1
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Humphrey ED, Sukhodolets MV. Isolation and Partial Characterization of Novel, Structurally Uniform (Hfq 6) n≥8 Assemblies Carrying Accessory Transcription and Translation Factors. Biochemistry 2024; 63:1647-1662. [PMID: 38869079 DOI: 10.1021/acs.biochem.3c00728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
In growing E. coli cells, the transcription-translation complexes (TTCs) form characteristic foci; however, the exact molecular composition of these superstructures is not known with certainty. Herein, we report that, during our recently developed "fast" procedures for purification of E. coli RNA polymerase (RP), a fraction of the RP's α/RpoA subunits is displaced from the core RP complexes and copurifies with multiprotein superstructures carrying the nucleic acid-binding protein Hfq and the ribosomal protein S6. We show that the main components of these large multiprotein assemblies are fixed protein copy-number (Hfq6)n≥8 complexes; these complexes have a high level of structural uniformity and are distinctly unlike the previously described (Hfq6)n "head-to-tail" polymers. We describe purification of these novel, structurally uniform (Hfq6)n≥8 complexes to near homogeneity and show that they also contain small nonprotein molecules and accessory S6. We demonstrate that Hfq, S6, and RP have similar solubility profiles and present evidence pointing to a role of the Hfq C-termini in superstructure formation. Taken together, our data offer new insights into the composition of the macromolecular assemblies likely acting as scaffolds for transcription complexes and ribosomes during bacterial cells' active growth.
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Affiliation(s)
- Elijah D Humphrey
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
| | - Maxim V Sukhodolets
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
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2
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Liu X, Wang X, Yang C, Wang G, Fan B, Shang Y, Dang C, Xie C, Wang Z. Genome-wide identification of TaCIPK gene family members in wheat and their roles in host response to Blumeria graminis f. sp. tritici infection. Int J Biol Macromol 2023; 248:125691. [PMID: 37422244 DOI: 10.1016/j.ijbiomac.2023.125691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023]
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive disease affecting wheat crops worldwide. Functional genes can be activated in response to Bgt inoculations. Calcineurin B-like protein (CBL) together with CBL-interacting protein kinase (CIPK) forms the CBL-CIPK protein complex that participates in Ca2+ sensor kinase-related signaling pathways responding to abiotic and biotic stresses. In this study, we performed a genome-wide screening and identified 27 CIPK subfamilies (123 CIPK transcripts, TaCIPKs) including 55 new and 47 updated TaCIPKs in wheat. Phylogenetic analysis revealed that 123 TaCIPKs could be divided into four groups. Segmental duplications and tandem repeats promoted the expansion of the TaCIPK family. Gene function was further evidenced by differences in gene structure, cis-elements, and protein domains. TaCIPK15-4A was cloned in this study. TaCIPK15-4A contained 17 serine, seven tyrosine, and 15 threonine phosphorylation sites and localized in the plasma membrane and cytoplasm. TaCIPK15-4A expression was induced after Bgt inoculation. Virus-induced gene silencing and overexpression experiments indicated that TaCIPK15-4A could play a positive role in wheat disease resistance to Bgt. Overall, these results provide insights into the role of the TaCIPK gene family in wheat resistance and could be beneficial for further research to prevent Bgt infection.
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Affiliation(s)
- Xiaoying Liu
- College of Life Science, Tianjin Normal University, Tianjin, 30087, China
| | - Xueqing Wang
- College of Life Science, Tianjin Normal University, Tianjin, 30087, China
| | - Chenxiao Yang
- College of Life Science, Tianjin Normal University, Tianjin, 30087, China
| | - Guangyu Wang
- College of Life Science, Tianjin Normal University, Tianjin, 30087, China
| | - Baoli Fan
- College of Life Science, Tianjin Normal University, Tianjin, 30087, China
| | - Yuntao Shang
- Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, 30087, China
| | - Chen Dang
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agro-biotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chaojie Xie
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agro-biotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhenying Wang
- College of Life Science, Tianjin Normal University, Tianjin, 30087, China.
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3
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Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmüller H, Nováček J, Wilson DN. Structural conservation of antibiotic interaction with ribosomes. Nat Struct Mol Biol 2023; 30:1380-1392. [PMID: 37550453 PMCID: PMC10497419 DOI: 10.1038/s41594-023-01047-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/26/2023] [Indexed: 08/09/2023]
Abstract
The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.
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Affiliation(s)
- Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Timm O Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Bertrand Beckert
- Dubochet Center for Imaging at EPFL-UNIL, Batiment Cubotron, Lausanne, Switzerland
| | | | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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4
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Tsirogianni A, Kournoutou GG, Mpogiatzoglou M, Dinos G, Athanassopoulos CM. Chloramphenicol Derivatization in Its Primary Hydroxyl Group with Basic Amino Acids Leads to New Pharmacophores with High Antimicrobial Activity. Antibiotics (Basel) 2023; 12:antibiotics12050832. [PMID: 37237735 DOI: 10.3390/antibiotics12050832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/05/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
In a previous study published by our group, successful modification of the antibiotic chloramphenicol (CHL) was reported, which was achieved by replacing the dichloroacetyl tail with alpha and beta amino acids, resulting in promising new antibacterial pharmacophores. In this study, CHL was further modified by linking the basic amino acids lysine, ornithine, and histidine to the primary hydroxyl group of CHL via triazole, carbamate, or amide bonding. Our results showed that while linking the basic amino acids retained antibacterial activity, it was somewhat reduced compared to CHL. However, in vitro testing demonstrated that all derivatives were comparable in activity to CHL and competed for the same ribosomal binding site with radioactive chloramphenicol. The amino acid-CHL tethering modes were evaluated either with carbamate (7, 8) derivatives, which exhibited higher activity, or with amide- (4-6) or triazole-bridged compounds (1-3), which were equally potent. Our findings suggest that these new pharmacophores have potential as antimicrobial agents, though further optimization is needed.
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Affiliation(s)
- Artemis Tsirogianni
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, GR-26504 Patras, Greece
| | - Georgia G Kournoutou
- Department of Biochemistry, School of Medicine, University of Patras, GR-26504 Patras, Greece
| | - Maria Mpogiatzoglou
- Department of Biochemistry, School of Medicine, University of Patras, GR-26504 Patras, Greece
| | - George Dinos
- Department of Biochemistry, School of Medicine, University of Patras, GR-26504 Patras, Greece
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5
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Wee LM, Tong AB, Florez Ariza AJ, Cañari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell 2023; 186:1244-1262.e34. [PMID: 36931247 PMCID: PMC10135430 DOI: 10.1016/j.cell.2023.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the majority of the effects of coupling. Also, by cryo-EM, we observed that RNAPs with a terminal mismatch adopt a backtracked conformation, while a coupled ribosome allosterically induces these polymerases toward a catalytically active anti-swiveled state. Finally, we demonstrate that prolonged RNAP pausing is detrimental to cell viability, which could be prevented by polymerase reactivation through a coupled ribosome.
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Affiliation(s)
- Liang Meng Wee
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alexander B Tong
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Alfredo Jose Florez Ariza
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Cristhian Cañari-Chumpitaz
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patricia Grob
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos J Bustamante
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Department of Physics, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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6
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Schäkermann S, Dietze P, Bandow JE. Label-Free Quantitation of Ribosomal Proteins from Bacillus subtilis for Antibiotic Research. Methods Mol Biol 2023; 2601:363-378. [PMID: 36445595 DOI: 10.1007/978-1-0716-2855-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Current research is focusing on ribosome heterogeneity as a response to changing environmental conditions and stresses. Altered stoichiometry and composition of ribosomal proteins as well as association of additional protein factors are mechanisms for shaping the protein expression profile or hibernating ribosomes. In this updated chapter, we present a method for the isolation of ribosomes to analyze antibiotic-induced changes in the composition of ribosomes in Bacillus subtilis or other bacteria. Ribosomes and associated proteins are isolated by ultracentrifugation, and proteins are identified and quantified using label-free mass spectrometry.
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Affiliation(s)
| | - Pascal Dietze
- Ruhr-Universität Bochum, Applied Microbiology, Bochum, Germany
| | - Julia E Bandow
- Ruhr-Universität Bochum, Applied Microbiology, Bochum, Germany
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7
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Thabet SG, Alomari DZ, Börner A, Brinch-Pedersen H, Alqudah AM. Elucidating the genetic architecture controlling antioxidant status and ionic balance in barley under salt stress. PLANT MOLECULAR BIOLOGY 2022; 110:287-300. [PMID: 35918559 DOI: 10.1007/s11103-022-01302-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Association genetic analysis empowered us to identify candidate genes underlying natural variation of morpho-physiological, antioxidants, and grain yield-related traits in barley. Novel intriguing genomic regions were identified and dissected. Salinity stress is one of the abiotic stresses that influence the morpho-physiological, antioxidants, and yield-related traits in crop plants. The plants of a core set of 138 diverse barley accessions were analyzed after exposure to salt stress under field conditions during the reproductive phase. A genome-wide association scan (GWAS) was then conducted using 19,276 single nucleotide polymorphisms (SNPs) to uncover the genetic basis of morpho-physiological and grain-related traits. A wide range of responses to salt stress by the accessions was explored in the current study. GWAS detected 263 significantly associated SNPs with the antioxidants, K+/Na+ content ratio, and agronomic traits. Five genomic regions harbored interesting putative candidate genes within LD ± 1.2 Mbp. Choromosome 2H harbored many candidate genes associated with the antioxidants ascorbic acid (AsA) and glutathione (GSH), such as superoxide dismutase (SOD), ascorbate peroxidase (APX), and glutathione reductase (GR), under salt stress. Markedly, an A:C SNP at 153,773,211 bp on chromosome 7H is located inside the gene HORVU.MOREX.r3.7HG0676830 (153,772,300-153,774,057 bp) that was annotated as L-gulonolactone oxidase, regulating the natural variation of SOD_S and APX_S. The allelic variation at this SNP reveals a negative selection of accessions carrying the C allele, predominantly found in six-rowed spring landraces originating from Far-, Near-East, and central Asia carrying photoperiod sensitive alleles having lower activity of enzymatic antioxidants. The SNP-trait associations detected in the current study constitute a benchmark for developing molecular selection tools for antioxidant compound selection in barley.
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Affiliation(s)
- Samar G Thabet
- Department of Botany, Faculty of Science, Fayoum University, 63514, Fayoum, Egypt
| | - Dalia Z Alomari
- Department of Agroecology, Aarhus University, Flakkebjerg, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr 3, 06466, Seeland, Germany
| | - Henrik Brinch-Pedersen
- Department of Agroecology, Aarhus University, Flakkebjerg, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Ahmad M Alqudah
- Department of Agroecology, Aarhus University, Flakkebjerg, Forsøgsvej 1, 4200, Slagelse, Denmark.
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8
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Annealing synchronizes the 70 S ribosome into a minimum-energy conformation. Proc Natl Acad Sci U S A 2022; 119:2111231119. [PMID: 35177473 PMCID: PMC8872765 DOI: 10.1073/pnas.2111231119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2022] [Indexed: 11/18/2022] Open
Abstract
Researchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate that simulated annealing on biological macromolecules helps predict the final structures with minimum free energy. Experimental validation of this homogenizing effect and further exploration of its applications are fascinating scientific questions that remain elusive. Here, we chose the apo-state 70S ribosome from Escherichia coli as a model, wherein the 30S subunit undergoes a thermally driven intersubunit rotation and exhibits substantial structural flexibility as well as distinct free energy. We experimentally demonstrate that annealing at a fast cooling rate enhances the 70S ribosome homogeneity and improves local resolution on the 30S subunit. After annealing, the 70S ribosome is in a nonrotated state with respect to corresponding intermediate structures in unannealed or heated ribosomes. Manifold-based analysis further indicates that the annealed 70S ribosome takes a narrow conformational distribution and exhibits a minimum-energy state in the free-energy landscape. Our experimental results offer a facile yet robust approach to enhance protein stability, which is ideal for high-resolution cryogenic electron microscopy. Beyond structure determination, annealing shows great potential for synchronizing proteins on a single-molecule level and can be extended to study protein folding and explore conformational and energy landscapes.
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9
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El-Shahir AA, El-Tayeh NA, Ali OM, Abdel Latef AAH, Loutfy N. The Effect of Endophytic Talaromyces pinophilus on Growth, Absorption and Accumulation of Heavy Metals of Triticum aestivum Grown on Sandy Soil Amended by Sewage Sludge. PLANTS (BASEL, SWITZERLAND) 2021; 10:2659. [PMID: 34961130 PMCID: PMC8704920 DOI: 10.3390/plants10122659] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 05/24/2023]
Abstract
Sewage sludge improves agricultural soil and plant growth, but there are risks associated with its use, including high heavy metal content. In this study, experiments were carried out to investigate the role of endophytic Talaromyces pinophilus MW695526 on the growth of Triticum aestivum cultivated in soil amended with sewage sludge and its phytoremediation ability. T. pinophilus could produce gibberellic acid (GA) and stimulate T. aestivum to accumulate GA. The results showed that inoculation with T. pinophilus boosted plant growth criteria, photosynthetic pigments, osmolytes (soluble proteins, soluble sugars and total amino acids), enzymatic antioxidants (catalase, superoxide dismutase and peroxidase), K, Ca and Mg. On the other hand, it reduced Na, Na/K ratio, Cd, Ni, Cu and Zn in the growth media as well as in the shoot and root of T. aestivum. The results suggest that endophytic T. pinophilus can work as a barrier to reduce the absorption of heavy metals in T. aestivum cultivated in soil amended with sewage sludge.
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Affiliation(s)
- Amany A. El-Shahir
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt; (N.A.E.-T.); (N.L.)
| | - Noha A. El-Tayeh
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt; (N.A.E.-T.); (N.L.)
| | - Omar M. Ali
- Department of Chemistry, Turabah University College, Turabah Branch, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Arafat Abdel Hamed Abdel Latef
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt; (N.A.E.-T.); (N.L.)
| | - Naglaa Loutfy
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt; (N.A.E.-T.); (N.L.)
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10
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Ur Rahman S, Basit A, Ara N, Ullah I, Rehman AU. Morpho-physiological Responses of Tomato Genotypes Under Saline Conditions. GESUNDE PFLANZEN 2021; 73:541-553. [DOI: 10.1007/s10343-021-00576-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/20/2021] [Indexed: 10/26/2023]
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11
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Gamper H, Mao Y, Masuda I, McGuigan H, Blaha G, Wang Y, Xu S, Hou YM. Twice exploration of tRNA +1 frameshifting in an elongation cycle of protein synthesis. Nucleic Acids Res 2021; 49:10046-10060. [PMID: 34417618 PMCID: PMC8464047 DOI: 10.1093/nar/gkab734] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 12/18/2022] Open
Abstract
Inducing tRNA +1 frameshifting to read a quadruplet codon has the potential to incorporate a non-natural amino acid into the polypeptide chain. While this strategy is being considered for genome expansion in biotechnology and bioengineering endeavors, a major limitation is a lack of understanding of where the shift occurs in an elongation cycle of protein synthesis. Here, we use the high-efficiency +1-frameshifting SufB2 tRNA, containing an extra nucleotide in the anticodon loop, to address this question. Physical and kinetic measurements of the ribosome reading frame of SufB2 identify twice exploration of +1 frameshifting in one elongation cycle, with the major fraction making the shift during translocation from the aminoacyl-tRNA binding (A) site to the peptidyl-tRNA binding (P) site and the remaining fraction making the shift within the P site upon occupancy of the A site in the +1-frame. We demonstrate that the twice exploration of +1 frameshifting occurs during active protein synthesis and that each exploration is consistent with ribosomal conformational dynamics that permits changes of the reading frame. This work indicates that the ribosome itself is a determinant of changes of the reading frame and reveals a mechanistic parallel of +1 frameshifting with –1 frameshifting.
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Affiliation(s)
- Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Yujia Mao
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Henri McGuigan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Shoujun Xu
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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12
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Cui J, Tcherkez G. Potassium dependency of enzymes in plant primary metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:522-530. [PMID: 34174657 DOI: 10.1016/j.plaphy.2021.06.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Potassium is a macroelement essential to many aspects of plant life, such as photosynthesis, phloem transport or cellular electrochemistry. Many enzymes in animals or microbes are known to be stimulated or activated by potassium (K+ ions). Several plant enzymes are also strictly K+-dependent, and this can be critical when plants are under K deficiency and thus intracellular K+ concentration is low. Although metabolic effects of low K conditions have been documented, there is presently no review focusing on roles of K+ for enzyme catalysis or activation in plants. In this mini-review, we compile the current knowledge on K+-requirement of plant enzymes and take advantage of structural data to present biochemical roles of K+. This information is instrumental to explain direct effects of low K+ content on metabolism and this is illustrated with recent metabolomics data.
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Affiliation(s)
- Jing Cui
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, Australia
| | - Guillaume Tcherkez
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, Australia; Institut de Recherche en Horticulture et Semences, INRAe Angers, Université d'Angers, 42 rue Georges Morel, 49070, Beaucouzé, France.
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13
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Gaonkar S, Rodrigues BF. Arbuscular mycorrhizal fungal status in mangroves of Pichavaram Forest, Tamil Nadu, India. Trop Ecol 2021. [DOI: 10.1007/s42965-021-00167-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Tsirogianni A, Kournoutou GG, Bougas A, Poulou-Sidiropoulou E, Dinos G, Athanassopoulos CM. New Chloramphenicol Derivatives with a Modified Dichloroacetyl Tail as Potential Antimicrobial Agents. Antibiotics (Basel) 2021; 10:antibiotics10040394. [PMID: 33917453 PMCID: PMC8067500 DOI: 10.3390/antibiotics10040394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/01/2021] [Accepted: 04/03/2021] [Indexed: 12/02/2022] Open
Abstract
To combat the dangerously increasing pathogenic resistance to antibiotics, we developed new pharmacophores by chemically modifying a known antibiotic, which remains to this day the most familiar and productive way for novel antibiotic development. We used as a starting material the chloramphenicol base, which is the free amine group counterpart of the known chloramphenicol molecule antibiotic upon removal of its dichloroacetyl tail. To this free amine group, we tethered alpha- and beta-amino acids, mainly glycine, lysine, histidine, ornithine and/or beta-alanine. Furthermore, we introduced additional modifications to the newly incorporated amine groups either with protecting groups triphenylmethyl- (Trt) and tert-butoxycarbonyl- (Boc) or with the dichloroacetic group found also in the chloramphenicol molecule. The antimicrobial activity of all compounds was tested both in vivo and in vitro, and according to the results, the bis-dichloroacetyl derivative of ornithine displayed the highest antimicrobial activity both in vivo and in vitro and seems to be a dynamic new pharmacophore with room for further modification and development.
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Affiliation(s)
- Artemis Tsirogianni
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, 26504 Patras, Greece;
| | - Georgia G. Kournoutou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.G.K.); (A.B.); (E.P.-S.)
| | - Anthony Bougas
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.G.K.); (A.B.); (E.P.-S.)
| | - Eleni Poulou-Sidiropoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.G.K.); (A.B.); (E.P.-S.)
| | - George Dinos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.G.K.); (A.B.); (E.P.-S.)
- Correspondence: (G.D.); (C.M.A.); Tel.: +30-2610-969-125 (G.D.); +30-2610-997-909 (C.M.A.)
| | - Constantinos M. Athanassopoulos
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, 26504 Patras, Greece;
- Correspondence: (G.D.); (C.M.A.); Tel.: +30-2610-969-125 (G.D.); +30-2610-997-909 (C.M.A.)
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15
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Alzahib RH, Migdadi HM, Al Ghamdi AA, Alwahibi MS, Ibrahim AA, Al-Selwey WA. Assessment of Morpho-Physiological, Biochemical and Antioxidant Responses of Tomato Landraces to Salinity Stress. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10040696. [PMID: 33916328 PMCID: PMC8065849 DOI: 10.3390/plants10040696] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/17/2021] [Accepted: 03/24/2021] [Indexed: 05/26/2023]
Abstract
Understanding salt tolerance in tomato (Solanum lycopersicum L.) landraces will facilitate their use in genetic improvement. The study assessed the morpho-physiological variability of Hail tomato landraces in response to different salinity levels at seedling stages and recommended a tomato salt-tolerant landrace for future breeding programs. Three tomato landraces, Hail 548, Hail 747, and Hail 1072 were tested under three salinity levels: 75, 150, and 300 mM NaCl. Salinity stress reduced shoots' fresh and dry weight by 71% and 72%, and roots were 86.5% and 78.6%, respectively. There was 22% reduced chlorophyll content, carotene content by 18.6%, and anthocyanin by 41.1%. Proline content increased for stressed treatments. The 300 mM NaCl treatment recorded the most proline content increases (67.37 mg/g fresh weight), with a percent increase in proline reaching 61.67% in Hail 747. Superoxide dismutase (SOD) activity decreased by 65% in Hail 548, while it relatively increased in Hail 747 and Hail 1072 treated with 300 mM NaCl. Catalase (CAT) activity was enhanced by salt stress in Hail 548 and recorded 7.6%, increasing at 75 and 5.1% at 300 mM NaCl. It revealed a reduction in malondialdehyde (MDA) at the 300 mM NaCl concentration in both Hail 548 and Hail 1072 landraces. Increasing salt concentrations showed a reduction in transpiration rate of 70.55%, 7.13% in stomatal conductance, and 72.34% in photosynthetic rate. K+/Na+ ratios decreased from 56% for 75 mM NaCl to 85% for 300 mM NaCl treatments in all genotypes. The response to salt stress in landraces involved some modifications in morphology, physiology, and metabolism. The landrace Hail 548 may have better protection against salt stress and observed protection against reactive oxygen species (ROS) by increasing enzymatic "antioxidants" activity under salt stress.
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Affiliation(s)
- Reem H. Alzahib
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (R.H.A.); (A.A.A.G.); (M.S.A.)
| | - Hussein M. Migdadi
- College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (A.A.I.); (W.A.A.-S.)
| | - Abdullah A. Al Ghamdi
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (R.H.A.); (A.A.A.G.); (M.S.A.)
| | - Mona S. Alwahibi
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (R.H.A.); (A.A.A.G.); (M.S.A.)
| | - Abdullah A. Ibrahim
- College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (A.A.I.); (W.A.A.-S.)
| | - Wadei A. Al-Selwey
- College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (A.A.I.); (W.A.A.-S.)
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16
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Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nat Commun 2020; 11:5569. [PMID: 33149120 PMCID: PMC7642426 DOI: 10.1038/s41467-020-19372-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/08/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.
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Affiliation(s)
- Linda Schulte
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany
| | - Jiafei Mao
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
| | - Julian Reitz
- Institute for Biophysics, Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, Frankfurt, Germany
| | - Sridhar Sreeramulu
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany
| | - Denis Kudlinzki
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany
| | - Victor-Valentin Hodirnau
- Institute for Biophysics, Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, Frankfurt, Germany.,Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Krishna Saxena
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany
| | - Florian Buhr
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany.,Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | | | | | - Achilleas S Frangakis
- Institute for Biophysics, Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, Frankfurt, Germany.
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt, Germany.
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany.
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17
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Current Advances in Plant Growth Promoting Bacteria Alleviating Salt Stress for Sustainable Agriculture. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10207025] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Humanity in the modern world is confronted with diverse problems at several levels. The environmental concern is probably the most important as it threatens different ecosystems, food, and farming as well as humans, animals, and plants. More specifically, salinization of agricultural soils is a global concern because of on one side, the permanent increase of the areas affected, and on the other side, the disastrous damage caused to various plants affecting hugely crop productivity and yields. Currently, great attention is directed towards the use of Plant Growth Promoting Bacteria (PGPB). This alternative method, which is healthy, safe, and ecological, seems to be very promising in terms of simultaneous salinity alleviation and improving crop productivity. This review attempts to deal with different aspects of the current advances concerning the use of PGPBs for saline stress alleviation. The objective is to explain, discuss, and present the current progress in this area of research. We firstly discuss the implication of PGPB on soil desalinization. We present the impacts of salinity on crops. We look for the different salinity origin and its impacts on plants. We discuss the impacts of salinity on soil. Then, we review various recent progress of hemophilic PGPB for sustainable agriculture. We categorize the mechanisms of PGPB toward salinity tolerance. We discuss the use of PGPB inoculants under salinity that can reduce chemical fertilization. Finally, we present some possible directions for future investigation. It seems that PGPBs use for saline stress alleviation gain more importance, investigations, and applications. Regarding the complexity of the mechanisms implicated in this domain, various aspects remain to be elucidated.
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18
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Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G, Su M, Ebright RH. Structural basis of transcription-translation coupling. Science 2020; 369:1359-1365. [PMID: 32820061 DOI: 10.1126/science.abb5317] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 07/17/2020] [Indexed: 12/19/2022]
Abstract
In bacteria, transcription and translation are coupled processes in which the movement of RNA polymerase (RNAP)-synthesizing messenger RNA (mRNA) is coordinated with the movement of the first ribosome-translating mRNA. Coupling is modulated by the transcription factors NusG (which is thought to bridge RNAP and the ribosome) and NusA. Here, we report cryo-electron microscopy structures of Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A, previously termed "expressome"). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling.
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Affiliation(s)
- Chengyuan Wang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Vadim Molodtsov
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Emre Firlar
- Rutgers New Jersey CryoEM/CryoET Core Facility and Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Jason T Kaelber
- Rutgers New Jersey CryoEM/CryoET Core Facility and Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Min Su
- Life Sciences Institute, University of Michigan, Ann Arbor, MI,48109, USA.
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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19
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Adaptation of Plants to Salt Stress: Characterization of Na+ and K+ Transporters and Role of CBL Gene Family in Regulating Salt Stress Response. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9110687] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Salinity is one of the most serious factors limiting the productivity of agricultural crops, with adverse effects on germination, plant vigor, and crop yield. This salinity may be natural or induced by agricultural activities such as irrigation or the use of certain types of fertilizer. The most detrimental effect of salinity stress is the accumulation of Na+ and Cl− ions in tissues of plants exposed to soils with high NaCl concentrations. The entry of both Na+ and Cl− into the cells causes severe ion imbalance, and excess uptake might cause significant physiological disorder(s). High Na+ concentration inhibits the uptake of K+, which is an element for plant growth and development that results in lower productivity and may even lead to death. The genetic analyses revealed K+ and Na+ transport systems such as SOS1, which belong to the CBL gene family and play a key role in the transport of Na+ from the roots to the aerial parts in the Arabidopsis plant. In this review, we mainly discuss the roles of alkaline cations K+ and Na+, Ion homeostasis-transport determinants, and their regulation. Moreover, we tried to give a synthetic overview of soil salinity, its effects on plants, and tolerance mechanisms to withstand stress.
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20
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Lema M, Ali MY, Retuerto R. Domestication influences morphological and physiological responses to salinity in Brassica oleracea seedlings. AOB PLANTS 2019; 11:plz046. [PMID: 31579110 PMCID: PMC6757351 DOI: 10.1093/aobpla/plz046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/29/2019] [Indexed: 05/28/2023]
Abstract
Brassica oleracea cultivars include important vegetable and forage crops grown worldwide, whereas the wild counterpart occurs naturally on European sea cliffs. Domestication and selection processes have led to phenotypic and genetic divergence between domesticated plants and their wild ancestors that inhabit coastal areas and are exposed to saline conditions. Salinity is one of the most limiting factors for crop production. However, little is known about how salinity affects plants in relation to domestication of B. oleracea. The objective of this study was to determine the influence of domestication status (wild, landrace or cultivar) on the response of different B. oleracea crops to salinity, as measured by seed germination, plant growth, water content and mineral concentration parameters at the seedling stage. For this purpose, two independent pot experiments were conducted with six accessions of B. oleracea, including cabbage (group capitata) and kale (group acephala), in a growth chamber under controlled environmental conditions. In both taxonomic groups, differences in domestication status and salt stress significantly affected all major process such as germination, changes in dry matter, water relations and mineral uptake. In the acephala experiment, the domestication × salinity interaction significantly affected water content parameters and shoot Na+ allocation. At early stages of development, wild plants are more succulent than cultivated plants and have a higher capacity to maintain lower Na+ concentrations in their shoots in response to increasing levels of salinity. Different responses of domesticated and cultivated accessions in relation to these traits indicated a high level of natural variation in wild B. oleracea. Exclusion of Na+ from shoots and increasing succulence may enhance salt tolerance in B. oleracea exposed to extreme salinity in the long term. The wild germplasm can potentially be used to improve the salt tolerance of crops by the identification of useful genes and incorporation of these into salinity-sensitive cultivars.
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Affiliation(s)
- M Lema
- Department of Functional Biology, Faculty of Biology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Md Y Ali
- Agrotechnology Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - R Retuerto
- Department of Functional Biology, Faculty of Biology, University of Santiago de Compostela, Santiago de Compostela, Spain
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21
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Pletnev PI, Nesterchuk MV, Rubtsova MP, Serebryakova MV, Dmitrieva K, Osterman IA, Bogdanov AA, Sergiev PV. Oligoglutamylation of E. coli ribosomal protein S6 is under growth phase control. Biochimie 2019; 167:61-67. [PMID: 31520657 DOI: 10.1016/j.biochi.2019.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022]
Abstract
Ribosomal protein S6 in Escherichia coli is modified by ATP-dependent glutamate ligase RimK. Up to four glutamate residues are added to the C-terminus of S6 protein. In this work we demonstrated that unlike the majority of ribosome modifications in E. coli, oligoglutamylation of S6 protein is regulated and happens only in the stationary phase of bacterial culture. Only S6 protein incorporated into assembled small ribosomal subunits, but not newly made free S6 protein is a substrate for RimK protein. Overexpression of the rimK gene leads to the modification of S6 protein even in the exponential phase of bacterial culture. Thus, it is unlikely that any stationary phase specific factor is needed for the modification. We propose a model that S6 modification is regulated solely via the rate of ribosome biosynthesis at limiting concentration of RimK enzyme.
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Affiliation(s)
- Philipp I Pletnev
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia; Skolkovo Institute for Science and Technology, Moscow, 143025, Russia
| | | | - Maria P Rubtsova
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia; Skolkovo Institute for Science and Technology, Moscow, 143025, Russia
| | - Marina V Serebryakova
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia; Skolkovo Institute for Science and Technology, Moscow, 143025, Russia
| | - Ksenia Dmitrieva
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia
| | - Ilya A Osterman
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia; Skolkovo Institute for Science and Technology, Moscow, 143025, Russia
| | - Alexey A Bogdanov
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia
| | - Petr V Sergiev
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia; Skolkovo Institute for Science and Technology, Moscow, 143025, Russia.
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22
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Rahman MA, Thomson MJ, De Ocampo M, Egdane JA, Salam MA, Shah-E-Alam M, Ismail AM. Assessing trait contribution and mapping novel QTL for salinity tolerance using the Bangladeshi rice landrace Capsule. RICE (NEW YORK, N.Y.) 2019; 12:63. [PMID: 31410650 PMCID: PMC6692794 DOI: 10.1186/s12284-019-0319-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/25/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Salinity is one of the most widespread abiotic stresses affecting rice productivity worldwide. The purpose of this study was to establish the relative importance of different traits associated with salinity tolerance in rice and to identify new quantitative trait loci (QTL) conferring tolerance to salinity at seedling stage. A total of 231 F2:3 plants derived from a cross between a sensitive variety BRRI dhan29 (BR29 hereafter) and Capsule, a salt tolerant Bangladeshi indica landrace, were evaluated under salt stress in a phytotron. RESULTS Out of the 231 F2 plants, 47 highly tolerant and 47 most sensitive lines were selected, representing the two extreme tails of the phenotypic distribution. These 94 plants were genotyped for 105 simple sequence repeat (SSR) and insertion/deletion (InDel) markers. A genetic linkage map spanning approximately 1442.9 cM of the 12 linkage groups with an average marker distance of 13.7 cM was constructed. QTL were identified on the long arm of chromosome 1 for Na+ concentration, K+ concentration, Na+-K+ ratio and survival; chromosome 3 for Na+ concentration, survival and overall phenotypic evaluation using the Standard Evaluation system (SES); and chromosome 5 for SES. A total of 6 pairwise epistatic interactions were also detected between QTL-linked and QTL-unlinked regions. Graphical genotyping indicated an association between the phenotypes of the extreme families and their QTL genotypes. Path coefficient analysis revealed that Na+ concentration, survival, Na+-K+ ratio and the overall phenotypic performance (SES score) are the major traits associated with salinity tolerance of Capsule. CONCLUSIONS Capsule provides an alternative source of salinity tolerance aside from Pokkali and Nona Bokra, the two Indian salt tolerant landraces traditionally used for breeding salt tolerant rice varieties. Pyramiding the new QTL identified in this study with previously discovered loci, such as Saltol, will facilitate breeding varieties that are highly tolerant of salt stress.
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Affiliation(s)
- M Akhlasur Rahman
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | - Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Marjorie De Ocampo
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - James A Egdane
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - M A Salam
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | - M Shah-E-Alam
- Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Abdelbagi M Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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23
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Svetlov MS, Plessa E, Chen CW, Bougas A, Krokidis MG, Dinos GP, Polikanov YS. High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition. RNA (NEW YORK, N.Y.) 2019; 25:600-606. [PMID: 30733327 PMCID: PMC6467010 DOI: 10.1261/rna.069260.118] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/28/2019] [Indexed: 05/22/2023]
Abstract
The 70S ribosome is a major target for antibacterial drugs. Two of the classical antibiotics, chloramphenicol (CHL) and erythromycin (ERY), competitively bind to adjacent but separate sites on the bacterial ribosome: the catalytic peptidyl transferase center (PTC) and the nascent polypeptide exit tunnel (NPET), respectively. The previously reported competitive binding of CHL and ERY might be due either to a direct collision of the two drugs on the ribosome or due to a drug-induced allosteric effect. Because of the resolution limitations, the available structures of these antibiotics in complex with bacterial ribosomes do not allow us to discriminate between these two possible mechanisms. In this work, we have obtained two crystal structures of CHL and ERY in complex with the Thermus thermophilus 70S ribosome at a higher resolution (2.65 and 2.89 Å, respectively) allowing unambiguous placement of the drugs in the electron density maps. Our structures provide evidence of the direct collision of CHL and ERY on the ribosome, which rationalizes the observed competition between the two drugs.
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Affiliation(s)
- Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Elena Plessa
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Chih-Wei Chen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Anthony Bougas
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Marios G Krokidis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - George P Dinos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Yury S Polikanov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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24
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Waduge P, Sakakibara Y, Chow CS. Chemical probing for examining the structure of modified RNAs and ligand binding to RNA. Methods 2019; 156:110-120. [DOI: 10.1016/j.ymeth.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/04/2018] [Accepted: 10/22/2018] [Indexed: 12/15/2022] Open
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25
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Asif MA, Schilling RK, Tilbrook J, Brien C, Dowling K, Rabie H, Short L, Trittermann C, Garcia A, Barrett-Lennard EG, Berger B, Mather DE, Gilliham M, Fleury D, Tester M, Roy SJ, Pearson AS. Mapping of novel salt tolerance QTL in an Excalibur × Kukri doubled haploid wheat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2179-2196. [PMID: 30062653 PMCID: PMC6154029 DOI: 10.1007/s00122-018-3146-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/14/2018] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE Novel QTL for salinity tolerance traits have been detected using non-destructive and destructive phenotyping in bread wheat and were shown to be linked to improvements in yield in saline fields. Soil salinity is a major limitation to cereal production. Breeding new salt-tolerant cultivars has the potential to improve cereal crop yields. In this study, a doubled haploid bread wheat mapping population, derived from the bi-parental cross of Excalibur × Kukri, was grown in a glasshouse under control and salinity treatments and evaluated using high-throughput non-destructive imaging technology. Quantitative trait locus (QTL) analysis of this population detected multiple QTL under salt and control treatments. Of these, six QTL were detected in the salt treatment including one for maintenance of shoot growth under salinity (QG(1-5).asl-7A), one for leaf Na+ exclusion (QNa.asl-7A) and four for leaf K+ accumulation (QK.asl-2B.1, QK.asl-2B.2, QK.asl-5A and QK:Na.asl-6A). The beneficial allele for QG(1-5).asl-7A (the maintenance of shoot growth under salinity) was present in six out of 44 mainly Australian bread and durum wheat cultivars. The effect of each QTL allele on grain yield was tested in a range of salinity concentrations at three field sites across 2 years. In six out of nine field trials with different levels of salinity stress, lines with alleles for Na+ exclusion and/or K+ maintenance at three QTL (QNa.asl-7A, QK.asl-2B.2 and QK:Na.asl-6A) excluded more Na+ or accumulated more K+ compared to lines without these alleles. Importantly, the QK.asl-2B.2 allele for higher K+ accumulation was found to be associated with higher grain yield at all field sites. Several alleles at other QTL were associated with higher grain yields at selected field sites.
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Affiliation(s)
- Muhammad A Asif
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Rhiannon K Schilling
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Joanne Tilbrook
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
- Plant Industries Development, Department of Primary Industry and Resources, PO Box 3000, Darwin, NT, 0801, Australia
| | - Chris Brien
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, Urrbrae, SA, 5064, Australia
- Phenomics and Bioinformatics Research Center, The University of South Australia, GPO Box 2471, Mawson Lakes, 5001, SA, Australia
| | - Kate Dowling
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Huwaida Rabie
- Phenomics and Bioinformatics Research Center, The University of South Australia, GPO Box 2471, Mawson Lakes, 5001, SA, Australia
- Bethlehem University, Rue de Freres #9, Bethlehem, West Bank, Palestine
| | - Laura Short
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Christine Trittermann
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Alexandre Garcia
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Edward G Barrett-Lennard
- School of Agriculture and Environment (M084), The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, 6151, WA, Australia
| | - Bettina Berger
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Diane E Mather
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Matthew Gilliham
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Delphine Fleury
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Mark Tester
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Stuart J Roy
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia.
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia.
| | - Allison S Pearson
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
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26
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Hashem A, Alqarawi AA, Radhakrishnan R, Al-Arjani ABF, Aldehaish HA, Egamberdieva D, Abd_Allah EF. Arbuscular mycorrhizal fungi regulate the oxidative system, hormones and ionic equilibrium to trigger salt stress tolerance in Cucumis sativus L. Saudi J Biol Sci 2018; 25:1102-1114. [PMID: 30174509 PMCID: PMC6117372 DOI: 10.1016/j.sjbs.2018.03.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/28/2018] [Accepted: 03/18/2018] [Indexed: 11/20/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) association increases plant stress tolerance. This study aimed to determine the mitigation effect of AMF on the growth and metabolic changes of cucumbers under adverse impact of salt stress. Salinity reduced the water content and synthesis of pigments. However, AMF inoculation ameliorated negative effects by enhancing the biomass, synthesis of pigments, activity of antioxidant enzymes, including superoxide dismutase, catalase, ascorbate peroxidase and glutathione reductase, and the content of ascorbic acid, which might be the result of lower level lipid peroxidation and electrolyte leakage. An accumulation of phenols and proline in AMF-inoculated plants also mediated the elimination of superoxide radicals. In addition, jasmonic acid, salicylic acid and several important mineral elements (K, Ca, Mg, Zn, Fe, Mn and Cu) were enhanced with significant reductions in the uptake of deleterious ions like Na+. These results suggested that AMF can protect cucumber growth from salt stress.
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Affiliation(s)
- Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza 12511, Egypt
| | - Abdulaziz A. Alqarawi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia
| | | | - Al-Bandari Fahad Al-Arjani
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia
| | - Horiah Abdulaziz Aldehaish
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia
| | | | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia
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27
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Fan H, Conn AB, Williams PB, Diggs S, Hahm J, Gamper HB, Hou YM, O'Leary SE, Wang Y, Blaha GM. Transcription-translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits. Nucleic Acids Res 2017; 45:11043-11055. [PMID: 28977553 PMCID: PMC5737488 DOI: 10.1093/nar/gkx719] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/09/2017] [Indexed: 11/12/2022] Open
Abstract
In prokaryotes, RNA polymerase and ribosomes can bind concurrently to the same RNA transcript, leading to the functional coupling of transcription and translation. The interactions between RNA polymerase and ribosomes are crucial for the coordination of transcription with translation. Here, we report that RNA polymerase directly binds ribosomes and isolated large and small ribosomal subunits. RNA polymerase and ribosomes form a one-to-one complex with a micromolar dissociation constant. The formation of the complex is modulated by the conformational and functional states of RNA polymerase and the ribosome. The binding interface on the large ribosomal subunit is buried by the small subunit during protein synthesis, whereas that on the small subunit remains solvent-accessible. The RNA polymerase binding site on the ribosome includes that of the isolated small ribosomal subunit. This direct interaction between RNA polymerase and ribosomes may contribute to the coupling of transcription to translation.
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Affiliation(s)
- Haitian Fan
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Adam B Conn
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Preston B Williams
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Stephen Diggs
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Joseph Hahm
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Seán E O'Leary
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Gregor M Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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28
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Schavemaker PE, Śmigiel WM, Poolman B. Ribosome surface properties may impose limits on the nature of the cytoplasmic proteome. eLife 2017; 6:e30084. [PMID: 29154755 PMCID: PMC5726854 DOI: 10.7554/elife.30084] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022] Open
Abstract
Much of the molecular motion in the cytoplasm is diffusive, which possibly limits the tempo of processes. We studied the dependence of protein mobility on protein surface properties and ionic strength. We used surface-modified fluorescent proteins (FPs) and determined their translational diffusion coefficients (D) in the cytoplasm of Escherichia coli, Lactococcus lactis and Haloferax volcanii. We find that in E. coli D depends on the net charge and its distribution over the protein, with positive proteins diffusing up to 100-fold slower than negative ones. This effect is weaker in L. lactis and Hfx. volcanii due to electrostatic screening. The decrease in mobility is probably caused by interaction of positive FPs with ribosomes as shown in in vivo diffusion measurements and confirmed in vitro with purified ribosomes. Ribosome surface properties may thus limit the composition of the cytoplasmic proteome. This finding lays bare a paradox in the functioning of prokaryotic (endo)symbionts.
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Affiliation(s)
| | | | - Bert Poolman
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenNetherlands
- Zernike Institute for Advanced MaterialsUniversity of GroningenGroningenNetherlands
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29
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Sakakibara Y, Chow CS. Pseudouridine modifications influence binding of aminoglycosides to helix 69 of bacterial ribosomes. Org Biomol Chem 2017; 15:8535-8543. [PMID: 28959821 PMCID: PMC5663508 DOI: 10.1039/c7ob02147j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Development of antibiotics that target new regions of functionality is a possible way to overcome antibiotic resistance. In this study, the interactions of aminoglycoside antibiotics with helix 69 of the E. coli 23S rRNA in the context of complete 70S ribosomes or the isolated 50S subunit were investigated by using chemical probing and footprinting analysis. Helix 69 is a dynamic RNA motif that plays major roles in bacterial ribosome activity. Neomycin, paromomycin, and gentamicin interact with the stem region of helix 69 in complete 70S ribosomes, but have diminished binding to the isolated 50S subunit. Pseudouridine modifications in helix 69 were shown to impact the aminoglycoside interactions. These results suggest a requirement for a specific conformational state of helix 69 for efficient aminoglycoside binding, and imply that this motif may be a suitable target for mechanism-based therapeutics.
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Affiliation(s)
- Yogo Sakakibara
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
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30
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Bougas A, Vlachogiannis IA, Gatos D, Arenz S, Dinos GP. Dual effect of chloramphenicol peptides on ribosome inhibition. Amino Acids 2017; 49:995-1004. [PMID: 28283906 DOI: 10.1007/s00726-017-2406-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/28/2017] [Indexed: 11/29/2022]
Abstract
Chloramphenicol peptides were recently established as useful tools for probing nascent polypeptide chain interaction with the ribosome, either biochemically, or structurally. Here, we present a new 10mer chloramphenicol peptide, which exerts a dual inhibition effect on the ribosome function affecting two distinct areas of the ribosome, namely the peptidyl transferase center and the polypeptide exit tunnel. According to our data, the chloramphenicol peptide bound on the chloramphenicol binding site inhibits the formation of both acetyl-phenylalanine-puromycin and acetyl-lysine-puromycin, showing, however, a decreased peptidyl transferase inhibition compared to chloramphenicol-mediated inhibition per se. Additionally, we found that the same compound is a strong inhibitor of green fluorescent protein synthesis in a coupled in vitro transcription-translation assay as well as a potent inhibitor of lysine polymerization in a poly(A)-programmed ribosome, showing that an additional inhibitory effect may exist. Since chemical protection data supported the interaction of the antibiotic with bases A2058 and A2059 near the entrance of the tunnel, we concluded that the extra inhibition effect on the synthesis of longer peptides is coming from interactions of the peptide moiety of the drug with residues comprising the ribosomal tunnel, and by filling up the tunnel and blocking nascent chain progression through the restricted tunnel. Therefore, the dual interaction of the chloramphenicol peptide with the ribosome increases its inhibitory effect and opens a new window for improving the antimicrobial potency of classical antibiotics or designing new ones.
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Affiliation(s)
- Anthony Bougas
- Department of Biochemistry, School of Medicine, University of Patras, 26500, Patras, Greece
| | | | - Dimitrios Gatos
- Department of Chemistry, University of Patras, Patras, Greece
| | - Stefan Arenz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University of Munich, Feodor- Lynen-Strasse 25, 81377, Munich, Germany
| | - George P Dinos
- Department of Biochemistry, School of Medicine, University of Patras, 26500, Patras, Greece.
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31
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Schäkermann S, Prochnow P, Bandow JE. Label-Free Quantitation of Ribosomal Proteins from Bacillus subtilis for Antibiotic Research. Methods Mol Biol 2017; 1520:291-306. [PMID: 27873260 DOI: 10.1007/978-1-4939-6634-9_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Current research is focusing on ribosome heterogeneity as a response to changing environmental conditions and stresses, such as antibiotic stress. Altered stoichiometry and composition of ribosomal proteins as well as association of additional protein factors are mechanisms for shaping the protein expression profile or hibernating ribosomes. Here, we present a method for the isolation of ribosomes to analyze antibiotic-induced changes in the composition of ribosomes in Bacillus subtilis or other bacteria. Ribosomes and associated proteins are isolated by ultracentrifugation and proteins are identified and quantified using label-free mass spectrometry.
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Affiliation(s)
- Sina Schäkermann
- Applied Microbiology, Ruhr-Universität Bochum, Universitätsstr. 150, Bochum, 44801, Germany.
| | - Pascal Prochnow
- Applied Microbiology, Ruhr-Universität Bochum, Universitätsstr. 150, Bochum, 44801, Germany
| | - Julia E Bandow
- Applied Microbiology, Ruhr-Universität Bochum, Universitätsstr. 150, Bochum, 44801, Germany
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32
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Heidrich CG, Mitova S, Schedlbauer A, Connell SR, Fucini P, Steenbergen JN, Berens C. The Novel Aminomethylcycline Omadacycline Has High Specificity for the Primary Tetracycline-Binding Site on the Bacterial Ribosome. Antibiotics (Basel) 2016; 5:antibiotics5040032. [PMID: 27669321 PMCID: PMC5187513 DOI: 10.3390/antibiotics5040032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 01/02/2023] Open
Abstract
Omadacycline is an aminomethylcycline antibiotic with potent activity against many Gram-positive and Gram-negative pathogens, including strains carrying the major efflux and ribosome protection resistance determinants. This makes it a promising candidate for therapy of severe infectious diseases. Omadacycline inhibits bacterial protein biosynthesis and competes with tetracycline for binding to the ribosome. Its interactions with the 70S ribosome were, therefore, analyzed in great detail and compared with tigecycline and tetracycline. All three antibiotics are inhibited by mutations in the 16S rRNA that mediate resistance to tetracycline in Brachyspira hyodysenteriae, Helicobacter pylori, Mycoplasma hominis, and Propionibacterium acnes. Chemical probing with dimethyl sulfate and Fenton cleavage with iron(II)-complexes of the tetracycline derivatives revealed that each antibiotic interacts in an idiosyncratic manner with the ribosome. X-ray crystallography had previously revealed one primary binding site for tetracycline on the ribosome and up to five secondary sites. All tetracyclines analyzed here interact with the primary site and tetracycline also with two secondary sites. In addition, each derivative displays a unique set of non-specific interactions with the 16S rRNA.
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Affiliation(s)
- Corina G Heidrich
- Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany.
| | - Sanya Mitova
- Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany.
| | | | - Sean R Connell
- Structural Biology Unit, CIC bioGUNE, 48160 Derio, Bizkaia, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
| | - Paola Fucini
- Structural Biology Unit, CIC bioGUNE, 48160 Derio, Bizkaia, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
| | | | - Christian Berens
- Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany.
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, 07743 Jena, Germany.
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33
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Han BG, Watson Z, Kang H, Pulk A, Downing KH, Cate J, Glaeser RM. Long shelf-life streptavidin support-films suitable for electron microscopy of biological macromolecules. J Struct Biol 2016; 195:238-244. [PMID: 27320699 DOI: 10.1016/j.jsb.2016.06.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/12/2016] [Accepted: 06/14/2016] [Indexed: 02/01/2023]
Abstract
We describe a rapid and convenient method of growing streptavidin (SA) monolayer crystals directly on holey-carbon EM grids. As expected, these SA monolayer crystals retain their biotin-binding function and crystalline order through a cycle of embedding in trehalose and, later, its removal. This fact allows one to prepare, and store for later use, EM grids on which SA monolayer crystals serve as an affinity substrate for preparing specimens of biological macromolecules. In addition, we report that coating the lipid-tail side of trehalose-embedded monolayer crystals with evaporated carbon appears to improve the consistency with which well-ordered, single crystals are observed to span over entire, 2μm holes of the support films. Randomly biotinylated 70S ribosomes are used as a test specimen to show that these support films can be used to obtain a high-resolution cryo-EM structure.
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Affiliation(s)
- Bong-Gyoon Han
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
| | - Zoe Watson
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Hannah Kang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
| | - Arto Pulk
- Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Kenneth H Downing
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
| | - Jamie Cate
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Robert M Glaeser
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
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34
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Shebl B, Menke DE, Pennella M, Poudyal RR, Burke DH, Cornish PV. Preparation of ribosomes for smFRET studies: A simplified approach. Arch Biochem Biophys 2016; 603:118-30. [PMID: 27208427 DOI: 10.1016/j.abb.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 11/18/2022]
Abstract
During the past decade, single-molecule studies of the ribosome have significantly advanced our understanding of protein synthesis. The broadest application of these methods has been towards the investigation of ribosome conformational dynamics using single-molecule Förster resonance energy transfer (smFRET). The recent advances in fluorescently labeled ribosomes and translation components have resulted in success of smFRET experiments. Various methods have been employed to target fluorescent dyes to specific locations within the ribosome. Primarily, these methods have involved additional steps including subunit dissociation and/or full reconstitution, which could result in ribosomes of reduced activity and translation efficiency. In addition, substantial time and effort are required to produce limited quantities of material. To enable rapid and large-scale production of highly active, fluorescently labeled ribosomes, we have developed a procedure that combines partial reconstitution with His-tag purification. This allows for a homogeneous single-step purification of mutant ribosomes and subsequent integration of labeled proteins. Ribosomes produced with this method are shown to be as active as ribosomes purified using classical methods. While we have focused on two labeling sites in this report, the method is generalizable and can in principle be extended to any non-essential ribosomal protein.
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Affiliation(s)
- Bassem Shebl
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Drew E Menke
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Min Pennella
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Raghav R Poudyal
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Peter V Cornish
- Department of Biochemistry, University of Missouri, Columbia, MO, USA.
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35
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Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions. Nat Commun 2015. [PMID: 26224058 PMCID: PMC4522699 DOI: 10.1038/ncomms8896] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin—paromomycin, ribostamycin and neamine—each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6′-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6′-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin–ribosome complex, we observe specific contacts between the apical tip of H69 and the 6′-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation. Ratchet-like rotation of the small ribosomal subunit relative to the large is essential to the translation mechanism. Here, the authors show that chemically related aminoglycoside antibiotics have distinct impacts on the nature and rate of the subunit rotation process within the intact ribosome.
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36
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Polikanov YS, Starosta AL, Juette MF, Altman RB, Terry DS, Lu W, Burnett BJ, Dinos G, Reynolds KA, Blanchard SC, Steitz TA, Wilson DN. Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A. Mol Cell 2015; 58:832-44. [PMID: 26028538 DOI: 10.1016/j.molcel.2015.04.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/23/2015] [Accepted: 04/07/2015] [Indexed: 01/12/2023]
Abstract
The increase in multi-drug-resistant bacteria is limiting the effectiveness of currently approved antibiotics, leading to a renewed interest in antibiotics with distinct chemical scaffolds. We have solved the structures of the Thermus thermophilus 70S ribosome with A-, P-, and E-site tRNAs bound and in complex with either the aminocyclitol-containing antibiotic hygromycin A (HygA) or the nucleoside antibiotic A201A. Both antibiotics bind at the peptidyl transferase center and sterically occlude the CCA-end of the A-tRNA from entering the A site of the peptidyl transferase center. Single-molecule Förster resonance energy transfer (smFRET) experiments reveal that HygA and A201A specifically interfere with full accommodation of the A-tRNA, leading to the presence of tRNA accommodation intermediates and thereby inhibiting peptide bond formation. Thus, our results provide not only insight into the mechanism of action of HygA and A201A, but also into the fundamental process of tRNA accommodation during protein synthesis.
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Affiliation(s)
- Yury S Polikanov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Agata L Starosta
- Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Manuel F Juette
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Roger B Altman
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Wanli Lu
- Department of Chemistry, Portland State University, Portland, OR 97207, USA
| | - Benjamin J Burnett
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - George Dinos
- Department of Biochemistry, School of Medicine, University of Patras, 26500 Patras, Greece
| | - Kevin A Reynolds
- Department of Chemistry, Portland State University, Portland, OR 97207, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA; Tri-Institutional Training Program in Chemical Biology, New York, NY 10065, USA.
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Daniel N Wilson
- Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany; Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany.
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37
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Krokidis M, Bougas A, Stavropoulou M, Kalpaxis D, Dinos GP. The slow dissociation rate of K-1602 contributes to the enhanced inhibitory activity of this novel alkyl-aryl-bearing fluoroketolide. J Enzyme Inhib Med Chem 2015; 31:276-82. [PMID: 25807301 DOI: 10.3109/14756366.2015.1018246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ketolides belong to the latest generation of macrolides and are not only effective against macrolide susceptible bacterial strains but also against some macrolide resistant strains. Here we present data providing insights into the mechanism of action of K-1602, a novel alkyl-aryl-bearing fluoroketolide. According to our data, the K-1602 interacts with the ribosome as a one-step slow binding inhibitor, displaying an association rate constant equal to 0.28 × 10(4) M(-1) s(-1) and a dissociation rate constant equal to 0.0025 min(-1). Both constants contribute to produce an overall inhibition constant Ki equal to 1.49 × 10(-8) M, which correlates very well with the superior activity of this compound when compared with many other ketolides or fluoroketolides.
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Affiliation(s)
- Marios Krokidis
- a Department of Pharmacology , Medical School, University of Athens , Athens , Greece
| | - Anthony Bougas
- b Laboratory of Biochemistry , School of Medicine, University of Patras , Patras , Greece , and
| | - Maria Stavropoulou
- c Department of Chemistry , Technical University of Munich , Munich , Germany
| | - Dimitrios Kalpaxis
- b Laboratory of Biochemistry , School of Medicine, University of Patras , Patras , Greece , and
| | - George P Dinos
- b Laboratory of Biochemistry , School of Medicine, University of Patras , Patras , Greece , and
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Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome. Proc Natl Acad Sci U S A 2014; 111:16274-9. [PMID: 25368144 DOI: 10.1073/pnas.1414401111] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Negamycin is a natural product with broad-spectrum antibacterial activity and efficacy in animal models of infection. Although its precise mechanism of action has yet to be delineated, negamycin inhibits cellular protein synthesis and causes cell death. Here, we show that single point mutations within 16S rRNA that confer resistance to negamycin are in close proximity of the tetracycline binding site within helix 34 of the small subunit head domain. As expected from its direct interaction with this region of the ribosome, negamycin was shown to displace tetracycline. However, in contrast to tetracycline-class antibiotics, which serve to prevent cognate tRNA from entering the translating ribosome, single-molecule fluorescence resonance energy transfer investigations revealed that negamycin specifically stabilizes near-cognate ternary complexes within the A site during the normally transient initial selection process to promote miscoding. The crystal structure of the 70S ribosome in complex with negamycin, determined at 3.1 Å resolution, sheds light on this finding by showing that negamycin occupies a site that partially overlaps that of tetracycline-class antibiotics. Collectively, these data suggest that the small subunit head domain contributes to the decoding mechanism and that small-molecule binding to this domain may either prevent or promote tRNA entry by altering the initial selection mechanism after codon recognition and before GTPase activation.
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Lu Z, Barnard D, Shaikh TR, Meng X, Mannella CA, Yassin A, Agrawal R, Wagenknecht T, Lu TM. Gas-Assisted Annular Microsprayer for Sample Preparation for Time-Resolved Cryo-Electron Microscopy. JOURNAL OF MICROMECHANICS AND MICROENGINEERING : STRUCTURES, DEVICES, AND SYSTEMS 2014; 24:115001. [PMID: 25530679 PMCID: PMC4266110 DOI: 10.1088/0960-1317/24/11/115001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Time-resolved cryo electron microscopy (TRCEM) has emerged as a powerful technique for transient structural characterization of isolated biomacromolecular complexes in their native state within the time scale of seconds to milliseconds. For TRCEM sample preparation, microfluidic device [9] has been demonstrated to be a promising approach to facilitate TRCEM biological sample preparation. It is capable of achieving rapidly aqueous sample mixing, controlled reaction incubation, and sample deposition on electron microscopy (EM) grids for rapid freezing. One of the critical challenges is to transfer samples to cryo-EM grids from the microfluidic device. By using microspraying method, the generated droplet size needs to be controlled to facilitate the thin ice film formation on the grid surface for efficient data collection, while not too thin to be dried out before freezing, i.e., optimized mean droplet size needs to be achieved. In this work, we developed a novel monolithic three dimensional (3D) annular gas-assisted microfluidic sprayer using 3D MEMS (MicroElectroMechanical System) fabrication techniques. The microsprayer demonstrated dense and consistent microsprays with average droplet size between 6-9 μm, which fulfilled the above droplet size requirement for TRCEM sample preparation. With droplet density of around 12-18 per grid window (window size is 58×58 μm), and the data collectible thin ice region of >50% total wetted area, we collected ~800-1000 high quality CCD micrographs in a 6-8 hour period of continuous effort. This level of output is comparable to what were routinely achieved using cryo-grids prepared by conventional blotting and manual data collection. In this case, weeks of data collection process with the previous device [9] has shortened to a day or two. And hundreds of microliter of valuable sample consumption can be reduced to only a small fraction.
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Affiliation(s)
- Zonghuan Lu
- Center for Integrated Electronics, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - David Barnard
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Tanvir R. Shaikh
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
- CEITEC, Masaryk University, Brno, Czech Republic
| | - Xing Meng
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Carmen A. Mannella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Aymen Yassin
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
- Department of Microbiology and Immunology, Cairo University, Cairo, Egypt
| | - Rajendra Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Terence Wagenknecht
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Toh-Ming Lu
- Center for Integrated Electronics, Rensselaer Polytechnic Institute, Troy, NY 12180
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Augé RM, Toler HD, Saxton AM. Arbuscular mycorrhizal symbiosis and osmotic adjustment in response to NaCl stress: a meta-analysis. FRONTIERS IN PLANT SCIENCE 2014; 5:562. [PMID: 25368626 PMCID: PMC4201091 DOI: 10.3389/fpls.2014.00562] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/30/2014] [Indexed: 05/03/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis can enhance plant resistance to NaCl stress in several ways. Two fundamental roles involve osmotic and ionic adjustment. By stimulating accumulation of solutes, the symbiosis can help plants sustain optimal water balance and diminish Na(+) toxicity. The size of the AM effect on osmolytes has varied widely and is unpredictable. We conducted a meta-analysis to determine the size of the AM effect on 22 plant solute characteristics after exposure to NaCl and to examine how experimental conditions have influenced the AM effect. Viewed across studies, AM symbioses have had marked effects on plant K(+), increasing root and shoot K(+) concentrations by an average of 47 and 42%, respectively, and root and shoot K(+)/Na(+) ratios by 47 and 58%, respectively. Among organic solutes, soluble carbohydrates have been most impacted, with AM-induced increases of 28 and 19% in shoots and roots. The symbiosis has had no consistent effect on several characteristics, including root glycine betaine concentration, root or shoot Cl(-) concentrations, leaf Ψπ, or shoot proline or polyamine concentrations. The AM effect has been very small for shoot Ca(++) concentration and root concentrations of Na(+), Mg(++) and proline. Interpretations about AM-conferred benefits regarding these compounds may be best gauged within the context of the individual studies. Shoot and root K(+)/Na(+) ratios and root proline concentration showed significant between-study heterogeneity, and we examined nine moderator variables to explore what might explain the differences in mycorrhizal effects on these parameters. Moderators with significant impacts included AM taxa, host type, presence or absence of AM growth promotion, stress severity, and whether NaCl constituted part or all of the experimental saline stress treatment. Meta-regression of shoot K(+)/Na(+) ratio showed a positive response to root colonization, and root K(+)/Na(+) ratio a negative response to time of exposure to NaCl.
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Affiliation(s)
- Robert M. Augé
- Department of Plant Sciences, University of TennesseeKnoxville, TN, USA
| | - Heather D. Toler
- Department of Plant Sciences, University of TennesseeKnoxville, TN, USA
| | - Arnold M. Saxton
- Department of Animal Sciences, University of TennesseeKnoxville, TN, USA
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41
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Initial bridges between two ribosomal subunits are formed within 9.4 milliseconds, as studied by time-resolved cryo-EM. Proc Natl Acad Sci U S A 2014; 111:9822-7. [PMID: 24958863 DOI: 10.1073/pnas.1406744111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Association of the two ribosomal subunits during the process of translation initiation is a crucial step of protein synthesis. The two subunits (30S and 50S) of the bacterial 70S ribosome are held together by 12 dynamic bridges involving RNA-RNA, RNA-protein, and protein-protein interactions. The process of bridge formation, such as whether all these bridges are formed simultaneously or in a sequential order, is poorly understood. To understand such processes, we have developed and implemented a class of microfluidic devices that mix two components to completion within 0.4 ms and spray the mixture in the form of microdroplets onto an electron microscopy grid, yielding a minimum reaction time of 9.4 ms before cryofixation. Using these devices, we have obtained cryo-EM data corresponding to reaction times of 9.4 and 43 ms and have determined 3D structures of ribosomal subunit association intermediates. Molecular analyses of the cryo-EM maps reveal that eight intersubunit bridges (bridges B1a, B1b, B2a, B2b, B3, B7a, B7b, and B8) form within 9.4 ms, whereas the remaining four bridges (bridges B2c, B4, B5, and B6) take longer than 43 ms to form, suggesting that bridges are formed in a stepwise fashion. Our approach can be used to characterize sequences of various dynamic functional events on complex macromolecular assemblies such as ribosomes.
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42
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McGinnis JL, Weeks KM. Ribosome RNA assembly intermediates visualized in living cells. Biochemistry 2014; 53:3237-47. [PMID: 24818530 DOI: 10.1021/bi500198b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In cells, RNAs likely adopt numerous intermediate conformations prior to formation of functional RNA-protein complexes. We used single-nucleotide resolution selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to probe the structure of Escherichia coli 16S rRNA in healthy growing bacteria. SHAPE-directed modeling indicated that the predominant steady-state RNA conformational ensemble in dividing cells had a base-paired structure different from that expected on the basis of comparative sequence analysis and high-resolution studies of the 30S ribosomal subunit. We identified the major cause of these differences by stopping ongoing in-cell transcription (in essence, an in-cell RNA structure pulse-chase experiment) which caused the RNA to chase into a structure that closely resembled the expected one. Most helices that formed alternate RNA conformations under growth conditions interact directly with tertiary-binding ribosomal proteins and form a C-shape that surrounds the mRNA channel and decoding site. These in-cell experiments lead to a model in which ribosome assembly factors function as molecular struts to preorganize this intermediate and emphasize that the final stages of ribonucleoprotein assembly involve extensive protein-facilitated RNA conformational changes.
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Affiliation(s)
- Jennifer L McGinnis
- Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States
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43
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Yang Z, Guo Q, Goto S, Chen Y, Li N, Yan K, Zhang Y, Muto A, Deng H, Himeno H, Lei J, Gao N. Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence. Protein Cell 2014; 5:394-407. [PMID: 24671761 PMCID: PMC3996153 DOI: 10.1007/s13238-014-0044-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 02/26/2014] [Indexed: 12/20/2022] Open
Abstract
The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA precursors, as well as modifications of selected bases. In the cell, a large number of factors are required to ensure the efficiency and fidelity of subunit production. Here we characterize the immature 30S subunits accumulated in a factor-null Escherichia coli strain (∆rsgA∆rbfA). The immature 30S subunits isolated with varying salt concentrations in the buffer system show interesting differences on both protein composition and structure. Specifically, intermediates derived under the two contrasting salt conditions (high and low) likely reflect two distinctive assembly stages, the relatively early and late stages of the 3' domain assembly, respectively. Detailed structural analysis demonstrates a mechanistic coupling between the maturation of the 5' end of the 17S rRNA and the assembly of the 30S head domain, and attributes a unique role of S5 in coordinating these two events. Furthermore, our structural results likely reveal the location of the unprocessed terminal sequences of the 17S rRNA, and suggest that the maturation events of the 17S rRNA could be employed as quality control mechanisms on subunit production and protein translation.
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Affiliation(s)
- Zhixiu Yang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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Ahanger MA, Hashem A, Abd-Allah EF, Ahmad P. Arbuscular Mycorrhiza in Crop Improvement under Environmental Stress. EMERGING TECHNOLOGIES AND MANAGEMENT OF CROP STRESS TOLERANCE 2014:69-95. [DOI: 10.1016/b978-0-12-800875-1.00003-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Hameed A, Dilfuza E, Abd-Allah EF, Hashem A, Kumar A, Ahmad P. Salinity Stress and Arbuscular Mycorrhizal Symbiosis in Plants. USE OF MICROBES FOR THE ALLEVIATION OF SOIL STRESSES, VOLUME 1 2014:139-159. [DOI: 10.1007/978-1-4614-9466-9_7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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46
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Golovina AY, Dzama MM, Petriukov KS, Zatsepin TS, Sergiev PV, Bogdanov AA, Dontsova OA. Method for site-specific detection of m6A nucleoside presence in RNA based on high-resolution melting (HRM) analysis. Nucleic Acids Res 2013; 42:e27. [PMID: 24265225 PMCID: PMC3936739 DOI: 10.1093/nar/gkt1160] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemical landscape of natural RNA species is decorated with the large number of modified nucleosides. Some of those could easily be detected by reverse transcription, while others permit only high-performance liquid chromatography or mass-spectrometry detection. Presence of m6A nucleoside at a particular position of long RNA molecule is challenging to observe. Here we report an easy and high-throughput method for detection of m6A nucleosides in RNA based on high-resolution melting analysis. The method relies on the previous knowledge of the modified nucleoside position at a particular place of RNA and allows rapid screening for conditions or genes necessary for formation of that modification.
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Affiliation(s)
- Anna Y Golovina
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia, Department of Bioinformatics and Bioengineering, Lomonosov Moscow State University, Moscow 119992, Russia and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
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47
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Insights into the mode of action of novel fluoroketolides, potent inhibitors of bacterial protein synthesis. Antimicrob Agents Chemother 2013; 58:472-80. [PMID: 24189263 DOI: 10.1128/aac.01994-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ketolides, the third generation of expanded-spectrum macrolides, have in the last years become a successful weapon in the endless war against macrolide-resistant pathogens. Ketolides are semisynthetic derivatives of the naturally produced macrolide erythromycin, displaying not only improved activity against some erythromycin-resistant strains but also increased bactericidal activity as well as inhibitory effects at lower drug concentrations. In this study, we present a series of novel ketolides carrying alkyl-aryl side chains at the C-6 position of the lactone ring and, additionally, one or two fluorine atoms attached either directly to the lactone ring at the C-2 position or indirectly via the C-13 position. According to our genetic and biochemical studies, these novel ketolides occupy the known macrolide binding site at the entrance of the ribosomal tunnel and exhibit lower MIC values against wild-type or mutant strains than erythromycin. In most cases, the ketolides display activities comparable to or better than the clinically used ketolide telithromycin. Chemical protection experiments using Escherichia coli ribosomes bearing U2609C or U754A mutations in 23S rRNA suggest that the alkyl-aryl side chain establishes an interaction with the U2609-A752 base pair, analogous to that observed with telithromycin but unlike the interactions formed by cethromycin. These findings reemphasize the versatility of the alkyl-aryl side chains with respect to species specificity, which will be important for future design of improved antimicrobial agents.
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Deng X, Zhou S, Hu W, Feng J, Zhang F, Chen L, Huang C, Luo Q, He Y, Yang G, He G. Ectopic expression of wheat TaCIPK14, encoding a calcineurin B-like protein-interacting protein kinase, confers salinity and cold tolerance in tobacco. PHYSIOLOGIA PLANTARUM 2013; 149:367-77. [PMID: 23534344 DOI: 10.1111/ppl.12046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 02/22/2013] [Accepted: 02/22/2013] [Indexed: 05/08/2023]
Abstract
Calcineurin B-like protein-interacting protein kinases (CIPKs) are components of Ca(2+) signaling in responses to abiotic stresses. In this work, the full-length cDNA of a novel CIPK gene (TaCIPK14) was isolated from wheat and was found to have significant sequence similarity to OsCIPK14/15. Subcellular localization assay revealed the presence of TaCIPK14 throughout the cell. qRT-PCR analysis showed that TaCIPK14 was upregulated under cold conditions or when treated with salt, PEG or exogenous stresses related signaling molecules including ABA, ethylene and H2 O2 . Transgenic tobaccos overexpressing TaCIPK14 exhibited higher contents of chlorophyll and sugar, higher catalase activity, while decreased amounts of H2 O2 and malondialdehyde, and lesser ion leakage under cold and salt stresses. In addition, overexpression also increased seed germination rate, root elongation and decreased Na(+) content in the transgenic lines under salt stress. Higher expression of stress-related genes was observed in lines overexpressing TaCIPK14 compared to controls under stress conditions. In summary, these results suggested that TaCIPK14 is an abiotic stress-responsive gene in plants.
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Affiliation(s)
- Xiaomin Deng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, 430074, China
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On the use of the antibiotic chloramphenicol to target polypeptide chain mimics to the ribosomal exit tunnel. Biochimie 2013; 95:1765-72. [PMID: 23770443 DOI: 10.1016/j.biochi.2013.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/04/2013] [Indexed: 11/23/2022]
Abstract
The ribosomal exit tunnel had recently become the centre of many functional and structural studies. Accumulated evidence indicates that the tunnel is not simply a passive conduit for the nascent chain, but a rather functionally important compartment where nascent peptide sequences can interact with the ribosome to signal translation to slow down or even stop. To explore further this interaction, we have synthesized short peptides attached to the amino group of a chloramphenicol (CAM) base, such that when bound to the ribosome these compounds mimic a nascent peptidyl-tRNA chain bound to the A-site of the peptidyltransferase center (PTC). Here we show that these CAM-peptides interact with the PTC of the ribosome while their effectiveness can be modulated by the sequence of the peptide, suggesting a direct interaction of the peptide with the ribosomal tunnel. Indeed, chemical footprinting in the presence of CAM-P2, one of the tested CAM-peptides, reveals protection of 23S rRNA nucleotides located deep within the tunnel, indicating a potential interaction with specific components of the ribosomal tunnel. Collectively, our findings suggest that the CAM-based peptide derivatives will be useful tools for targeting polypeptide chain mimics to the ribosomal tunnel, allowing their conformation and interaction with the ribosomal tunnel to be explored using further biochemical and structural methods.
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50
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Kotani T, Akabane S, Takeyasu K, Ueda T, Takeuchi N. Human G-proteins, ObgH1 and Mtg1, associate with the large mitochondrial ribosome subunit and are involved in translation and assembly of respiratory complexes. Nucleic Acids Res 2013; 41:3713-22. [PMID: 23396448 PMCID: PMC3616715 DOI: 10.1093/nar/gkt079] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The bacterial homologues of ObgH1 and Mtg1, ObgE and RbgA, respectively, have been suggested to be involved in the assembly of large ribosomal subunits. We sought to elucidate the functions of ObgH1 and Mtg1 in ribosome biogenesis in human mitochondria. ObgH1 and Mtg1 are localized in mitochondria in association with the inner membrane, and are exposed on the matrix side. Mtg1 and ObgH1 specifically associate with the large subunit of the mitochondrial ribosome in GTP-dependent manner. The large ribosomal subunit stimulated the GTPase activity of Mtg1, whereas only the intrinsic GTPase activity was detectable with ObgH1. The knockdown of Mtg1 decreased the overall mitochondrial translation activity, and caused defects in the formation of respiratory complexes. On the other hand, the depletion of ObgH1 led to the specific activation of the translation of subunits of Complex V, and disrupted its proper formation. Our results suggested that Mtg1 and ObgH1 function with the large subunit of the mitochondrial ribosome, and are also involved in both the translation and assembly of respiratory complexes. The fine coordination of ribosome assembly, translation and respiratory complex formation in mammalian mitochondria is affirmed.
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Affiliation(s)
- Tetsuya Kotani
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
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