will facilitate the design of novel, more potent and selective anti-cancer chemotherapeutic agents.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Kristyna Slychko
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Donna J Arndt-Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Thomas M Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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16
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Pospieszna B, Kusy K, Slominska EM, Ciekot-Sołtysiak M, Zieliński J. Sports Participation Promotes Beneficial Adaptations in the Erythrocyte Guanylate Nucleotide Pool in Male Athletes Aged 20-90 Years. Clin Interv Aging 2023; 18:987-997. [PMID: 37377627 PMCID: PMC10292611 DOI: 10.2147/cia.s406555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Introduction The guanine nucleotide pool (GTP, guanosine-5'-triphosphate; GDP, guanosine-5'-diphosphate, and GMP, guanosine-5'-monophosphate) is an essential energy donor in various biological processes (eg protein synthesis and gluconeogenesis) and secures several vital regulatory functions in the human body. The study aimed to predict the trends of age-related changes in erythrocyte guanine nucleotides and examine whether competitive sport and related physical training promote beneficial adaptations in erythrocyte guanylate concentrations. Methods The study included 86 elite endurance runners (EN) aged 20-81 years, 58 sprint-trained athletes (SP) aged 21-90 years, and 62 untrained individuals (CO) aged 20-68 years. Results The concentration of erythrocyte GTP and total guanine nucleotides (TGN) were highest in the SP group, lower in the EN group, and lowest in the CO group. Both athletic groups had higher guanylate energy charge (GEC) values than the CO group (p = 0.012). Concentrations of GTP, TGN, and GEC value significantly decreased, while GDP and GMP concentrations progressively increased with age. Conclusion Such a profile of change suggests a deterioration of the GTP-related regulatory function in older individuals. Our study explicitly shows that lifelong sports participation, especially of sprint-oriented nature, allows for maintaining a higher erythrocyte guanylate pool concentration, supporting cells' energy metabolism, regulatory and transcription properties, and thus more efficient overall body functioning.
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Affiliation(s)
- Barbara Pospieszna
- Department of Athletics, Strength and Conditioning, Poznan University of Physical Education, Poznan, Poland
| | - Krzysztof Kusy
- Department of Athletics, Strength and Conditioning, Poznan University of Physical Education, Poznan, Poland
| | | | - Monika Ciekot-Sołtysiak
- Department of Athletics, Strength and Conditioning, Poznan University of Physical Education, Poznan, Poland
| | - Jacek Zieliński
- Department of Athletics, Strength and Conditioning, Poznan University of Physical Education, Poznan, Poland
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17
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Takizawa Y, Kizawa M, Niwa N, Komura Y, Takahashi M, Koda D, Kurita T, Nakajima T. Specific inhibitory effects of guanosine on breast cancer cell proliferation. Biochem Biophys Res Commun 2023; 673:67-72. [PMID: 37356147 DOI: 10.1016/j.bbrc.2023.06.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]
Abstract
Breast cancer is the most commonly diagnosed cancer and the leading cause of cancer-related death. Drug therapy for breast cancer is currently selected based on the subtype classification; however, many anticancer drugs are highly cytotoxic. Since intracellular levels of GTP are elevated in many cancer cells that undergo a specific cell proliferation cycle, GTP has potential as a target for cancer therapy. The present study focused on nucleosides and nucleotides and examined intracellular GTP-dependent changes in cell proliferation rates in normal (MCF-12A) and cancer (MCF-7) breast cell lines. Decreased cell proliferation due to a reduction in intracellular GTP levels by mycophenolic acid (MPA), an inosine monophosphate dehydrogenase inhibitor, was observed in both cell lines. The inhibitory effects of MPA on cell proliferation were suppressed when it was applied in combination with Guanosine (Guo), a substrate for GTP salvage synthesis, while the single exposure to Guo suppressed the proliferation of MCF-7 cells only. Although the underlying mechanisms remain unclear, since the inhibitory effects of Guo on cell proliferation did not correlate with GTP or ATP intracellular levels or the GTP/ATP ratio, there may be another cause besides GTP metabolism. Guo inhibited the proliferation of MCF-7, a human breast cancer cell line, but not MCF-12A, a human normal breast cell line. Further studies are needed to investigate the potential of applying Guo as a target for the development of a novel cancer treatment system.
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Affiliation(s)
- Yusuke Takizawa
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan.
| | - Masayuki Kizawa
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Nobuyuki Niwa
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Yuya Komura
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Masato Takahashi
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Daiki Koda
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Takuro Kurita
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Takanori Nakajima
- Division of Clinical Pharmaceutics, Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
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18
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Palácio PB, de Freitas Soares GC, Lima GMB, Cunha PLO, Varela ALN, Facundo HT. Competitive interaction between ATP and GTP regulates mitochondrial ATP-sensitive potassium channels. Chem Biol Interact 2023:110560. [PMID: 37244398 DOI: 10.1016/j.cbi.2023.110560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/28/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Mitochondrial ATP-sensitive K+ channels (mitoKATP) have been recently characterized structurally, and possess a protein through which K+ enters mitochondria (MitoKIR), and a regulatory subunit (mitoSUR). The mitoSUR regulatory subunit is an ATP-binding cassette (ABC) protein isoform 8 (ABCB8). Opening these channels is known to be cardioprotective, but the molecular and physiological mechanisms that activate them are not fully known. Here, to better understand the molecular and physiological mechanisms of activators (GTP) and inhibitors (ATP) on the activity of mitoKATP, we exposed isolated mitochondria to both nucleotides. We also used molecular docking directed to the nucleotide-binding domain of human ABCB8/mitoSUR to test a comparative model of ATP and GTP effects. As expected, we find that ATP dose-dependently inhibits mitoKATP activity (IC50 = 21.24 ± 1.4 mM). However, simultaneous exposure of mitochondria to GTP dose-dependently (EC50 = 13.19 ± 1.33 mM) reversed ATP inhibition. Pharmacological and computational studies suggest that GTP reverses ATP activity competitively. Docking directed to the site of crystallized ADP reveals that both nucleotides bind to mitoSUR with high affinity, with their phosphates directed to the Mg2+ ion and the walker A motif of the protein (SGGGKTT). These effects, when combined, result in GTP binding, ATP displacement, mitochondrial ATP-sensitive K+ transport, and lower formation of reactive oxygen species. Overall, our findings demonstrate the basis for ATP and GTP binding in mitoSUR using a combination of biochemical, pharmacological, and computational experiments. Future studies may reveal the extent to which the balance between ATP and GTP actions contributes toward cardioprotection against ischemic events.
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19
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Becerra SC, Christy BA, Herzig MC, Bynum JA, Darlington DN. Metabolic effects of radiation on red blood cells from cold stored whole blood. Transfusion 2023; 63 Suppl 3:S199-S207. [PMID: 37029665 DOI: 10.1111/trf.17345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/24/2023] [Accepted: 03/20/2023] [Indexed: 04/09/2023]
Abstract
BACKGROUND The risk of military and civilian radiation exposure is increasing, and determining the effects of exposure is a high priority. Irradiation of the nearby blood supply after a nuclear event may impede mobilization of blood products for resuscitation at a time of great need. RBCs are administered to patients with trauma and hemorrhage to transport and deliver oxygen and avoid tissue hypoxia. Here we determine the effects of ionizing radiation on the energy metabolome of RBCs isolated from cold stored whole blood to determine if their stability is compromised by radiation exposure. STUDY DESIGN AND METHODS Whole blood from healthy volunteers was subjected to 0, 25, or 75 Gy of X-irradiation, and stored at 4°C. RBCs were isolated from stored WB at 0, 1, 7, 14, and 21 days of storage. The levels of extracted Krebs cycle intermediates, nicotinamide adenine dinucleotides, and phosphorylated derivatives of adenosine and guanosine were determined by tandem mass spectroscopy. RESULTS Irradiation at either 25Gy or 75Gy had no significant effect on any parameter measured compared to control (0Gy). However, there was a significant change over time in storage for ATP, GDP, and guanosine. DISCUSSION Irradiation at doses up to 75Gy had no effect on the energy metabolome of RBCs prepared from blood stored at 4°C for up to 21 days, suggesting that the RBC energy metabolome is not affected by radiation exposure and the blood can still be used for resuscitation in trauma patients.
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Affiliation(s)
- Sandra C Becerra
- Pathology, Epidemiology and Biostatistics, United States Army Institute of Surgical Research, Fort Sam Houston, Texas, 78234, USA
| | - Barbara A Christy
- Blood and Shock Research, United States Army Institute of Surgical Research, Fort Sam Houston, Texas, 78234, USA
- Department of Molecular Medicine, UT Health San Antonio, San Antonio, Texas, 78229, USA
| | - Maryanne C Herzig
- Blood and Shock Research, United States Army Institute of Surgical Research, Fort Sam Houston, Texas, 78234, USA
| | - James A Bynum
- Blood and Shock Research, United States Army Institute of Surgical Research, Fort Sam Houston, Texas, 78234, USA
- Department of Surgery, UT Health San Antonio, San Antonio, Texas, 78229, USA
| | - Daniel N Darlington
- Blood and Shock Research, United States Army Institute of Surgical Research, Fort Sam Houston, Texas, 78234, USA
- Department of Surgery, UT Health San Antonio, San Antonio, Texas, 78229, USA
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20
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Huang N, Yang D, Chen H, Xiao Y, Wen J, Long Y, Zheng H. Colorimetric detection of biothiols and Hg 2+ based on the peroxidase-like activity of GTP. Spectrochim Acta A Mol Biomol Spectrosc 2023; 290:122263. [PMID: 36571862 DOI: 10.1016/j.saa.2022.122263] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/25/2022] [Accepted: 12/17/2022] [Indexed: 06/18/2023]
Abstract
Guanosine-5'-triphosphate (GTP) not only plays a key role in a majority of cellular processes but also be proposed as a peroxidase-like mimic. Compared with nanozymes, GTP shows good tolerance under harsh conditions, which can be used to construct an easy colorimetric analysis for the detection of biomolecules. Here, on the basis of the peroxidase-like activity of GTP which can catalyze the oxidation of 3,3',5,5'-tetramethyl benzidine dihydrochloride (TMB), colorimetric sensing was established for biothiols and Hg2+. Biothiols reduced the oxTMB back to colorless TMB, and Hg2+ restored the formation of oxTMB, leading to the recovery of color. This method not only provides a platform for the detection of metal ions and biothiols, but also shows that GTP has great potential for analytical detection.
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Affiliation(s)
- Na Huang
- College of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, China
| | - Dan Yang
- College of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, China
| | - Huanhuan Chen
- College of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, China
| | - Yu Xiao
- College of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, China
| | - Jiahui Wen
- College of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, China
| | - Yijuan Long
- College of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, China
| | - Huzhi Zheng
- College of Chemistry and Chemical Engineering, Southwest University, Beibei, Chongqing 400715, China.
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21
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Jiang TT, Ji CL, Yu LJ, Song MK, Li Y, Liao Q, Wei T, Olatunji OJ, Zuo J, Han J. Resveratrol-induced SIRT1 activation inhibits glycolysis-fueled angiogenesis under rheumatoid arthritis conditions independent of HIF-1α. Inflamm Res 2023; 72:1021-1035. [PMID: 37016140 DOI: 10.1007/s00011-023-01728-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/22/2023] [Accepted: 03/28/2023] [Indexed: 04/06/2023] Open
Abstract
OBJECTIVE This study investigated the impacts of SIRT1 activation on rheumatoid arthritis (RA)-related angiogenesis. METHODS HUVECs were cultured by different human serum. Intracellular metabolites were quantified by UPLC-MS. Next, HUVECs and rat vascular epithelial cells under different inflammatory conditions were treated by a SIRT1 agonist resveratrol (RSV). Cytokines and biochemical indicators were detected by corresponding kits. Protein and mRNA expression levels were assessed by immunoblotting and PCR methods, respectively. Angiogenesis capabilities were evaluated by migration, wound-healing and tube-formation experiments. To down-regulate certain signals, gene-specific siRNA were applied. RESULTS Metabolomics study revealed the accelerated glycolysis in RA serum-treated HUVECs. It led to ATP accumulation, but did not affect GTP levels. RSV inhibited pro-angiogenesis cytokines production and glycolysis in both the cells, and impaired the angiogenesis potentials. These effects were mimicked by an energy metabolism interrupter bikini in lipopolysaccharide (LPS)-primed HUVECs, largely independent of HIF-1α. Both RSV and bikinin can inhibit the activation of the GTP-dependent pathway Rho/ROCK and reduce VEGF production. Abrogation of RhoA signaling reinforced HIF-1α silencing-brought changes in LPS-stimulated HUVECs, and overshadowed the anti-angiogenesis potentials of RSV. CONCLUSION Glycolysis provides additional energy to sustain Rho/ROCK activation in RA subjects, which promotes VEGF-driven angiogenesis and can be inhibited by SIRT1 activation.
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Affiliation(s)
- Tian-Tian Jiang
- Xin'an Medicine Research Center, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital), Wuhu, 241000, China
| | - Cong-Lan Ji
- School of Pharmacy, Anhui College of Traditional Chinese Medicine, Wuhu, 241000, China
| | - Li-Jun Yu
- Xin'an Medicine Research Center, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital), Wuhu, 241000, China
- Research Center of Integration of Traditional Chinese and Western Medicine, Wannan Medical College, Wuhu, China
| | - Meng-Ke Song
- Xin'an Medicine Research Center, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital), Wuhu, 241000, China
- Research Center of Integration of Traditional Chinese and Western Medicine, Wannan Medical College, Wuhu, China
| | - Yan Li
- Xin'an Medicine Research Center, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital), Wuhu, 241000, China
| | - Qiang Liao
- Xin'an Medicine Research Center, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital), Wuhu, 241000, China
- Research Center of Integration of Traditional Chinese and Western Medicine, Wannan Medical College, Wuhu, China
| | - Tuo Wei
- Xin'an Medicine Research Center, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital), Wuhu, 241000, China
| | | | - Jian Zuo
- Xin'an Medicine Research Center, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital), Wuhu, 241000, China.
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine, Institution of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, 230000, China.
- Anhui Provincial Engineering Laboratory for Screening and Re-Evaluation of Active Compounds of Herbal Medicines in Southern Anhui, Wuhu, 241000, China.
| | - Jun Han
- Anhui Provincial Engineering Laboratory for Screening and Re-Evaluation of Active Compounds of Herbal Medicines in Southern Anhui, Wuhu, 241000, China.
- School of Pharmacy, Wannan Medical College, Wuhu, 241000, China.
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22
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Martínez RAS, Pinky PD, Harlan BA, Brewer GJ. GTP energy dependence of endocytosis and autophagy in the aging brain and Alzheimer's disease. GeroScience 2023; 45:757-780. [PMID: 36622562 PMCID: PMC9886713 DOI: 10.1007/s11357-022-00717-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
Increased interest in the aging and Alzheimer's disease (AD)-related impairments in autophagy in the brain raise important questions about regulation and treatment. Since many steps in endocytosis and autophagy depend on GTPases, new measures of cellular GTP levels are needed to evaluate energy regulation in aging and AD. The recent development of ratiometric GTP sensors (GEVALS) and findings that GTP levels are not homogenous inside cells raise new issues of regulation of GTPases by the local availability of GTP. In this review, we highlight the metabolism of GTP in relation to the Rab GTPases involved in formation of early endosomes, late endosomes, and lysosomal transport to execute the autophagic degradation of damaged cargo. Specific GTPases control macroautophagy (mitophagy), microautophagy, and chaperone-mediated autophagy (CMA). By inference, local GTP levels would control autophagy, if not in excess. Additional levels of control are imposed by the redox state of the cell, including thioredoxin involvement. Throughout this review, we emphasize the age-related changes that could contribute to deficits in GTP and AD. We conclude with prospects for boosting GTP levels and reversing age-related oxidative redox shift to restore autophagy. Therefore, GTP levels could regulate the numerous GTPases involved in endocytosis, autophagy, and vesicular trafficking. In aging, metabolic adaptation to a sedentary lifestyle could impair mitochondrial function generating less GTP and redox energy for healthy management of amyloid and tau proteostasis, synaptic function, and inflammation.
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Affiliation(s)
| | - Priyanka D. Pinky
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
| | - Benjamin A. Harlan
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
| | - Gregory J. Brewer
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
- Center for Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA 92697 USA
- MIND Institute, University of California Irvine, Irvine, CA 92697 USA
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23
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Carrilero L, Urwin L, Ward E, Choudhury NR, Monk IR, Turner CE, Stinear TP, Corrigan RM. Stringent Response-Mediated Control of GTP Homeostasis Is Required for Long-Term Viability of Staphylococcus aureus. Microbiol Spectr 2023; 11:e0044723. [PMID: 36877013 PMCID: PMC10101089 DOI: 10.1128/spectrum.00447-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 03/07/2023] Open
Abstract
Staphylococcus aureus is an opportunistic bacterial pathogen that often results in difficult-to-treat infections. One mechanism used by S. aureus to enhance survival during infection is the stringent response. This is a stress survival pathway that utilizes the nucleotides (p)ppGpp to reallocate bacterial resources, shutting down growth until conditions improve. Small colony variants (SCVs) of S. aureus are frequently associated with chronic infections, and this phenotype has previously been linked to a hyperactive stringent response. Here, we examine the role of (p)ppGpp in the long-term survival of S. aureus under nutrient-restricted conditions. When starved, a (p)ppGpp-null S. aureus mutant strain ((p)ppGpp0) initially had decreased viability. However, after 3 days we observed the presence and dominance of a population of small colonies. Similar to SCVs, these small colony isolates (p0-SCIs) had reduced growth but remained hemolytic and sensitive to gentamicin, phenotypes that have been tied to SCVs previously. Genomic analysis of the p0-SCIs revealed mutations arising within gmk, encoding an enzyme in the GTP synthesis pathway. We show that a (p)ppGpp0 strain has elevated levels of GTP, and that the mutations in the p0-SCIs all lower Gmk enzyme activity and consequently cellular GTP levels. We further show that in the absence of (p)ppGpp, cell viability can be rescued using the GuaA inhibitor decoyinine, which artificially lowers the intracellular GTP concentration. Our study highlights the role of (p)ppGpp in GTP homeostasis and underscores the importance of nucleotide signaling for long-term survival of S. aureus in nutrient-limiting conditions, such as those encountered during infections. IMPORTANCE Staphylococcus aureus is a human pathogen that upon invasion of a host encounters stresses, such as nutritional restriction. The bacteria respond by switching on a signaling cascade controlled by the nucleotides (p)ppGpp. These nucleotides function to shut down bacterial growth until conditions improve. Therefore, (p)ppGpp are important for bacterial survival and have been implicated in promoting chronic infections. Here, we investigate the importance of (p)ppGpp for long-term survival of bacteria in nutrient-limiting conditions similar to those in a human host. We discovered that in the absence of (p)ppGpp, bacterial viability decreases due to dysregulation of GTP homeostasis. However, the (p)ppGpp-null bacteria were able to compensate by introducing mutations in the GTP synthesis pathway that led to a reduction in GTP build-up and a rescue of viability. This study therefore highlights the importance of (p)ppGpp for the regulation of GTP levels and for long-term survival of S. aureus in restricted environments.
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Affiliation(s)
- Laura Carrilero
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Lucy Urwin
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ezra Ward
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Naznin R. Choudhury
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire E. Turner
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca M. Corrigan
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
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24
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Fleming IR, Hannan JP, Swisher GH, Tesdahl CD, Martyr JG, Cordaro NJ, Erbse AH, Falke JJ. Binding of active Ras and its mutants to the Ras binding domain of PI-3-kinase: A quantitative approach to K D measurements. Anal Biochem 2023; 663:115019. [PMID: 36526022 PMCID: PMC9884175 DOI: 10.1016/j.ab.2022.115019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Ras family GTPases (H/K/N-Ras) modulate numerous effectors, including the lipid kinase PI3K (phosphatidylinositol-3-kinase) that generates growth signal lipid PIP3 (phosphatidylinositol-3,4,5-triphosphate). Active GTP-Ras binds PI3K with high affinity, thereby stimulating PIP3 production. We hypothesize the affinity of this binding interaction could be significantly increased or decreased by Ras mutations at PI3K contact positions, with clinical implications since some Ras mutations at PI3K contact positions are disease-linked. To enable tests of this hypothesis, we have developed an approach combining UV spectral deconvolution, HPLC, and microscale thermophoresis to quantify the KD for binding. The approach measures the total Ras concentration, the fraction of Ras in the active state, and the affinity of active Ras binding to its docking site on PI3K Ras binding domain (RBD) in solution. The approach is illustrated by KD measurements for the binding of active H-Ras and representative mutants, each loaded with GTP or GMPPNP, to PI3Kγ RBD. The findings demonstrate that quantitation of the Ras activation state increases the precision of KD measurements, while also revealing that Ras mutations can increase (Q25L), decrease (D38E, Y40C), or have no effect (G13R) on PI3K binding affinity. Significant Ras affinity changes are predicted to alter PI3K regulation and PIP3 growth signals.
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Affiliation(s)
- Ian R Fleming
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - George Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Corey D Tesdahl
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Justin G Martyr
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA.
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25
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Shemesh A, Ghareeb H, Dharan R, Levi-Kalisman Y, Metanis N, Ringel I, Raviv U. Effect of tubulin self-association on GTP hydrolysis and nucleotide exchange reactions. Biochim Biophys Acta Proteins Proteom 2023; 1871:140869. [PMID: 36400388 DOI: 10.1016/j.bbapap.2022.140869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 10/13/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
We investigated how the self-association of isolated tubulin dimers affects the rate of GTP hydrolysis and the equilibrium of nucleotide exchange. Both reactions are relevant for microtubule (MT) dynamics. We used HPLC to determine the concentrations of GDP and GTP and thereby the GTPase activity of SEC-eluted tubulin dimers in assembly buffer solution, free of glycerol and tubulin aggregates. When GTP hydrolysis was negligible, the nucleotide exchange mechanism was studied by determining the concentrations of tubulin-free and tubulin-bound GTP and GDP. We observed no GTP hydrolysis below the critical conditions for MT assembly (either below the critical tubulin concentration and/or at low temperature), despite the assembly of tubulin 1D curved oligomers and single-rings, showing that their assembly did not involve GTP hydrolysis. Under conditions enabling spontaneous slow MT assembly, a slow pseudo-first-order GTP hydrolysis kinetics was detected, limited by the rate of MT assembly. Cryo-TEM images showed that GTP-tubulin 1D oligomers were curved also at 36 °C. Nucleotide exchange depended on the total tubulin concentration and the molar ratio between tubulin-free GDP and GTP. We used a thermodynamic model of isodesmic tubulin self-association, terminated by the formation of tubulin single-rings to determine the molar fractions of dimers with exposed and buried nucleotide exchangeable sites (E-sites). Our analysis shows that the GDP to GTP exchange reaction equilibrium constant was an order-of-magnitude larger for tubulin dimers with exposed E-sites than for assembled dimers with buried E-sites. This conclusion may have implications on the dynamics at the tip of the MT plus end.
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Affiliation(s)
- Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Hiba Ghareeb
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yael Levi-Kalisman
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
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26
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Zhang Q, Cui K, Yang X, He Q, Yu J, Yang L, Yao G, Guo W, Luo Z, Liu Y, Chen Y, He Z, Lan P. c-Myc-IMPDH1/2 axis promotes tumourigenesis by regulating GTP metabolic reprogramming. Clin Transl Med 2023; 13:e1164. [PMID: 36629054 PMCID: PMC9832425 DOI: 10.1002/ctm2.1164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Metabolic reprogramming is a hallmark of cancer. Metabolic rate-limiting enzymes and oncogenic c-Myc (Myc) play critical roles in metabolic reprogramming to affect tumourigenesis. However, a systematic assessment of metabolic rate-limiting enzymes and their relationship with Myc in human cancers is lacking. METHODS Multiple Pan-cancer datasets were used to develop the transcriptome, genomic alterations, clinical outcomes and Myc correlation landscapes of 168 metabolic rate-limiting enzymes across 20 cancers. Real-time quantitative PCR and immunoblotting were, respectively, used to examine the mRNA and protein of inosine monophosphate dehydrogenase 1 (IMPDH1) in human colorectal cancer (CRC), azoxymethane/dextran sulphate sodium-induced mouse CRC and spontaneous intestinal tumours from APCMin/+ mice. Clone formation, CCK-8 and subcutaneous xenograft model were applied to investigate the possible mechanisms connecting IMPDH1 to CRC growth. Co-immunoprecipitation and protein half-life assay were used to explore the mechanisms underlying the regulation of IMPDH1. RESULTS We explored the global expression patterns, dysregulation profiles, genomic alterations and clinical relevance of 168 metabolic rate-limiting enzymes across human cancers. Importantly, a series of enzymes were associated with Myc, especially top three upregulated enzymes (TK1, RRM2 and IMPDH1) were positively correlated with Myc in multiple cancers. As a proof-of-concept exemplification, we demonstrated that IMPDH1, a rate-limiting enzyme in GTP biosynthesis, is highly upregulated in CRC and promotes CRC growth in vitro and in vivo. Mechanistically, IMPDH2 stabilizes IMPDH1 by decreasing the polyubiquitination levels of IMPDH1, and Myc promotes the de novo GTP biosynthesis by the transcriptional activation of IMPDH1/2. Finally, we confirmed that the Myc-IMPDH1/2 axis is dysregulated across human cancers. CONCLUSIONS Our study highlights the essential roles of metabolic rate-limiting enzymes in tumourigenesis and their crosstalk with Myc, and the Myc-IMPDH1/2 axis promotes tumourigenesis by altering GTP metabolic reprogramming. Our results propose the inhibition of IMPDH1 as a viable option for cancer treatment.
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Affiliation(s)
- Qiang Zhang
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Kaisa Cui
- Wuxi Cancer InstituteAffiliated Hospital of Jiangnan UniversityWuxiJiangsuChina
| | - Xiaoya Yang
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Qilang He
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jing Yu
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of GastroenterologyGuangzhouGuangdongChina
| | - Li Yang
- Zhumadian Central HospitalHuanghuai UniversityZhumadianHenanChina
| | - Gang Yao
- The People's Hospital of Zhengyang CountyZhumadianHenanChina
| | - Weiwei Guo
- The People's Hospital of Zhengyang CountyZhumadianHenanChina
| | - Zhanhao Luo
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of GastroenterologyGuangzhouGuangdongChina
| | - Yugeng Liu
- Center for Synthetic MicrobiomeInstitute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdongChina
| | - Yuan Chen
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zhen He
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of GastroenterologyGuangzhouGuangdongChina
| | - Ping Lan
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of GastroenterologyGuangzhouGuangdongChina
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27
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Bao HY, Wang W, Sun HB, Chen JZ. Binding modes of GDP, GTP and GNP to NRAS deciphered by using Gaussian accelerated molecular dynamics simulations. SAR QSAR Environ Res 2023; 34:65-89. [PMID: 36762439 DOI: 10.1080/1062936x.2023.2165542] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/31/2022] [Indexed: 06/18/2023]
Abstract
Probing binding modes of GDP, GTP and GNP to NRAS are of significance for understanding the regulation mechanism on the activity of RAS proteins. Four separate Gaussian accelerated molecular dynamics (GaMD) simulations were performed on the apo, GDP-, GTP- and GNP-bound NRAS. Dynamics analyses suggest that binding of three ligands highly affects conformational states of the switch domains from NRAS, which disturbs binding of NRAS to its effectors. The analyses of free energy landscapes (FELs) indicate that binding of GDP, GTP and GNP induces more energetic states of NRAS compared to the apo NRAS but the presence of GNP makes the switch domains more ordered than binding of GDP and GNP. The information of interaction networks of ligands with NRAS reveals that the π-π interaction of residue F28 and the salt bridge interactions of K16 and D119 with ligands stabilize binding of GDP, GTP and GNP to NRAS. Meanwhile magnesium ion plays a bridge role in interactions of ligands with NRAS, which is favourable for associations of GDP, GTP and GNP with NRAS. This work is expected to provide useful information for deeply understanding the function and activity of NRAS.
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Affiliation(s)
- H Y Bao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Z Chen
- School of Science, Shandong Jiaotong University, Jinan, China
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28
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Luo M, Han Z, Huang G, Li R, Liu Y, Lu J, Liu L, Miao R. Structural comparison of unconventional G protein YchF with heterotrimeric G protein and small G protein. Plant Signal Behav 2022; 17:2024405. [PMID: 35135414 PMCID: PMC8959515 DOI: 10.1080/15592324.2021.2024405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Guanine nucleotide-binding (G) proteins, namely, phosphate-binding (P) loop GTPases, play a critical role in life processes among different species. Based on the structural characteristics, G proteins can be divided into heterotrimeric G proteins, small G proteins and multiple unique unconventional G proteins. The highly conserved unconventional G protein YchF is composed of a core G domain, an inserted coiled-coil domain, and a TGS domain from the N-terminus to the C-terminus. In this review, we compared the structural characteristics of the G domain in rice OsYchF1 with those of Rattus norvegicus heterotrimeric G protein α-subunit and human small G protein Ras-related G protein C and analyzed the binding modes of these G proteins with GTP or ATP by performing molecular dynamics simulations. In summary, it will provide new insights into the enormous diversity of biological function of G proteins.
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Affiliation(s)
- Maozhen Luo
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiwei Han
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guoye Huang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rongfang Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junjie Lu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rui Miao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- CONTACT Rui Miao College of Life Sciences, Fujian Agriculture and Forestry University, Jinshan, Fuzhou350002, China
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29
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Noronha FS, Jose TT, George A, George LS. Effectiveness of Gatekeeper Training Program ( GTP) on awareness, attitude, mental help seeking intention and gatekeeper behavior among Koraga tribe: A study protocol. F1000Res 2022; 11:291. [PMID: 36704047 PMCID: PMC9839944 DOI: 10.12688/f1000research.109497.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Aim: This study aims to build the capacity of the people at grass root level as gatekeepers of mental health. It will assess the effectiveness of the Gatekeeper Training Program (GTP) on gatekeeper behaviour, awareness, attitude, and mental help seeking intention. Design: An evaluative research approach in two phases. Phase 1: Cross-sectional house-to-house exploratory survey. Phase 2: A quasi-experimental design with multiple follow ups at 0, 6 and 12 months. Method: Data will be collected using standardized tools like Mental Health Knowledge Questionnaire (MHKQ), Community Attitude towards Mentally Ill (CAMIS), Mental Help Seeking Intention (MHSIS) and Gatekeeper Behavior Scale (GBS). For Phase 1, a house-to-house survey will be conducted among the selected colonies of Koraga tribe to determine their awareness, attitude, and mental help seeking intention regarding common mental health problems. Phase 2 includes identification of the leaders/representatives of the selected tribal colonies, and involving them in GTP. Pre-test and multiple post-test will be conducted in Phase 2 at 0, 6, 12 months. The study is funded by Indian Council of Medical Research from 16 August 2021 for 3 years duration. Discussion: Treatment gap in psychiatric disorders remains an issue of great concern. Evidence based research promotes task shifting approaches in dealing with mental health problems in the community. Capacity building programs like GTP for the underprivileged section of the society are important especially in low and middle income group of countries. Impact: This need based GTP, will ensure mental health first aid in the society. Early identification of people with mental health problems at their doorsteps has huge impact on the prognosis of the illness, closing the treatment gap and stigma reduction.
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Affiliation(s)
- Flavia Sharlet Noronha
- Psychiatric (Mental Health) Nursing, Manipal College of Nursing, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
| | - Tessy Treesa Jose
- Psychiatric (Mental Health) Nursing, Manipal College of Nursing, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India,
| | - Anice George
- Pediatric Nursing, Manipal College of Nursing, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
| | - Linu Sara George
- Fundamentals of Nursing, Manipal College of Nursing, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
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Jacewicz A, Dantuluri S, Shuman S. Structures of RNA ligase RtcB in complexes with divalent cations and GTP. RNA 2022; 28:1509-1518. [PMID: 36130078 PMCID: PMC9745838 DOI: 10.1261/rna.079327.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Pyrococcus horikoshii (Pho) RtcB exemplifies a family of binuclear transition metal- and GTP-dependent RNA ligases that join 3'-phosphate and 5'-OH ends via RtcB-(histidinyl-N)-GMP and RNA3'pp5'G intermediates. We find that guanylylation of PhoRtcB is optimal with manganese and less effective with cobalt and nickel. Zinc and copper are inactive and potently inhibit manganese-dependent guanylylation. We report crystal structures of PhoRtcB in complexes with GTP and permissive (Mn, Co, Ni) or inhibitory (Zn, Cu) metals. Zinc and copper occupy the M1 and M2 sites adjacent to the GTP phosphates, as do manganese, cobalt, and nickel. The identity/positions of enzymic ligands for M1 (His234, His329, Cys98) and M2 (Cys98, Asp95, His203) are the same for permissive and inhibitory metals. The differences pertain to: (i) the coordination geometries and phosphate contacts of the metals; and (ii) the orientation of the His404 nucleophile with respect to the GTP α-phosphate and pyrophosphate leaving group. M2 metal coordination geometry correlates with metal cofactor activity, whereby inhibitory Zn2 and Cu2 assume a tetrahedral configuration and contact only the GTP γ-phosphate, whereas Mn2, Co2, and Ni2 coordination complexes are pentahedral and contact the β- and γ-phosphates. The His404-Nε-Pα-O(α-β) angle is closer to apical in Mn (179°), Co (171°), and Ni (169°) structures than in Zn (160°) and Cu (155°) structures. The octahedral Mn1 geometry in our RtcB•GTP•Mn2+ structure, in which Mn1 contacts α-, β-, and γ-phosphates, transitions to a tetrahedral configuration after formation of RtcB•(His404)-GMP•Mn2+ and departure of pyrophosphate.
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Affiliation(s)
- Agata Jacewicz
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Swathi Dantuluri
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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Wolff DW, Bianchi-Smiraglia A, Nikiforov MA. Compartmentalization and regulation of GTP in control of cellular phenotypes. Trends Mol Med 2022; 28:758-769. [PMID: 35718686 PMCID: PMC9420775 DOI: 10.1016/j.molmed.2022.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 10/18/2022]
Abstract
Genetic or pharmacological inhibition of enzymes involved in GTP biosynthesis has substantial biological effects, underlining the need to better understand the function of GTP levels in regulation of cellular processes and the significance of targeting GTP biosynthesis enzymes for therapeutic intervention. Our current understanding of spatiotemporal regulation of GTP metabolism and its role in physiological and pathological cellular processes is far from complete. Novel methodologies such as genetically encoded sensors of free GTP offered insights into intracellular distribution and function of GTP molecules. In the current Review, we provide analysis of recent discoveries in the field of GTP metabolism and evaluate the key enzymes as molecular targets.
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Affiliation(s)
- David W Wolff
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA.
| | - Anna Bianchi-Smiraglia
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Mikhail A Nikiforov
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA.
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Wolff DW, Deng Z, Bianchi-Smiraglia A, Foley CE, Han Z, Wang X, Shen S, Rosenberg MM, Moparthy S, Yun DH, Chen J, Baker BK, Roll MV, Magiera AJ, Li J, Hurley E, Feltri ML, Cox AO, Lee J, Furdui CM, Liu L, Bshara W, LaConte LE, Kandel ES, Pasquale EB, Qu J, Hedstrom L, Nikiforov MA. Phosphorylation of guanosine monophosphate reductase triggers a GTP-dependent switch from pro- to anti-oncogenic function of EPHA4. Cell Chem Biol 2022; 29:970-984.e6. [PMID: 35148834 PMCID: PMC9620470 DOI: 10.1016/j.chembiol.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 11/19/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022]
Abstract
Signal transduction pathways post-translationally regulating nucleotide metabolism remain largely unknown. Guanosine monophosphate reductase (GMPR) is a nucleotide metabolism enzyme that decreases GTP pools by converting GMP to IMP. We observed that phosphorylation of GMPR at Tyr267 is critical for its activity and found that this phosphorylation by ephrin receptor tyrosine kinase EPHA4 decreases GTP pools in cell protrusions and levels of GTP-bound RAC1. EPHs possess oncogenic and tumor-suppressor activities, although the mechanisms underlying switches between these two modes are poorly understood. We demonstrated that GMPR plays a key role in EPHA4-mediated RAC1 suppression. This supersedes GMPR-independent activation of RAC1 by EPHA4, resulting in a negative overall effect on melanoma cell invasion and tumorigenicity. Accordingly, EPHA4 levels increase during melanoma progression and inversely correlate with GMPR levels in individual melanoma tumors. Therefore, phosphorylation of GMPR at Tyr267 is a metabolic signal transduction switch controlling GTP biosynthesis and transformed phenotypes.
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Affiliation(s)
- David W. Wolff
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
| | - Zhiyong Deng
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
| | - Anna Bianchi-Smiraglia
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Colleen E. Foley
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Zhannan Han
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
| | - Xingyou Wang
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | | | - Sudha Moparthy
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
| | - Dong Hyun Yun
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
| | - Jialin Chen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
| | - Brian K. Baker
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
| | - Matthew V. Roll
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
| | - Andrew J. Magiera
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Edward Hurley
- Department of Biochemistry and Neurology, Hunter James Kelly Research Institute, University at Buffalo, Buffalo NY, USA
| | - Maria Laura Feltri
- Department of Biochemistry and Neurology, Hunter James Kelly Research Institute, University at Buffalo, Buffalo NY, USA
| | - Anderson O. Cox
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem NC, USA
| | - Jingyun Lee
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem NC, USA
| | - Cristina M. Furdui
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem NC, USA
| | - Liang Liu
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
| | - Wiam Bshara
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo NY 14203, USA
| | - Leslie E.W. LaConte
- Fralin Biomedical Research Institute at Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
| | - Eugene S. Kandel
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Elena B. Pasquale
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jun Qu
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA
| | - Lizbeth Hedstrom
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA,Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Mikhail A. Nikiforov
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA,Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA,Corresponding author and lead contact: Mikhail A. Nikiforov,
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Takeuchi K, Ikeda Y, Senda M, Harada A, Okuwaki K, Fukuzawa K, Nakagawa S, Yu HY, Nagase L, Imai M, Sasaki M, Lo YH, Ito D, Osaka N, Fujii Y, Sasaki AT, Senda T. The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity. Structure 2022; 30:886-899.e4. [PMID: 35504278 PMCID: PMC9177683 DOI: 10.1016/j.str.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/22/2021] [Accepted: 04/06/2022] [Indexed: 10/18/2022]
Abstract
Unlike most kinases, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) utilizes GTP as a physiological phosphate donor and regulates cell growth under stress (i.e., GTP-dependent stress resilience). However, the genesis and evolution of its GTP responsiveness remain unknown. Here, we reveal that PI5P4Kβ has acquired GTP preference by generating a short dual-nucleotide-recognizing motif called the guanine efficient association (GEA) motif. Comparison of nucleobase recognition with 660 kinases and 128 G proteins has uncovered that most kinases and PI5P4Kβ use their main-chain atoms for adenine recognition, while the side-chain atoms are required for guanine recognition. Mutational analysis of the GEA motif revealed that the acquisition of GTP reactivity is accompanied by an extended activity toward inosine triphosphate (ITP) and xanthosine triphosphate (XTP). Along with the evolutionary analysis data that point to strong negative selection of the GEA motif, these results suggest that the GTP responsiveness of PI5P4Kβ has evolved from a compromised trade-off between activity and specificity, underpinning the development of the GTP-dependent stress resilience.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery and Cellular Molecular Biotechnology Research Institute, National Institute of Advanced Science and Technology, Aomi, Koto, Tokyo 135-0063, Japan; Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan.
| | - Yoshiki Ikeda
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Ayaka Harada
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Koji Okuwaki
- Department of Chemistry and Research Center for Smart Molecules, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Tokyo 142-8501, Japan
| | - So Nakagawa
- Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Hong Yang Yu
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Lisa Nagase
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Misaki Imai
- Molecular Profiling Research Center for Drug Discovery and Cellular Molecular Biotechnology Research Institute, National Institute of Advanced Science and Technology, Aomi, Koto, Tokyo 135-0063, Japan; Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Mika Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yu-Hua Lo
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Doshun Ito
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Natsuki Osaka
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Yuki Fujii
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, Cincinnati, OH 45267, USA.
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan; Department of Accelerator Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), Oho, Tsukuba, Ibaraki 305-0801, Japan; Faculty of Pure and Applied Sciences, University of Tsukuba, Tennodai, Ibaraki 305-8571, Japan.
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Chakraborty A, Halder S, Kishore P, Saha D, Saha S, Sikder K, Basu A. The structure-function analysis of Obg-like GTPase proteins along the evolutionary tree from bacteria to humans. Genes Cells 2022; 27:469-481. [PMID: 35610748 PMCID: PMC9545696 DOI: 10.1111/gtc.12942] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 11/28/2022]
Abstract
Obg proteins belong to P-loop guanine triphosphatase (GTPase) that are conserved from bacteria to humans. Like other GTPases, Obg cycles between guanine triphosphate (GTP) bound "on" state and guanine diphosphate (GDP)-bound "off" state, thereby controlling various cellular processes. Different members of this group have unique structural characteristics; a conserved glycine-rich N-terminal domain known as obg fold, a central conserved nucleotide binding domain, and a less conserved C-terminal domain of other functions. Obg is a ribosome dependent GTPase helps in ribosome maturation by interacting with several proteins of the 50S subunit of the ribosome. Obg proteins have been widely considered as a regulator of cellular functions, helping in DNA replication, cell division. Apart from that, this protein also takes part in various stress adaptation pathways like a stringent response, sporulation, and general stress response. In this particular review, the structural features of ObgE have been highlighted and how the structure plays important role in interacting with regulators like GTP, ppGpp that are crucial for executing biological function has been orchestrated. In particular, we believe that Obg-like proteins can provide a link between different global pathways that are necessary for fine-tuning cellular processes to maintain the cellular energy status.
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Affiliation(s)
- Asmita Chakraborty
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sheta Halder
- Department of Biotechnology, Amity University Kolkata, Kolkata, India
| | - Purvi Kishore
- Department of Biotechnology, Amity University Kolkata, Kolkata, India
| | - Disha Saha
- Department of Biotechnology, Amity University Kolkata, Kolkata, India
| | - Sujata Saha
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Kunal Sikder
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Arnab Basu
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
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Shahroor MA, Lasorsa FM, Porcelli V, Dweikat I, Di Noia MA, Gur M, Agostino G, Shaag A, Rinaldi T, Gasparre G, Guerra F, Castegna A, Todisco S, Abu-Libdeh B, Elpeleg O, Palmieri L. PNC2 (SLC25A36) Deficiency Associated With the Hyperinsulinism/Hyperammonemia Syndrome. J Clin Endocrinol Metab 2022; 107:1346-1356. [PMID: 34971397 DOI: 10.1210/clinem/dgab932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT The hyperinsulinism/hyperammonemia (HI/HA) syndrome, the second-most common form of congenital hyperinsulinism, has been associated with dominant mutations in GLUD1, coding for the mitochondrial enzyme glutamate dehydrogenase, that increase enzyme activity by reducing its sensitivity to allosteric inhibition by GTP. OBJECTIVE To identify the underlying genetic etiology in 2 siblings who presented with the biochemical features of HI/HA syndrome but did not carry pathogenic variants in GLUD1, and to determine the functional impact of the newly identified mutation. METHODS The patients were investigated by whole exome sequencing. Yeast complementation studies and biochemical assays on the recombinant mutated protein were performed. The consequences of stable slc25a36 silencing in HeLa cells were also investigated. RESULTS A homozygous splice site variant was identified in solute carrier family 25, member 36 (SLC25A36), encoding the pyrimidine nucleotide carrier 2 (PNC2), a mitochondrial nucleotide carrier that transports pyrimidine as well as guanine nucleotides across the inner mitochondrial membrane. The mutation leads to a 26-aa in-frame deletion in the first repeat domain of the protein, which abolishes transport activity. Furthermore, knockdown of slc25a36 expression in HeLa cells caused a marked reduction in the mitochondrial GTP content, which likely leads to a hyperactivation of glutamate dehydrogenase in our patients. CONCLUSION We report for the first time a mutation in PNC2/SLC25A36 leading to HI/HA and provide functional evidence of the molecular mechanism responsible for this phenotype. Our findings underscore the importance of mitochondrial nucleotide metabolism and expand the role of mitochondrial transporters in insulin secretion.
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Affiliation(s)
- Maher A Shahroor
- Department of Pediatrics and Genetics, Al Makassed Hospital and Al-Quds University, 95908 Jerusalem, Palestine
- Department of Neonatology, Sunnybrook Health Sciences Center, University of Toronto, M4N 3M5 Toronto, Canada
| | - Francesco M Lasorsa
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, 70125 Bari, Italy
| | - Vito Porcelli
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Imad Dweikat
- Metabolic Unit, An-Najah National University, P467 Nablus, Palestine
| | - Maria Antonietta Di Noia
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Michal Gur
- Department of Genetics, Hadassah, Hebrew University Medical Center, 91120 Jerusalem, Israel
| | - Giulia Agostino
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Avraham Shaag
- Department of Genetics, Hadassah, Hebrew University Medical Center, 91120 Jerusalem, Israel
| | - Teresa Rinaldi
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology "Charles Darwin", University of Rome La Sapienza, 00185 Rome, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences (DIMEC), Unit of Medical Genetics and Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
| | - Flora Guerra
- Department of Medical and Surgical Sciences (DIMEC), Unit of Medical Genetics and Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
| | - Alessandra Castegna
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, 70125 Bari, Italy
| | - Simona Todisco
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Bassam Abu-Libdeh
- Department of Pediatrics and Genetics, Al Makassed Hospital and Al-Quds University, 95908 Jerusalem, Palestine
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, 91120 Jerusalem, Israel
| | - Luigi Palmieri
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, 70125 Bari, Italy
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Adriaansen J, Stanton J, Schaut W, Bowden R. Compliance and cost control for cryopreservation of cellular starting materials: An industry perspective. Cytotherapy 2022:S1465-3249(22)00051-2. [PMID: 35304076 DOI: 10.1016/j.jcyt.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/15/2022] [Accepted: 02/07/2022] [Indexed: 11/20/2022]
Abstract
Over the last decade, cancer immunotherapy has progressed from an academically interesting field to one of the most promising forms of new treatments in which not the cancer but the immune system is treated. In particular, genetic modification for purposeful redirection of autologous T cells is providing hope to many treatment-resistant patients. This personalized form of medicine is radically different from more traditional oncologic drugs. With these evolving medical advancements and more cellular therapies becoming available, some regulatory agencies have created new regulatory requirements to manage the production of these types of products. The regulations are specifically suited for the manufacture of gene and cell therapy products, as they use a risk-based approach towards product development and manufacturing, when there is limited characterization available. The correct interpretation of how and when requirements apply is crucial, since theoretical approaches to implementing GMP can easily lead to disproportionate and unwarranted restrictions that may not address the specific risks that regulators were intending to control. This is especially relevant for cell collection and biopreservation preceding the manufacturing process for products manufactured from autologous T cells. Both the fresh and cryopreserved apheresis materials can be filed as minimally manipulated starting materials to the authorities. The preservation of such cellular material can then routinely be managed using the available regulations for tissues and cells, allowing for a more fit-for-purpose approach to the control measures implemented.
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Strogulski NR, Stefani MA, Böhmer AE, Hansel G, Rodolphi MS, Kopczynski A, de Oliveira VG, Stefani ET, Portela JV, Schmidt AP, Oses JP, Smith DH, Portela LV. Cerebrospinal fluid purinomics as a biomarker approach to predict outcome after severe traumatic brain injury. J Neurochem 2022; 161:173-186. [PMID: 35157328 PMCID: PMC9035090 DOI: 10.1111/jnc.15590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/31/2022] [Indexed: 11/27/2022]
Abstract
Severe traumatic brain injury (TBI) is associated with high rates of mortality and long-term disability linked to neurochemical abnormalities. Although purine-derivatives play important roles in TBI pathogenesis in preclinical models, little is known about potential changes in purine levels and their implications in human TBI. We assessed cerebrospinal fluid (CSF) levels of purines in severe TBI patients as potential biomarkers that predict mortality and long-term dysfunction. This was a cross-sectional study performed in 17 severe TBI patients (Glasgow Coma Scale < 8) and 51 controls. Two to four hours after admission to ICU, patients were submitted to ventricular drainage and CSF collection for quantification of adenine and guanine purine-derivatives by HPLC. TBI patients survival was followed up to 3 days from admission. A neurofunctional assessment was performed through the modified Rankin Scale (mRS) two years after ICU admission. Purine levels were compared between control and TBI patients, and between surviving and non-surviving patients. Relative to controls, TBI patients presented increased CSF levels of GDP, guanosine, adenosine, inosine, hypoxanthine, and xanthine. Further, GTP, GDP, IMP, and xanthine levels were different between surviving and non-surviving patients. Among the purines, guanosine was associated with improved mRS (p=0.042; r= -0.506). Remarkably, GTP displayed predictive value (AUC=0.841, p=0.024) for discriminating survival vs. non-survival patients up to three days from admission. These results support TBI-specific purine signatures, suggesting GTP as a promising biomarker of mortality, and guanosine as an indicator of long-term functional disability.
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Affiliation(s)
- Nathan R Strogulski
- Laboratory of Neurotrauma e Biomarkers, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Marco Antonio Stefani
- Laboratory of Neuroanatomy, Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Ana Elisa Böhmer
- Laboratory of Neurotrauma e Biomarkers, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Gisele Hansel
- Neuroinflammation and Neuroimmunology Laboratory, Brain Institute of Rio Grande do Sul, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Marcelo S Rodolphi
- Laboratory of Neurotrauma e Biomarkers, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Afonso Kopczynski
- Laboratory of Neurotrauma e Biomarkers, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Vitória G de Oliveira
- Laboratory of Neurotrauma e Biomarkers, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Eduarda T Stefani
- Laboratory of Neuroanatomy, Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Juliana V Portela
- Laboratory of Neurotrauma e Biomarkers, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - André P Schmidt
- Laboratory of Neurotrauma e Biomarkers, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Department of Anesthesia and Perioperative Medicine, Hospital de Clínicas de Porto Alegre (HCPA), UFRGS, Porto Alegre, RS, Brazil. Department of Anesthesia, Santa Casa de Porto Alegre, Universidade Federal de Ciências Médicas de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil. Department of Anesthesia, Hospital Nossa Senhora da Conceição, Porto Alegre, RS, Brazil
| | - Jean Pierre Oses
- Programa de Pós-Graduação em Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Douglas H Smith
- Penn Center for Brain Injury and Repair and Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Luis V Portela
- Laboratory of Neurotrauma e Biomarkers, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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Zhang J, Xu J, Li H, Zhang Y, Ma Z, Bechthold A, Yu X. Enhancement of toyocamycin production through increasing supply of precursor GTP in Streptomyces diastatochromogenes 1628. J Basic Microbiol 2022; 62:750-759. [PMID: 35076122 DOI: 10.1002/jobm.202100622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/03/2022] [Accepted: 01/08/2022] [Indexed: 11/07/2022]
Abstract
The nucleoside antibiotic toyocamycin (TM), which is produced by Streptomyces diastatochromogenes 1628, exhibits potent activity against a broad range of phytopathogenic fungi. TM was synthesized through a multi-step reaction, using guanosine triphosphate (GTP) as precursor. Based on a comparison of proteomics data from S. diastatochromogenes 1628 and rifamycin-resistant mutant 1628-T15 with high yield of TM, we determined that the differentially expressed protein X0NBV6 called ribose-phosphate pyrophosphokinase (RHP), which is a rate-limiting enzyme involved in the de novo biosynthesis of GTP, exhibits a higher expression level in mutant 1628-T15. In this study, to elucidate the relationships between RHP, GTP, and TM production, the gene rhp sd encoding RHP was cloned and overexpressed in S. diastatochromogenes strain 1628. The recombinant strain S. diastatochromogenes 1628-RHP exhibited better performance at the transcriptional level of the rhp sd gene, as well as RHP enzymatic activity, intracellular GTP concentration, and TM production, compared to S. diastatochromogenes 1628. Finally, the yield of TM produced by S. diastatochromogenes 1628-RHP (340.2 mg/L) was 133.3% higher than that produced by S. diastatochromogenes1628. Moreover, the transcriptional level of toy genes involved in TM biosynthesis was enhanced due to the overexpression of the rhp sd gene.
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Affiliation(s)
- Jinyao Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Jie Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Huijie Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Yongyong Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Andreas Bechthold
- Pharmaceutical Biology and Biotechnology, Institute for Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
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LaFrance BJ, Roostalu J, Henkin G, Greber BJ, Zhang R, Normanno D, McCollum CO, Surrey T, Nogales E. Structural transitions in the GTP cap visualized by cryo-electron microscopy of catalytically inactive microtubules. Proc Natl Acad Sci U S A 2022; 119:e2114994119. [PMID: 34996871 DOI: 10.1073/pnas.2114994119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2021] [Indexed: 01/27/2023] Open
Abstract
Microtubules (MTs) are polymers of αβ-tubulin heterodimers that stochastically switch between growth and shrinkage phases. This dynamic instability is critically important for MT function. It is believed that GTP hydrolysis within the MT lattice is accompanied by destabilizing conformational changes and that MT stability depends on a transiently existing GTP cap at the growing MT end. Here, we use cryo-electron microscopy and total internal reflection fluorescence microscopy of GTP hydrolysis-deficient MTs assembled from mutant recombinant human tubulin to investigate the structure of a GTP-bound MT lattice. We find that the GTP-MT lattice of two mutants in which the catalytically active glutamate in α-tubulin was substituted by inactive amino acids (E254A and E254N) is remarkably plastic. Undecorated E254A and E254N MTs with 13 protofilaments both have an expanded lattice but display opposite protofilament twists, making these lattices distinct from the compacted lattice of wild-type GDP-MTs. End-binding proteins of the EB family have the ability to compact both mutant GTP lattices and to stabilize a negative twist, suggesting that they promote this transition also in the GTP cap of wild-type MTs, thereby contributing to the maturation of the MT structure. We also find that the MT seam appears to be stabilized in mutant GTP-MTs and destabilized in GDP-MTs, supporting the proposal that the seam plays an important role in MT stability. Together, these structures of catalytically inactive MTs add mechanistic insight into the GTP state of MTs, the stability of the GTP- and GDP-bound lattice, and our overall understanding of MT dynamic instability.
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Jennings MD, Pavitt GD. Quantifying the Binding of Fluorescently Labeled Guanine Nucleotides and Initiator tRNA to Eukaryotic Translation Initiation Factor 2. Methods Mol Biol 2022; 2428:89-99. [PMID: 35171475 DOI: 10.1007/978-1-0716-1975-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The translation initiation factor eIF2 is critical for protein synthesis initiation, and its regulation is central to the integrated stress response (ISR). eIF2 is a G protein, and the activity is regulated by its GDP or GTP-binding status, such that only GTP-bound eIF2 has high affinity for initiator methionyl tRNA. In the ISR, regulatory signaling reduces the availability of eIF2-GTP and so downregulates protein synthesis initiation in cells. Fluorescence spectroscopy can be used as an analytical tool to study protein-ligand interactions in vitro. Here we describe methods to purify eIF2 and assays of its activity, employing analogs of GDP, GTP, and methionyl initiator tRNA ligands to accurately measure their binding affinities.
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Affiliation(s)
- Martin D Jennings
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
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Liu Y, Wang W, Li C, Li M, Zhang C, Dong M, Wang L, Song L. CgRab1 regulates Cgcathepsin L1 expression and participates in the phagocytosis of haemocytes in oyster Crassostrea gigas. Fish Shellfish Immunol 2022; 120:536-546. [PMID: 34952195 DOI: 10.1016/j.fsi.2021.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Rab protein plays an important role in a variety of cellular activities, especially the fusion process of the inner membrane during endocytosis. In the present study, a Rab1 protein (CgRab1) was identified from the Pacific oyster Crassostrea gigas. The full-length cDNA sequence of CgRab1 was of 2248 bp with an open reading frame of 618 bp, encoding a polypeptide of 205 amino acids containing a Rab domain. The deduced amino acid sequence of CgRab1 shared 94.2% and 89.3% identity with Rab1 from Pomacea canaliculata and Homo sapiens respectively. In the phylogenetic tree, CgRab1 was firstly clustered with the Rab1s from Aplysia californica and Pomacea canaliculata to form a sister group with Rab1 from invertebrates. The recombinant CgRab1 protein (rCgRab1) was able to bind GTP. The mRNA transcripts of CgRab1 were highly expressed in oyster haemocytes, and its expression level in oyster haemocytes was significantly up-regulated at 24 h after the stimulations with Vibro splendidus, which was 2.43-fold (p < 0.01) of that in the control group. After the expression of CgRab1 was knocked down (0.38-fold of that in EGFP-RNAi experimental group) by RNAi,the protein expression of Cgcathepsin L1 were reduced (0.63-fold, p < 0.01) compared with that in EGFP-RNAi experimental group. The phagocytic rate and phagocytic index of haemocytes in CgRab1-RNAi oysters decreased after V. splendidus stimulation, which was 0.50-fold (p < 0.01) and 0.58-fold (p < 0.01) of that in EGFP-RNAi experimental group. These results indicated that CgRab1 was involved in the process of haemocytes phagocytosis by regulating the expression of Cgcathepsin L1 in oyster C. gigas.
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Affiliation(s)
- Yu Liu
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Meijia Li
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Chi Zhang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Miren Dong
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
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Hannan JP, Swisher GH, Martyr JG, Cordaro NJ, Erbse AH, Falke JJ. HPLC method to resolve, identify and quantify guanine nucleotides bound to recombinant ras GTPase. Anal Biochem 2021; 631:114338. [PMID: 34433016 PMCID: PMC8511091 DOI: 10.1016/j.ab.2021.114338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/31/2022]
Abstract
The Ras superfamily of small G proteins play central roles in diverse signaling pathways. Superfamily members act as molecular on-off switches defined by their occupancy with GTP or GDP, respectively. In vitro functional studies require loading with a hydrolysis-resistant GTP analogue to increase the on-state lifetime, as well as knowledge of fractional loading with activating and inactivating nucleotides. The present study describes a method combining elements of previous approaches with new, optimized features to analyze the bound nucleotide composition of a G protein loaded with activating (GMPPNP) or inactivating (GDP) nucleotide. After nucleotide loading, the complex is washed to remove unbound nucleotides then bound nucleotides are heat-extracted and subjected to ion-paired, reverse-phase HPLC-UV to resolve, identify and quantify the individual nucleotide components. These data enable back-calculation to the nucleotide composition and fractional activation of the original, washed G protein population prior to heat extraction. The method is highly reproducible. Application to multiple HRas preparations and mutants confirms its ability to fully extract and analyze bound nucleotides, and to resolve the fractional on- and off-state populations. Furthermore, the findings yield a novel hypothesis for the molecular disease mechanism of Ras mutations at the E63 and Y64 positions.
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Affiliation(s)
- Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - G Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Justin G Martyr
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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Guardia CM, Hierro A, Gershlick DC. Editorial: Energy Requirements in Membrane Trafficking. Front Cell Dev Biol 2021; 9:750633. [PMID: 34722535 PMCID: PMC8551823 DOI: 10.3389/fcell.2021.750633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 11/21/2022] Open
Affiliation(s)
- Carlos M. Guardia
- Section on Intracellular Protein Trafficking, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Aitor Hierro
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro, Bilbao, Spain
| | - David C. Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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Walker B, Jing Z, Ren P. Molecular dynamics free energy simulations of ATP:Mg 2+ and ADP:Mg 2+ using the polarizable force field AMOEBA. Mol Simul 2021; 47:439-448. [PMID: 34421214 DOI: 10.1080/08927022.2020.1725003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
ATPases and GTPases are two important classes of protein that play critical roles in energy transduction, cellular signaling, gene regulation and catalysis. These proteins use cofactors such as nucleoside di and tri-phosphates (NTP, NDP) and can detect the difference between NDP and NTP which then induce different protein conformations. Mechanisms that drive proteins into the NTP or NDP conformation may depend on factors such as ligand structure and how Mg2+ coordinates with the ligand, amino acids in the pocket and water molecules. Here, we have used the advanced electrostatic and polarizable force field AMOEBA and molecular dynamics free energy simulations (MDFE) to examine the various binding mechanisms of ATP:Mg2+ and ADP:Mg2+.We compared the ATP:Mg2+ binding with previous studies using non-polarizable force fields and experimental data on the binding affinity. It was found that the total free energy of binding for ATP:Mg2+ (-7.00 ± 2.13 kcal/mol) is in good agreement with experimental values (-8.6 ± .2 kcal/mol)1. In addition, parameters for relevant protonation states of ATP, ADP, GTP and GDP have been derived. These parameters will allow for researchers to investigate biochemical phenomena involving NTP's and NDP's with greater accuracy than previous studies involving non-polarizable force fields.
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Affiliation(s)
- Brandon Walker
- Department of Biomedical Engineering at The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhifeng Jing
- Department of Biomedical Engineering at The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering at The University of Texas at Austin, Austin, Texas 78712, United States
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Park S, Kim D, Park Y, Cho H, Kim D, Kwon S. 5G Security Threat Assessment in Real Networks. Sensors (Basel) 2021; 21:5524. [PMID: 34450971 DOI: 10.3390/s21165524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/02/2022]
Abstract
Advances in mobile communication networks from 2G to 5G have brought unprecedented traffic growth, and 5G mobile communication networks are expected to be used in a variety of industries based on innovative technologies, fast not only in terms of extremely low latency but massive access devices. Various types of services, such as enhanced mobile broadband (eMBB), massive machine type communication (mMTC), and ultra-reliable and low latency communication (uRLLC), represent an increase in the number of attacks on users’ personal information, confidential information, and privacy information. Therefore, security assessments are essential to verify and cope with these various attacks. In this research, we (1) looked at 5G mobile communication network backgrounds and problems to investigate existing vulnerabilities and (2) assessed the current situation through evaluation of 5G security threats in real-world mobile networks in service.
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Kovacikova K, Gorostiola González M, Jones R, Reguera J, Gigante A, Pérez-Pérez MJ, Pürstinger G, Moesslacher J, Langer T, Jeong LS, Delang L, Neyts J, Snijder EJ, van Westen GJP, van Hemert MJ. Structural Insights into the Mechanisms of Action of Functionally Distinct Classes of Chikungunya Virus Nonstructural Protein 1 Inhibitors. Antimicrob Agents Chemother 2021; 65:e0256620. [PMID: 33875421 DOI: 10.1128/AAC.02566-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Chikungunya virus (CHIKV) nonstructural protein 1 (nsP1) harbors the methyltransferase (MTase) and guanylyltransferase (GTase) activities needed for viral RNA capping and represents a promising antiviral drug target. We compared the antiviral efficacies of nsP1 inhibitors belonging to the MADTP, CHVB, and FHNA series (6′-fluoro-homoneplanocin A [FHNA], its 3′-keto form, and 6′-β-fluoro-homoaristeromycin). Cell-based phenotypic cross-resistance assays revealed that the CHVB and MADTP series had similar modes of action that differed from that of the FHNA series. In biochemical assays with purified Semliki Forest virus and CHIKV nsP1, CHVB compounds strongly inhibited MTase and GTase activities, while MADTP-372 had a moderate inhibitory effect. FHNA did not directly inhibit the enzymatic activity of CHIKV nsP1. The first-of-their-kind molecular-docking studies with the cryo-electron microscopy (cryo-EM) structure of CHIKV nsP1, which is assembled into a dodecameric ring, revealed that the MADTP and CHVB series bind at the S-adenosylmethionine (SAM)-binding site in the capping domain, where they would function as competitive or noncompetitive inhibitors. The FHNA series was predicted to bind at the secondary binding pocket in the ring-aperture membrane-binding and oligomerization (RAMBO) domain, potentially interfering with the membrane binding and oligomerization of nsP1. Our cell-based and enzymatic assays, in combination with molecular docking and mapping of compound resistance mutations to the nsP1 structure, allowed us to group nsP1 inhibitors into functionally distinct classes. This study identified druggable pockets in the nsP1 dodecameric structure and provides a basis for the rational design, optimization, and combination of inhibitors of this unique and promising antiviral drug target.
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Kofuji S, Sasaki AT. GTP metabolic reprogramming by IMPDH2: unlocking cancer cells' fuelling mechanism. J Biochem 2021; 168:319-328. [PMID: 32702086 DOI: 10.1093/jb/mvaa085] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/16/2020] [Indexed: 12/15/2022] Open
Abstract
Growing cells increase multiple biosynthetic processes in response to the high metabolic demands needed to sustain proliferation. The even higher metabolic requirements in the setting of cancer provoke proportionately greater biosynthesis. Underappreciated key aspects of this increased metabolic demand are guanine nucleotides and adaptive mechanisms to regulate their concentration. Using the malignant brain tumour, glioblastoma, as a model, we have demonstrated that one of the rate-limiting enzymes for guanosine triphosphate (GTP) synthesis, inosine monophosphate dehydrogenase-2 (IMPDH2), is increased and IMPDH2 expression is necessary for the activation of de novo GTP biosynthesis. Moreover, increased IMPDH2 enhances RNA polymerase I and III transcription directly linking GTP metabolism to both anabolic capacity as well as nucleolar enlargement historically observed as associated with cancer. In this review, we will review in detail the basis of these new discoveries and, more generally, summarize the current knowledge on the role of GTP metabolism in cancer.
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Affiliation(s)
- Satoshi Kofuji
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, 3125 Eden Ave., Cincinnati, OH 45267-0508, USA.,Department of Cancer Biology, University of Cincinnati College of Medicine, 3125 Eden Ave., OH 45267-0508, USA.,Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, 3113 Bellevue Ave, Cincinnati, OH 45267-0508, USA.,Institute for Advanced Biosciences, Keio University, Kakuganji 246-2, Mizukami, Tsuruoka City, Yamagata 997-0052, Japan
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Pathania A, Anba-Mondoloni J, Gominet M, Halpern D, Dairou J, Dupont L, Lamberet G, Trieu-Cuot P, Gloux K, Gruss A. (p)ppGpp/ GTP and Malonyl-CoA Modulate Staphylococcus aureus Adaptation to FASII Antibiotics and Provide a Basis for Synergistic Bi-Therapy. mBio 2021; 12:e03193-20. [PMID: 33531402 DOI: 10.1128/mBio.03193-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human bacterial pathogen for which new inhibitors are urgently needed. Antibiotic development has centered on the fatty acid synthesis (FASII) pathway, which provides the building blocks for bacterial membrane phospholipids. Fatty acid biosynthesis (FASII) enzymes are considered valid targets for antimicrobial drug development against the human pathogen Staphylococcus aureus. However, incorporation of host fatty acids confers FASII antibiotic adaptation that compromises prospective treatments. S. aureus adapts to FASII inhibitors by first entering a nonreplicative latency period, followed by outgrowth. Here, we used transcriptional fusions and direct metabolite measurements to investigate the factors that dictate the duration of latency prior to outgrowth. We show that stringent response induction leads to repression of FASII and phospholipid synthesis genes. (p)ppGpp induction inhibits synthesis of malonyl-CoA, a molecule that derepresses FapR, a key regulator of FASII and phospholipid synthesis. Anti-FASII treatment also triggers transient expression of (p)ppGpp-regulated genes during the anti-FASII latency phase, with concomitant repression of FapR regulon expression. These effects are reversed upon outgrowth. GTP depletion, a known consequence of the stringent response, also occurs during FASII latency, and is proposed as the common signal linking these responses. We next showed that anti-FASII treatment shifts malonyl-CoA distribution between its interactants FapR and FabD, toward FapR, increasing expression of the phospholipid synthesis genes plsX and plsC during outgrowth. We conclude that components of the stringent response dictate malonyl-CoA availability in S. aureus FASII regulation, and contribute to latency prior to anti-FASII-adapted outgrowth. A combinatory approach, coupling a (p)ppGpp inducer and an anti-FASII, blocks S. aureus outgrowth, opening perspectives for bi-therapy treatment.
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Swisher GH, Hannan JP, Cordaro NJ, Erbse AH, Falke JJ. Ras-guanine nucleotide complexes: A UV spectral deconvolution method to analyze protein concentration, nucleotide stoichiometry, and purity. Anal Biochem 2021; 618:114066. [PMID: 33485819 DOI: 10.1016/j.ab.2020.114066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/31/2022]
Abstract
The many members of the Ras superfamily are small GTPases that serve as molecular switches. These proteins bind the guanine nucleotides GTP and GDP with picomolar affinities, thereby stabilizing on- and off-signaling states, respectively. Quantitative in vitro Ras studies require accurate determination of total protein, its fractional occupancy with guanine nucleotide, and spectroscopic purity. Yet the high nucleotide affinity of Ras and the overlapping UV spectra of the protein and bound nucleotide make such determinations challenging. Here we describe a generalizable UV spectral deconvolution method to analyze the total protein concentration, total nucleotide stoichiometry, and purity of Ras complexes.
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Affiliation(s)
- G Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States.
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Ekka MK, Meena LS. Essential biochemical, biophysical and computational inputs on efficient functioning of Mycobacterium tuberculosis H 37Rv FtsY. Int J Biol Macromol 2021; 171:59-73. [PMID: 33412199 DOI: 10.1016/j.ijbiomac.2020.12.182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 11/19/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis H37Rv) utilizes the signal recognition particle pathway (SRP pathway) system for secretion of various proteins from ribosomes to the extracellular surface which plays an important role in the machinery running inside the bacterium. This system comprises of three major components FtsY, FfH and 4.5S rRNA. This manuscript highlights essential factors responsible for the optimized enzymatic activity of FtsY. Kinetic parameters include Vmax and Km for the hydrolysis of GTP by ftsY which were 20.25±5.16 μM/min/mg and 39.95±7.7 μM respectively. kcat and catalytic efficiency of the reaction were 0.012±0.003 s-1 and 0.00047±0.0001 μM/s-1 respectively. These values were affected upon changing the standard conditions. Cations (Mg2+ and Mn2+) play important role in FtsY enzymatic activity as increasing Mg2+ decrease the activity. Mn2+on the other hand is required at higher concentration around 60 mM for carrying optimum GTPase activity. FtsY is hydrolyzing ATP and GDP as well and GDP acts as an inhibitor of the reaction. MD simulation shows effective binding and stabilization of the FtsY complexed structure with GTP, GDP and ATP. Mutational analysis was done at two important residues of GTP binding motif of FtsY, namely, GXXXXGK (K236) and DXXG (D367) and showed that these mutations significantly decrease FtsY GTPase activity. FtsY is comprised of α helices, but this structural pattern was shown to change with increasing concentrations of GTP and ATP which symbolize that these ligands cause significant conformational change by variating the secondary structure to transduce signals required by downstream effectors. This binding favors the functional stabilization of FtsY by destabilization of α-helix integrity. Revealing the hidden aspects of the functioning of FtsY might be an essential part for the understanding of the SRP pathway which is one of the important contributors of M. tuberculosis virulence.
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Affiliation(s)
- Mary Krishna Ekka
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh 201 002, India
| | - Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh 201 002, India.
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