29 results on '"Ero R"'
Search Results
2. Structure of DsGPDH of Dunaliella salina
- Author
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He, Q., primary, Toh, J.D., additional, Ero, R., additional, Qiao, Z., additional, Kumar, V., additional, and Gao, Y.G., additional
- Published
- 2019
- Full Text
- View/download PDF
3. Ribosome Structure bound to ABC-F protein.
- Author
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Su, W.X., primary, Kumar, V., additional, Ero, R., additional, Andrew, S.W.W., additional, Jian, S., additional, and Yong-Gui, G., additional
- Published
- 2018
- Full Text
- View/download PDF
4. Structure of ribosome bound to cofactor at 5.7 angstrom resolution
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Kumar, V., primary, Ero, R., additional, Jian, G.K., additional, Ahmed, T., additional, Zhan, Y., additional, Bhushan, S., additional, and Gao, Y.G., additional
- Published
- 2016
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5. Structure of ribosome bound to cofactor at 3.8 angstrom resolution
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Kumar, V., primary, Ero, R., additional, Jian, G.K., additional, Ahmed, T., additional, Zhan, Y., additional, Bhushan, S., additional, and Gao, Y.G., additional
- Published
- 2016
- Full Text
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6. Complex of Thermous thermophilus ribosome bound to BipA-GDPCP
- Author
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Kumar, V., primary, Chen, Y., additional, Ahmed, T., additional, Tan, J., additional, Ero, R., additional, Bhushan, S., additional, and Gao, Y.-G., additional
- Published
- 2015
- Full Text
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7. Complex of Thermous thermophilus ribosome (A-and P-site tRNA) bound to BipA-GDPCP
- Author
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Kumar, V., primary, Chen, Y., additional, Ahmed, T., additional, Tan, J., additional, Ero, R., additional, Bhushan, S., additional, and Gao, Y.-G., additional
- Published
- 2015
- Full Text
- View/download PDF
8. Structure of apo BipA
- Author
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Kumar, V., primary, Chen, Y., additional, Ero, R., additional, Li, Z., additional, and Gao, Y., additional
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- 2015
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9. Structure of GDPCP BipA
- Author
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Kumar, V., primary, Chen, Y., additional, Ero, R., additional, Li, Z., additional, and Gao, Y., additional
- Published
- 2015
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10. Structure of ppGpp BipA
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Kumar, V., primary, Chen, Y., additional, Ero, R., additional, Li, Z., additional, and Gao, Y.-G., additional
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- 2015
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11. Structure of GDP bound BipA
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Kumar, V., primary, Chen, Y., additional, Ero, R., additional, Li, Z., additional, and Gao, Y.-G., additional
- Published
- 2015
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12. Crystal structure of signal transducing protein
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Ero, R., primary, Dimitrova, V.T., additional, Chen, Y., additional, Bu, W., additional, Feng, S., additional, Liu, T., additional, Wang, P., additional, Xue, C., additional, Tan, S.M., additional, and Gao, Y.G., additional
- Published
- 2015
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13. Ribosomal RNA modification enzymes stimulate large ribosome subunit assembly in E. coli.
- Author
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Ero R, Leppik M, Reier K, Liiv A, and Remme J
- Subjects
- Ribosome Subunits, Large, Bacterial metabolism, Ribosome Subunits, Large, Bacterial genetics, Methyltransferases metabolism, Methyltransferases genetics, RNA, Ribosomal metabolism, RNA, Ribosomal genetics, Ribosome Subunits, Large metabolism, Ribosome Subunits, Large genetics, Ribosomes metabolism, Ribosomes genetics, Escherichia coli genetics, Escherichia coli metabolism, Escherichia coli Proteins metabolism, Escherichia coli Proteins genetics, RNA, Ribosomal, 23S metabolism, RNA, Ribosomal, 23S genetics, RNA, Ribosomal, 23S chemistry
- Abstract
Ribosomal RNA modifications are introduced by specific enzymes during ribosome assembly in bacteria. Deletion of individual modification enzymes has a minor effect on bacterial growth, ribosome biogenesis, and translation, which has complicated the definition of the function of the enzymes and their products. We have constructed an Escherichia coli strain lacking 10 genes encoding enzymes that modify 23S rRNA around the peptidyl-transferase center. This strain exhibits severely compromised growth and ribosome assembly, especially at lower temperatures. Re-introduction of the individual modification enzymes allows for the definition of their functions. The results demonstrate that in addition to previously known RlmE, also RlmB, RlmKL, RlmN and RluC facilitate large ribosome subunit assembly. RlmB and RlmKL have functions in ribosome assembly independent of their modification activities. While the assembly stage specificity of rRNA modification enzymes is well established, this study demonstrates that there is a mutual interdependence between the rRNA modification process and large ribosome subunit assembly., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)
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- 2024
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14. Plasticity and conditional essentiality of modification enzymes for domain V of Escherichia coli 23S ribosomal RNA.
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Liljeruhm J, Leppik M, Bao L, Truu T, Calvo-Noriega M, Freyer NS, Liiv A, Wang J, Blanco RC, Ero R, Remme J, and Forster AC
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- Cell Cycle Proteins genetics, Escherichia coli metabolism, Methyltransferases metabolism, Protein Biosynthesis, RNA, Bacterial metabolism, RNA, Ribosomal metabolism, Ribosomes metabolism, Peptidyl Transferases genetics, RNA, Ribosomal, 23S chemistry
- Abstract
Escherichia coli rRNAs are post-transcriptionally modified at 36 positions but their modification enzymes are dispensable individually for growth, bringing into question their significance. However, a major growth defect was reported for deletion of the RlmE enzyme, which abolished a 2' O methylation near the peptidyl transferase center (PTC) of the 23S rRNA. Additionally, an adjacent 80-nt "critical region" around the PTC had to be modified to yield significant peptidyl transferase activity in vitro. Surprisingly, we discovered that an absence of just two rRNA modification enzymes is conditionally lethal (at 20°C): RlmE and RluC. At a permissive temperature (37°C), this double knockout was shown to abolish four modifications and be defective in ribosome assembly, though not more so than the RlmE single knockout. However, the double knockout exhibited an even lower rate of tripeptide synthesis than did the single knockout, suggesting an even more defective ribosomal translocation. A combination knockout of the five critical-region-modifying enzymes RluC, RlmKL, RlmN, RlmM, and RluE (not RlmE), which synthesize five of the seven critical-region modifications and 14 rRNA and tRNA modifications altogether, was viable (minor growth defect at 37°C, major at 20°C). This was surprising based on prior in vitro studies. This five-knockout combination had minimal effects on ribosome assembly and frameshifting at 37°C, but greater effects on ribosome assembly and in vitro peptidyl transferase activity at cooler temperatures. These results establish the conditional essentiality of bacterial rRNA modification enzymes and also reveal unexpected plasticity of modification of the PTC region in vivo., (© 2022 Liljeruhm et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)
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- 2022
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15. The mechanism of complex formation between calmodulin and voltage gated calcium channels revealed by molecular dynamics.
- Author
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Yaduvanshi S, Ero R, and Kumar V
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- Binding Sites, Protein Binding, Protein Conformation, Calcium metabolism, Calcium Channels chemistry, Calcium Channels metabolism, Calmodulin chemistry, Calmodulin metabolism, Molecular Dynamics Simulation
- Abstract
Calmodulin, a ubiquitous eukaryotic calcium sensor responsible for the regulation of many fundamental cellular processes, is a highly flexible protein and exhibits an unusually wide range of conformations. Furthermore, CaM is known to interact with more than 300 cellular targets. Molecular dynamics (MD) simulation trajectories suggest that EF-hand loops show different magnitudes of flexibility. Therefore, the four EF-hand motifs have different affinities for Ca2+ ions, which enables CaM to function on wide range of Ca2+ ion concentrations. EF-hand loops are 2-3 times more flexible in apo CaM whereas least flexible in Ca2+/CaM-IQ motif complexes. We report a unique intermediate conformation of Ca2+/CaM while transitioning from extended to compact form. We also report the complex formation process between Ca2+/CaM and IQ CaM-binding motifs. Our results showed how IQ motif recognise its binding site on the CaM and how CaM transforms from extended to compact form upon binding to IQ motif., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2021
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16. [ETIOLOGIES OF EXTREME HYPERFERRITINEMIA - ANALYSIS OF A LARGE DATABASE].
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Leibu-Ero R, Kuntzman Y, Shoenfeld Y, Comaneshter D, Cohen AD, and Amital H
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- Adult, Ferritins, Humans, Prognosis, Retrospective Studies, Hyperferritinemia, Still's Disease, Adult-Onset
- Abstract
Introduction: Besides its role in iron homeostasis and storage, ferritin is also regarded as an acute-phase reactant. Extreme Hyperferritinemia is seen in severe inflammatory conditions, severe infections, iron storage diseases and malignancies. A direct linkage between high ferritin levels and poor prognosis has been observed., Objectives: To characterize patients with extreme high ferritin levels in the serum for possible etiologies and assessment of the correlation between ferritin levels, prognosis and mortality., Methods: We conducted a retrospective cohort study between the years 2002-2016 using the large database of Clalit Health Services. Patients older than 18 years with ferritin levels above 10,000 ng/ml that were taken during hospitalization and ambulatory visits were included in the study. After examining the medical files of each patient, we evaluated the demographic characteristics, etiologies, clinical presentation and relevant laboratory parameters. We calculated the proportion of this data and compared it to the general population by using chi square test., Results: The incidence of extreme hyperferritinemia was statistically significant in patients with autoimmune and rheumatologic diseases in particular adult onset Still's disease compared to the general population. Among hospitalized patients, bacterial and viral infections were the leading cause in 62% of cases. In ambulatory patients, hyperferritinemia was mainly secondary to chronic blood transfusions in patients with hemoglobinopathies and poor compliance to iron chelators. Among 21 biopsies from involved organs including lymph nodes, bone marrow and liver, hemophagocytosis was only observed in 5 cases (6.8%)., Conclusions: Extreme hyperferritinemia with values higher than 10,000 ng/ml can be attributed to many inflammatory autoimmune conditions.
- Published
- 2021
17. Translational GTPase BipA Is Involved in the Maturation of a Large Subunit of Bacterial Ribosome at Suboptimal Temperature.
- Author
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Goh KJ, Ero R, Yan XF, Park JE, Kundukad B, Zheng J, Sze SK, and Gao YG
- Abstract
BPI-inducible protein A (BipA), a highly conserved paralog of the well-known translational GTPases LepA and EF-G, has been implicated in bacterial motility, cold shock, stress response, biofilm formation, and virulence. BipA binds to the aminoacyl-(A) site of the bacterial ribosome and establishes contacts with the functionally important regions of both subunits, implying a specific role relevant to the ribosome, such as functioning in ribosome biogenesis and/or conditional protein translation. When cultured at suboptimal temperatures, the Escherichia coli bipA genomic deletion strain (Δ bipA ) exhibits defects in growth, swimming motility, and ribosome assembly, which can be complemented by a plasmid-borne bipA supplementation or suppressed by the genomic rluC deletion. Based on the growth curve, soft agar swimming assay, and sucrose gradient sedimentation analysis, mutation of the catalytic residue His78 rendered plasmid-borne bipA unable to complement its deletion phenotypes. Interestingly, truncation of the C-terminal loop of BipA exacerbates the aforementioned phenotypes, demonstrating the involvement of BipA in ribosome assembly or its function. Furthermore, tandem mass tag-mass spectrometry analysis of the Δ bipA strain proteome revealed upregulations of a number of proteins (e.g., DeaD, RNase R, CspA, RpoS, and ObgE) implicated in ribosome biogenesis and RNA metabolism, and these proteins were restored to wild-type levels by plasmid-borne bipA supplementation or the genomic rluC deletion, implying BipA involvement in RNA metabolism and ribosome biogenesis. We have also determined that BipA interacts with ribosome 50S precursor (pre-50S), suggesting its role in 50S maturation and ribosome biogenesis. Taken together, BipA demonstrates the characteristics of a bona fide 50S assembly factor in ribosome biogenesis., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Goh, Ero, Yan, Park, Kundukad, Zheng, Sze and Gao.)
- Published
- 2021
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18. Ribosome Protection Proteins-"New" Players in the Global Arms Race with Antibiotic-Resistant Pathogens.
- Author
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Ero R, Yan XF, and Gao YG
- Subjects
- ATP-Binding Cassette Transporters metabolism, Anti-Bacterial Agents pharmacology, Bacteria drug effects, Bacterial Infections drug therapy, Bacterial Proteins metabolism, Drug Resistance, Bacterial drug effects, Drug Resistance, Multiple drug effects, Models, Molecular, Protein Biosynthesis drug effects, Ribosomal Proteins drug effects, Ribosomes drug effects, Drug Resistance, Microbial physiology, Ribosomal Proteins metabolism, Ribosomes metabolism
- Abstract
Bacteria have evolved an array of mechanisms enabling them to resist the inhibitory effect of antibiotics, a significant proportion of which target the ribosome. Indeed, resistance mechanisms have been identified for nearly every antibiotic that is currently used in clinical practice. With the ever-increasing list of multi-drug-resistant pathogens and very few novel antibiotics in the pharmaceutical pipeline, treatable infections are likely to become life-threatening once again. Most of the prevalent resistance mechanisms are well understood and their clinical significance is recognized. In contrast, ribosome protection protein-mediated resistance has flown under the radar for a long time and has been considered a minor factor in the clinical setting. Not until the recent discovery of the ATP-binding cassette family F protein-mediated resistance in an extensive list of human pathogens has the significance of ribosome protection proteins been truly appreciated. Understanding the underlying resistance mechanism has the potential to guide the development of novel therapeutic approaches to evade or overcome the resistance. In this review, we discuss the latest developments regarding ribosome protection proteins focusing on the current antimicrobial arsenal and pharmaceutical pipeline as well as potential implications for the future of fighting bacterial infections in the time of "superbugs."
- Published
- 2021
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19. Structural basis of human full-length kindlin-3 homotrimer in an auto-inhibited state.
- Author
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Bu W, Levitskaya Z, Loh ZY, Jin S, Basu S, Ero R, Yan X, Wang M, Ngan SFC, Sze SK, Tan SM, and Gao YG
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- Cell Movement, Humans, Integrins metabolism, K562 Cells, Membrane Proteins metabolism, Models, Molecular, Neoplasm Proteins metabolism, Protein Binding, Protein Domains, Structural Homology, Protein, Structure-Activity Relationship, Membrane Proteins antagonists & inhibitors, Membrane Proteins chemistry, Neoplasm Proteins antagonists & inhibitors, Neoplasm Proteins chemistry, Protein Multimerization
- Abstract
Kindlin-1, -2, and -3 directly bind integrin β cytoplasmic tails to regulate integrin activation and signaling. Despite their functional significance and links to several diseases, structural information on full-length kindlin proteins remains unknown. Here, we report the crystal structure of human full-length kindlin-3, which reveals a novel homotrimer state. Unlike kindlin-3 monomer, which is the major population in insect and mammalian cell expression systems, kindlin-3 trimer does not bind integrin β cytoplasmic tail as the integrin-binding pocket in the F3 subdomain of 1 protomer is occluded by the pleckstrin homology (PH) domain of another protomer, suggesting that kindlin-3 is auto-inhibited upon trimer formation. This is also supported by functional assays in which kindlin-3 knockout K562 erythroleukemia cells reconstituted with the mutant kindlin-3 containing trimer-disrupting mutations exhibited an increase in integrin-mediated adhesion and spreading on fibronectin compared with those reconstituted with wild-type kindlin-3. Taken together, our findings reveal a novel mechanism of kindlin auto-inhibition that involves its homotrimer formation., Competing Interests: The authors have declared that no competing interests exist.
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- 2020
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20. The unusual di-domain structure of Dunaliella salina glycerol-3-phosphate dehydrogenase enables direct conversion of dihydroxyacetone phosphate to glycerol.
- Author
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He Q, Toh JD, Ero R, Qiao Z, Kumar V, Serra A, Tan J, Sze SK, and Gao YG
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- Catalytic Domain, Chlorophyceae genetics, Chlorophyceae metabolism, Glycerolphosphate Dehydrogenase chemistry, Glycerolphosphate Dehydrogenase genetics, NAD metabolism, Protein Structure, Tertiary, Sequence Alignment, Chlorophyceae enzymology, Dihydroxyacetone Phosphate metabolism, Glycerol metabolism, Glycerolphosphate Dehydrogenase metabolism
- Abstract
Dunaliella has been extensively studied due to its intriguing adaptation to high salinity. Its di-domain glycerol-3-phosphate dehydrogenase (GPDH) isoform is likely to underlie the rapid production of the osmoprotectant glycerol. Here, we report the structure of the chimeric Dunaliella salina GPDH (DsGPDH) protein featuring a phosphoserine phosphatase-like domain fused to the canonical glycerol-3-phosphate (G3P) dehydrogenase domain. Biochemical assays confirm that DsGPDH can convert dihydroxyacetone phosphate (DHAP) directly to glycerol, whereas a separate phosphatase protein is required for this conversion process in most organisms. The structure of DsGPDH in complex with its substrate DHAP and co-factor nicotinamide adenine dinucleotide (NAD) allows the identification of the residues that form the active sites. Furthermore, the structure reveals an intriguing homotetramer form that likely contributes to the rapid biosynthesis of glycerol., (© 2019 The Authors The Plant Journal © 2019 John Wiley & Sons Ltd.)
- Published
- 2020
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21. Ribosome protection by ABC-F proteins-Molecular mechanism and potential drug design.
- Author
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Ero R, Kumar V, Su W, and Gao YG
- Subjects
- ATP-Binding Cassette Transporters chemistry, Animals, Anti-Bacterial Agents chemistry, Anti-Bacterial Agents metabolism, Bacteria metabolism, Bacterial Infections drug therapy, Bacterial Infections microbiology, Bacterial Proteins chemistry, Humans, Models, Molecular, ATP-Binding Cassette Transporters metabolism, Anti-Bacterial Agents pharmacology, Bacteria drug effects, Bacterial Proteins metabolism, Drug Design, Drug Resistance, Bacterial
- Abstract
Members of the ATP-binding cassette F (ABC-F) proteins confer resistance to several classes of clinically important antibiotics through ribosome protection. Recent structures of two ABC-F proteins, Pseudomonas aeruginosa MsrE and Bacillus subtilis VmlR bound to ribosome have shed light onto the ribosome protection mechanism whereby drug resistance is mediated by the antibiotic resistance domain (ARD) connecting the two ATP binding domains. ARD of the E site bound MsrE and VmlR extends toward the drug binding region within the peptidyl transferase center (PTC) and leads to conformational changes in the P site tRNA acceptor stem, the PTC, and the drug binding site causing the release of corresponding drugs. The structural similarities and differences of the MsrE and VmlR structures likely highlight an universal ribosome protection mechanism employed by antibiotic resistance (ARE) ABC-F proteins. The variable ARD domains enable this family of proteins to adapt the protection mechanism for several classes of ribosome-targeting drugs. ARE ABC-F genes have been found in numerous pathogen genomes and multi-drug resistance conferring plasmids. Collectively they mediate resistance to a broader range of antimicrobial agents than any other group of resistance proteins and play a major role in clinically significant drug resistance in pathogenic bacteria. Here, we review the recent structural and biochemical findings on these emerging resistance proteins, offering an update of the molecular basis and implications for overcoming ABC-F conferred drug resistance., (© 2019 The Protein Society.)
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- 2019
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22. Ribosome protection by antibiotic resistance ATP-binding cassette protein.
- Author
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Su W, Kumar V, Ding Y, Ero R, Serra A, Lee BST, Wong ASW, Shi J, Sze SK, Yang L, and Gao YG
- Subjects
- ATP-Binding Cassette Transporters chemistry, Adenosine Triphosphate metabolism, Bacterial Proteins chemistry, Binding Sites, Crystallography, X-Ray, Models, Molecular, Peptidyl Transferases chemistry, Peptidyl Transferases metabolism, Protein Biosynthesis, Protein Conformation, Ribosomes chemistry, ATP-Binding Cassette Transporters metabolism, Anti-Bacterial Agents pharmacology, Bacteria drug effects, Bacterial Proteins metabolism, Drug Resistance, Microbial, Ribosomes drug effects, Ribosomes metabolism
- Abstract
The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer resistance to ribosome-targeting antibiotics through a yet unknown mechanism. Among them, MsrE has been implicated in macrolide resistance. Here, we report the cryo-EM structure of ATP form MsrE bound to the ribosome. Unlike previously characterized ribosomal protection proteins, MsrE is shown to bind to ribosomal exit site. Our structure reveals that the domain linker forms a unique needle-like arrangement with two crossed helices connected by an extended loop projecting into the peptidyl-transferase center and the nascent peptide exit tunnel, where numerous antibiotics bind. In combination with biochemical assays, our structure provides insight into how MsrE binding leads to conformational changes, which results in the release of the drug. This mechanism appears to be universal for the ABC-F type ribosome protection proteins., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)
- Published
- 2018
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23. Selective Binding to mRNA Duplex Regions by Chemically Modified Peptide Nucleic Acids Stimulates Ribosomal Frameshifting.
- Author
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Puah RY, Jia H, Maraswami M, Toh DK, Ero R, Yang L, Patil KM, Ong AAL, Krishna MS, Sun R, Tong C, Huang M, Chen X, Loh TP, Gao YG, Liu DX, and Chen G
- Subjects
- Animals, Base Sequence, Binding Sites, Cell-Free System, Peptide Nucleic Acids chemistry, Peptide Nucleic Acids metabolism, Protein Biosynthesis, Rabbits, Frameshifting, Ribosomal drug effects, Peptide Nucleic Acids pharmacology, RNA, Double-Stranded metabolism, RNA, Messenger metabolism
- Abstract
Minus-one programmed ribosomal frameshifting (-1 PRF) allows the precise maintenance of the ratio between viral proteins and is involved in the regulation of the half-lives of cellular mRNAs. Minus-one ribosomal frameshifting is activated by several stimulatory elements such as a heptameric slippery sequence (X XXY YYZ) and an mRNA secondary structure (hairpin or pseudoknot) that is positioned 2-8 nucleotides downstream from the slippery site. Upon -1 RF, the ribosomal reading frame is shifted from the normal zero frame to the -1 frame with the heptameric slippery sequence decoded as XXX YYY Z instead of X XXY YYZ. Our research group has developed chemically modified peptide nucleic acid (PNA) L and Q monomers to recognize G-C and C-G Watson-Crick base pairs, respectively, through major-groove parallel PNA·RNA-RNA triplex formation. L- and Q-incorporated PNAs show selective binding to double-stranded RNAs (dsRNAs) over single-stranded RNAs (ssRNAs). The sequence specificity and structural selectivity of L- and Q-modified PNAs may allow the precise targeting of desired viral and cellular RNA structures, and thus may serve as valuable biological tools for mechanistic studies and potential therapeutics for fighting diseases. Here, for the first time, we demonstrate by cell-free in vitro translation assays using rabbit reticulocyte lysate that the dsRNA-specific chemically modified PNAs targeting model mRNA hairpins stimulate -1 RF (from 2% to 32%). An unmodified control PNA, however, shows nonspecific inhibition of translation. Our results suggest that the modified dsRNA-binding PNAs may be advantageous for targeting structured RNAs.
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- 2018
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24. Similarity and diversity of translational GTPase factors EF-G, EF4, and BipA: From structure to function.
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Ero R, Kumar V, Chen Y, and Gao YG
- Subjects
- Cryoelectron Microscopy, Crystallography, X-Ray, Models, Molecular, Peptide Elongation Factor G chemistry, Peptide Elongation Factor G metabolism, Protein Binding, Protein Conformation, Protein Domains, RNA, Messenger metabolism, RNA, Transfer metabolism, GTP Phosphohydrolases chemistry, GTP Phosphohydrolases metabolism
- Abstract
EF-G, EF4, and BipA are members of the translation factor family of GTPases with a common ribosome binding mode and GTPase activation mechanism. However, topological variations of shared as well as unique domains ensure different roles played by these proteins during translation. Recent X-ray crystallography and cryo-electron microscopy studies have revealed the structural basis for the involvement of EF-G domain IV in securing the movement of tRNAs and mRNA during translocation as well as revealing how the unique C-terminal domains of EF4 and BipA interact with the ribosome and tRNAs contributing to the regulation of translation under certain conditions. EF-G, EF-4, and BipA are intriguing examples of structural variations on a common theme that results in diverse behavior and function. Structural studies of translational GTPase factors have been greatly facilitated by the use of antibiotics, which have revealed their mechanism of action.
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- 2016
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25. Structure of the GTP Form of Elongation Factor 4 (EF4) Bound to the Ribosome.
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Kumar V, Ero R, Ahmed T, Goh KJ, Zhan Y, Bhushan S, and Gao YG
- Subjects
- Catalytic Domain, Cryoelectron Microscopy, Guanosine Diphosphate chemistry, Guanosine Triphosphate chemistry, Hydrogen Bonding, Hydrolysis, Models, Molecular, Protein Binding, Bacterial Proteins chemistry, GTP Phosphohydrolase-Linked Elongation Factors chemistry, Ribosome Subunits, Large, Bacterial chemistry, Ribosome Subunits, Small, Bacterial chemistry, Thermus thermophilus
- Abstract
Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in bacterial, mitochondrial, and chloroplast genomes, its exact biological function remains controversial. Here we present the cryo-EM reconstitution of the GTP form of EF4 bound to the ribosome with P and E site tRNAs at 3.8-Å resolution. Interestingly, our structure reveals an unrotated ribosome rather than a clockwise-rotated ribosome, as observed in the presence of EF4-GDP and P site tRNA. In addition, we also observed a counterclockwise-rotated form of the above complex at 5.7-Å resolution. Taken together, our results shed light on the interactions formed between EF4, the ribosome, and the P site tRNA and illuminate the GTPase activation mechanism at previously unresolved detail., (© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.)
- Published
- 2016
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26. Kindlin-3 interacts with the ribosome and regulates c-Myc expression required for proliferation of chronic myeloid leukemia cells.
- Author
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Qu J, Ero R, Feng C, Ong LT, Tan HF, Lee HS, Ismail MH, Bu WT, Nama S, Sampath P, Gao YG, and Tan SM
- Subjects
- Animals, Antibiotics, Antineoplastic pharmacology, Cell Proliferation drug effects, GTP-Binding Proteins metabolism, HEK293 Cells, Human Umbilical Vein Endothelial Cells, Humans, Integrin beta3 metabolism, K562 Cells, Leukemia, Myelogenous, Chronic, BCR-ABL Positive metabolism, Leukemia, Myelogenous, Chronic, BCR-ABL Positive pathology, Membrane Proteins antagonists & inhibitors, Membrane Proteins genetics, Mice, Mice, Inbred BALB C, Mice, Knockout, Neoplasm Proteins antagonists & inhibitors, Neoplasm Proteins genetics, Protein Binding, Proto-Oncogene Proteins c-myc genetics, RNA Interference, Receptors for Activated C Kinase, Receptors, Cell Surface metabolism, Recombinant Proteins biosynthesis, Recombinant Proteins chemistry, Recombinant Proteins isolation & purification, Signal Transduction drug effects, Sirolimus pharmacology, TOR Serine-Threonine Kinases metabolism, Membrane Proteins metabolism, Neoplasm Proteins metabolism, Proto-Oncogene Proteins c-myc metabolism, Ribosomes metabolism
- Abstract
Kindlins are FERM-containing cytoplasmic proteins that regulate integrin-mediated cell-cell and cell-extracellular matrix (ECM) attachments. Kindlin-3 is expressed in hematopoietic cells, platelets, and endothelial cells. Studies have shown that kindlin-3 stabilizes cell adhesion mediated by ß1, ß2, and ß3 integrins. Apart from integrin cytoplasmic tails, kindlins are known to interact with other cytoplasmic proteins. Here we demonstrate that kindlin-3 can associate with ribosome via the receptor for activated-C kinase 1 (RACK1) scaffold protein based on immunoprecipitation, ribosome binding, and proximity ligation assays. We show that kindlin-3 regulates c-Myc protein expression in the human chronic myeloid leukemia cell line K562. Cell proliferation was reduced following siRNA reduction of kindlin-3 expression and a significant reduction in tumor mass was observed in xenograft experiments. Mechanistically, kindlin-3 is involved in integrin α5ß1-Akt-mTOR-p70S6K signaling; however, its regulation of c-Myc protein expression could be independent of this signaling axis.
- Published
- 2015
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27. Structure of BipA in GTP form bound to the ratcheted ribosome.
- Author
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Kumar V, Chen Y, Ero R, Ahmed T, Tan J, Li Z, Wong AS, Bhushan S, and Gao YG
- Subjects
- Cryoelectron Microscopy, Crystallography, X-Ray, Models, Molecular, Protein Conformation, Escherichia coli Proteins chemistry, GTP Phosphohydrolases chemistry, Guanosine Triphosphate chemistry, Phosphoproteins chemistry, Ribosomes chemistry
- Abstract
BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive. Here, we present the crystal structures of apo form and GTP analog, GDP, and guanosine-3',5'-bisdiphosphate (ppGpp)-bound BipA. In addition to having a distinctive domain arrangement, the C-terminal domain of BipA has a unique fold. Furthermore, we report the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form and elucidate the unique structural attributes of BipA interactions with the ribosome and A-site tRNA in the light of its possible function in regulating translation.
- Published
- 2015
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28. Crystal structure of Gib2, a signal-transducing protein scaffold associated with ribosomes in Cryptococcus neoformans.
- Author
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Ero R, Dimitrova VT, Chen Y, Bu W, Feng S, Liu T, Wang P, Xue C, Tan SM, and Gao YG
- Subjects
- Adaptor Proteins, Signal Transducing chemistry, Amino Acid Sequence, Conserved Sequence, Cryptococcus neoformans growth & development, Eukaryotic Initiation Factor-4A metabolism, GTP-Binding Proteins chemistry, Humans, Molecular Sequence Data, Neoplasm Proteins chemistry, Protein Binding, Protein Conformation, Receptors for Activated C Kinase, Receptors, Cell Surface chemistry, Saccharomyces cerevisiae Proteins chemistry, Sequence Alignment, Cryptococcus neoformans metabolism, Fungal Proteins chemistry, Fungal Proteins metabolism, Models, Molecular, Ribosomes metabolism, Signal Transduction
- Abstract
The atypical Gβ-like/RACK1 Gib2 protein promotes cAMP signalling that plays a central role in regulating the virulence of Cryptococcus neoformans. Gib2 contains a seven-bladed β transducin structure and is emerging as a scaffold protein interconnecting signalling pathways through interactions with various protein partners. Here, we present the crystal structure of Gib2 at a 2.2-Å resolution. The structure allows us to analyse the association between Gib2 and the ribosome, as well as to identify the Gib2 amino acid residues involved in ribosome binding. Our studies not only suggest that Gib2 has a role in protein translation but also present Gib2 as a physical link at the crossroads of various regulatory pathways important for the growth and virulence of C. neoformans.
- Published
- 2015
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29. Corrigendum: Structure of EF-G-ribosome complex in a pretranslocation state.
- Author
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Chen Y, Feng S, Kumar V, Ero R, and Gao YG
- Published
- 2015
- Full Text
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