1
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Rasmussen RA, Wang S, Camarillo JM, Sosnowski V, Cho BK, Goo Y, Lucks J, O’Halloran T. Zur and zinc increase expression of E. coli ribosomal protein L31 through RNA-mediated repression of the repressor L31p. Nucleic Acids Res 2022; 50:12739-12753. [PMID: 36533433 PMCID: PMC9825181 DOI: 10.1093/nar/gkac1086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria can adapt in response to numerous stress conditions. One such stress condition is zinc depletion. The zinc-sensing transcription factor Zur regulates the way numerous bacterial species respond to severe changes in zinc availability. Under zinc sufficient conditions, Zn-loaded Zur (Zn2-Zur) is well-known to repress transcription of genes encoding zinc uptake transporters and paralogues of a few ribosomal proteins. Here, we report the discovery and mechanistic basis for the ability of Zur to up-regulate expression of the ribosomal protein L31 in response to zinc in E. coli. Through genetic mutations and reporter gene assays, we find that Zur achieves the up-regulation of L31 through a double repression cascade by which Zur first represses the transcription of L31p, a zinc-lacking paralogue of L31, which in turn represses the translation of L31. Mutational analyses show that translational repression by L31p requires an RNA hairpin structure within the l31 mRNA and involves the N-terminus of the L31p protein. This work uncovers a new genetic network that allows bacteria to respond to host-induced nutrient limiting conditions through a sophisticated ribosomal protein switching mechanism.
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Affiliation(s)
- Rebecca A Rasmussen
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
| | - Suning Wang
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Jeannie M Camarillo
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
| | - Victoria Sosnowski
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
| | - Byoung-Kyu Cho
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
- Mass Spectrometry Technology Access Center, Washington University in St Louis, School of Medicine, USA
| | - Young Ah Goo
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
- Mass Spectrometry Technology Access Center, Washington University in St Louis, School of Medicine, USA
| | - Julius B Lucks
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Thomas V O’Halloran
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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2
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Kolano L, Knappe D, Berg A, Berg T, Hoffmann R. Effect of amino acid substitutions on 70S ribosomal binding, cellular uptake, and antimicrobial activity of oncocin Onc112. Chembiochem 2021; 23:e202100609. [PMID: 34902208 PMCID: PMC9306569 DOI: 10.1002/cbic.202100609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/06/2022]
Abstract
Proline‐rich antimicrobial peptides (PrAMPs) are promising candidates for the treatment of infections caused by high‐priority human pathogens. Their mode of action consists of (I) passive diffusion across the outer membrane, (II) active transport through the inner membrane, and (III) inhibition of protein biosynthesis by blocking the exit tunnel of the 70S ribosome. We tested whether in vitro data on ribosomal binding and bacterial uptake could predict the antibacterial activity of PrAMPs against Gram‐negative and Gram‐positive bacteria. Ribosomal binding and bacterial uptake rates were measured for 47 derivatives of PrAMP Onc112 and compared to the minimal inhibitory concentrations (MIC) of each peptide. Ribosomal binding was evaluated for ribosome extracts from four Gram‐negative bacteria. Bacterial uptake was assessed by quantifying each peptide in the supernatants of bacterial cultures. Oncocin analogues with a higher net positive charge appeared to be more active, although their ribosome binding and uptake rates were not necessarily better than for Onc112. The data suggest a complex mode of action influenced by further factors improving or reducing the antibacterial activity, including diffusion through membranes, transport mechanism, secondary targets, off‐target binding, intracellular distribution, and membrane effects. Relying only on in vitro binding and uptake data may not be sufficient for the rational development of more active analogues.
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Affiliation(s)
- Lisa Kolano
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Daniel Knappe
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Angela Berg
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Thorsten Berg
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Ralf Hoffmann
- Institut für Bioanalytische Chemie, Biotechnologisch-Biomedizinisches Zentrum, Deutscher Platz 5, 04103, Leipzig, GERMANY
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3
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Henneberg F, Chari A. Chromatography-Free Purification Strategies for Large Biological Macromolecular Complexes Involving Fractionated PEG Precipitation and Density Gradients. Life (Basel) 2021; 11:1289. [PMID: 34947821 PMCID: PMC8707722 DOI: 10.3390/life11121289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/10/2021] [Accepted: 11/22/2021] [Indexed: 12/25/2022] Open
Abstract
A complex interplay between several biological macromolecules maintains cellular homeostasis. Generally, the demanding chemical reactions which sustain life are not performed by individual macromolecules, but rather by several proteins that together form a macromolecular complex. Understanding the functional interactions amongst subunits of these macromolecular machines is fundamental to elucidate mechanisms by which they maintain homeostasis. As the faithful function of macromolecular complexes is essential for cell survival, their mis-function leads to the development of human diseases. Furthermore, detailed mechanistic interrogation of the function of macromolecular machines can be exploited to develop and optimize biotechnological processes. The purification of intact macromolecular complexes is an essential prerequisite for this; however, chromatographic purification schemes can induce the dissociation of subunits or the disintegration of the whole complex. Here, we discuss the development and application of chromatography-free purification strategies based on fractionated PEG precipitation and orthogonal density gradient centrifugation that overcomes existing limitations of established chromatographic purification protocols. The presented case studies illustrate the capabilities of these procedures for the purification of macromolecular complexes.
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Affiliation(s)
- Fabian Henneberg
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany;
| | - Ashwin Chari
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany;
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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4
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Levy M, Falkovich R, Vonshak O, Bracha D, Tayar AM, Shimizu Y, Daube SS, Bar-Ziv RH. Boundary-Free Ribosome Compartmentalization by Gene Expression on a Surface. ACS Synth Biol 2021; 10:609-619. [PMID: 33595282 PMCID: PMC8023806 DOI: 10.1021/acssynbio.0c00613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 11/30/2022]
Abstract
The design of artificial cell models based on minimal surface-bound transcription-translation reactions aims to mimic the compartmentalization facilitated by organelles and inner interfaces in living cells. Dense DNA brushes as localized sources of RNA and proteins serve as synthetic operons that have recently proven useful for the autonomous synthesis and assembly of cellular machines. Here, we studied ribosome compartmentalization in a minimal gene-expression reaction on a surface in contact with a macroscopic reservoir. We first observed the accumulation and colocalization of RNA polymerases, ribosomes, nascent RNAs and proteins, in dense DNA brushes using evanescent field fluorescence, showing transcription-translation coupling in the brush. Fluorescence recovery after photobleaching showed that ribosomes engaged in translation in the brush had a 4-fold slower diffusion constant. In addition, ribosomes in the brush had over a 10-fold higher local concentration relative to free ribosomes, creating a boundary-free functional ribosome-rich compartment. To decouple translation from transcription, we immobilized dense phases of ribosomes next to DNA brushes. We demonstrated that immobilized ribosomes were capable of protein synthesis, forming 2D subcompartments of active ribosome patterns induced and regulated by DNA brush layout of coding and inhibitory genes. Localizing additional molecular components on the surface will further compartmentalize gene-expression reactions.
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Affiliation(s)
- Michael Levy
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Reuven Falkovich
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Ohad Vonshak
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Dan Bracha
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra M. Tayar
- Department
of Physics, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Yoshihiro Shimizu
- Laboratory
for Cell-Free Protein Synthesis, RIKEN Center
for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Shirley S. Daube
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Roy H. Bar-Ziv
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
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5
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Sorroche F, Morales V, Mouffok S, Pichereaux C, Garnerone AM, Zou L, Soni B, Carpéné MA, Gargaros A, Maillet F, Burlet-Schiltz O, Poinsot V, Polard P, Gough C, Batut J. The ex planta signal activity of a Medicago ribosomal uL2 protein suggests a moonlighting role in controlling secondary rhizobial infection. PLoS One 2020; 15:e0235446. [PMID: 33002000 PMCID: PMC7529298 DOI: 10.1371/journal.pone.0235446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/15/2020] [Indexed: 11/19/2022] Open
Abstract
We recently described a regulatory loop, which we termed autoregulation of infection (AOI), by which Sinorhizobium meliloti, a Medicago endosymbiont, downregulates the root susceptibility to secondary infection events via ethylene. AOI is initially triggered by so-far unidentified Medicago nodule signals named signal 1 and signal 1' whose transduction in bacteroids requires the S. meliloti outer-membrane-associated NsrA receptor protein and the cognate inner-membrane-associated adenylate cyclases, CyaK and CyaD1/D2, respectively. Here, we report on advances in signal 1 identification. Signal 1 activity is widespread as we robustly detected it in Medicago nodule extracts as well as in yeast and bacteria cell extracts. Biochemical analyses indicated a peptidic nature for signal 1 and, together with proteomic analyses, a universally conserved Medicago ribosomal protein of the uL2 family was identified as a candidate signal 1. Specifically, MtRPuL2A (MtrunA17Chr7g0247311) displays a strong signal activity that requires S. meliloti NsrA and CyaK, as endogenous signal 1. We have shown that MtRPuL2A is active in signaling only in a non-ribosomal form. A Medicago truncatula mutant in the major symbiotic transcriptional regulator MtNF-YA1 lacked most signal 1 activity, suggesting that signal 1 is under developmental control. Altogether, our results point to the MtRPuL2A ribosomal protein as the candidate for signal 1. Based on the Mtnf-ya1 mutant, we suggest a link between root infectiveness and nodule development. We discuss our findings in the context of ribosomal protein moonlighting.
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Affiliation(s)
- Fernando Sorroche
- Laboratoire des Interactions Plantes Microorganismes (LIPM), INRAE, CNRS, Castanet-Tolosan, France
| | - Violette Morales
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Saïda Mouffok
- Laboratoire des Interactions Plantes Microorganismes (LIPM), INRAE, CNRS, Castanet-Tolosan, France
| | - Carole Pichereaux
- Fédération de Recherche (FR3450), Agrobiosciences, Interactions et Biodiversité (AIB), CNRS, Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse UPS, CNRS, Toulouse, France
| | - A. Marie Garnerone
- Laboratoire des Interactions Plantes Microorganismes (LIPM), INRAE, CNRS, Castanet-Tolosan, France
| | - Lan Zou
- Laboratoire des Interactions Plantes Microorganismes (LIPM), INRAE, CNRS, Castanet-Tolosan, France
| | - Badrish Soni
- Laboratoire des Interactions Plantes Microorganismes (LIPM), INRAE, CNRS, Castanet-Tolosan, France
| | | | - Audrey Gargaros
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse UPS, CNRS, Toulouse, France
| | - Fabienne Maillet
- Laboratoire des Interactions Plantes Microorganismes (LIPM), INRAE, CNRS, Castanet-Tolosan, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse UPS, CNRS, Toulouse, France
| | - Verena Poinsot
- I2MC, Université de Toulouse UPS, INSERM, CNRS, Toulouse, France
| | - Patrice Polard
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Clare Gough
- Laboratoire des Interactions Plantes Microorganismes (LIPM), INRAE, CNRS, Castanet-Tolosan, France
| | - Jacques Batut
- Laboratoire des Interactions Plantes Microorganismes (LIPM), INRAE, CNRS, Castanet-Tolosan, France
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6
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Levy M, Falkovich R, Daube SS, Bar-Ziv RH. Autonomous synthesis and assembly of a ribosomal subunit on a chip. SCIENCE ADVANCES 2020; 6:eaaz6020. [PMID: 32494616 PMCID: PMC7159907 DOI: 10.1126/sciadv.aaz6020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/22/2020] [Indexed: 05/03/2023]
Abstract
Ribosome biogenesis is an efficient and complex assembly process that has not been reconstructed outside a living cell so far, yet is the most critical step for establishing a self-replicating artificial cell. We recreated the biogenesis of Escherichia coli's small ribosomal subunit by synthesizing and capturing all its ribosomal proteins and RNA on a chip. Surface confinement provided favorable conditions for autonomous stepwise assembly of new subunits, spatially segregated from original intact ribosomes. Our real-time fluorescence measurements revealed hierarchal assembly, cooperative interactions, unstable intermediates, and specific binding to large ribosomal subunits. Using only synthetic genes, our methodology is a crucial step toward creation of a self-replicating artificial cell and a general strategy for the mechanistic investigation of diverse multicomponent macromolecular machines.
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7
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Acquah C, Chan YW, Pan S, Yon LS, Ongkudon CM, Guo H, Danquah MK. Characterisation of aptamer-anchored poly(EDMA-co-GMA) monolith for high throughput affinity binding. Sci Rep 2019; 9:14501. [PMID: 31601836 PMCID: PMC6787036 DOI: 10.1038/s41598-019-50862-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/13/2019] [Indexed: 11/17/2022] Open
Abstract
Immobilisation of aptameric ligands on solid stationary supports for effective binding of target molecules requires understanding of the relationship between aptamer-polymer interactions and the conditions governing the mass transfer of the binding process. Herein, key process parameters affecting the molecular anchoring of a thrombin-binding aptamer (TBA) onto polymethacrylate monolith pore surface, and the binding characteristics of the resulting macroporous aptasensor were investigated. Molecular dynamics (MD) simulations of the TBA-thrombin binding indicated enhanced Guanine 4 (G4) structural stability of TBA upon interaction with thrombin in an ionic environment. Fourier-transform infrared spectroscopy and thermogravimetric analyses were used to characterise the available functional groups and thermo-molecular stability of the immobilised polymer generated with Schiff-base activation and immobilisation scheme. The initial degradation temperature of the polymethacrylate stationary support increased with each step of the Schiff-base process: poly(Ethylene glycol Dimethacrylate-co-Glycidyl methacrylate) or poly(EDMA-co-GMA) [196.0 °C (±1.8)]; poly(EDMA-co-GMA)-Ethylenediamine [235.9 °C (±6.1)]; poly(EDMA-co-GMA)-Ethylenediamine-Glutaraldehyde [255.4 °C (±2.7)]; and aptamer-modified monolith [273.7 °C (±2.5)]. These initial temperature increments reflected in the associated endothermic energies were determined with differential scanning calorimetry. The aptameric ligand density obtained after immobilisation was 480 pmol/μL. Increase in pH and ionic concentration affected the surface charge distribution and the binding characteristics of the aptamer-modified disk-monoliths, resulting in the optimum binding pH and ionic concentration of 8.0 and 5 mM Mg2+, respectively. These results are critical in understanding and setting parametric constraints indispensable to develop and enhance the performance of aptasensors.
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Affiliation(s)
- Caleb Acquah
- Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia.,School of Nutrition Science, Faculty of Health Science, University of Ottawa, K1N 6N5, Ontario, Canada
| | - Yi Wei Chan
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
| | - Sharadwata Pan
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, 85354, Germany
| | - Lau Sie Yon
- Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Clarence M Ongkudon
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
| | - Haobo Guo
- Department of Computer Science and Engineering, University of Tennessee, Chattanooga, TN, 37403, United States.,SimCenter, University of Tennessee, Chattanooga, TN, 37403, United States
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga, TN, 37403, United States.
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8
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Kranz A, Steinmann A, Degner U, Mengus-Kaya A, Matamouros S, Bott M, Polen T. Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H. BMC Genomics 2018; 19:753. [PMID: 30326828 PMCID: PMC6191907 DOI: 10.1186/s12864-018-5111-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/25/2018] [Indexed: 12/14/2022] Open
Abstract
Background Gluconobacter oxydans is a strictly aerobic Gram-negative acetic acid bacterium used industrially for oxidative biotransformations due to its exceptional type of catabolism. It incompletely oxidizes a wide variety of carbohydrates regio- and stereoselectively in the periplasm using membrane-bound dehydrogenases with accumulation of the products in the medium. As a consequence, only a small fraction of the carbon and energy source enters the cell, resulting in a low biomass yield. Additionally, central carbon metabolism is characterized by the absence of a functional glycolysis and absence of a functional tricarboxylic acid (TCA) cycle. Due to these features, G. oxydans is a highly interesting model organism. Here we analyzed global mRNA decay in G. oxydans to describe its characteristic features and to identify short-lived mRNAs representing potential bottlenecks in the metabolism for further growth improvement by metabolic engineering. Results Using DNA microarrays we estimated the mRNA half-lives in G. oxydans. Overall, the mRNA half-lives ranged mainly from 3 min to 25 min with a global mean of 5.7 min. The transcripts encoding GroES and GroEL required for proper protein folding ranked at the top among transcripts exhibiting both long half-lives and high abundance. The F-type H+-ATP synthase transcripts involved in energy metabolism ranked among the transcripts with the shortest mRNA half-lives. RNAseq analysis revealed low expression levels for genes of the incomplete TCA cycle and also the mRNA half-lives of several of those were short and below the global mean. The mRNA decay analysis also revealed an apparent instability of full-length 23S rRNA. Further analysis of the ribosome-associated rRNA revealed a 23S rRNA fragmentation pattern exhibiting new cleavage regions in 23S rRNAs which were previously not known. Conclusions The very short mRNA half-lives of the H+-ATP synthase, which is likely responsible for the ATP-proton motive force interconversion in G. oxydans under many or most conditions, is notably in contrast to mRNA decay data from other bacteria. Together with the short mRNA half-lives and low expression of some other central metabolic genes it could limit intended improvements of G. oxydans’ biomass yield by metabolic engineering. Also, further studies are needed to unravel the multistep process of the 23S rRNA fragmentation in G. oxydans. Electronic supplementary material The online version of this article (10.1186/s12864-018-5111-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Angela Kranz
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Andrea Steinmann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Ursula Degner
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Aliye Mengus-Kaya
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Susana Matamouros
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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9
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Yoshikawa H, Larance M, Harney DJ, Sundaramoorthy R, Ly T, Owen-Hughes T, Lamond AI. Efficient analysis of mammalian polysomes in cells and tissues using Ribo Mega-SEC. eLife 2018; 7:36530. [PMID: 30095066 PMCID: PMC6086667 DOI: 10.7554/elife.36530] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/28/2018] [Indexed: 12/14/2022] Open
Abstract
We describe Ribo Mega-SEC, a powerful approach for the separation and biochemical analysis of mammalian polysomes and ribosomal subunits using Size Exclusion Chromatography and uHPLC. Using extracts from either cells, or tissues, polysomes can be separated within 15 min from sample injection to fraction collection. Ribo Mega-SEC shows translating ribosomes exist predominantly in polysome complexes in human cell lines and mouse liver tissue. Changes in polysomes are easily quantified between treatments, such as the cellular response to amino acid starvation. Ribo Mega-SEC is shown to provide an efficient, convenient and highly reproducible method for studying functional translation complexes. We show that Ribo Mega-SEC is readily combined with high-throughput MS-based proteomics to characterize proteins associated with polysomes and ribosomal subunits. It also facilitates isolation of complexes for electron microscopy and structural studies.
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Affiliation(s)
- Harunori Yoshikawa
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark Larance
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Dylan J Harney
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Tony Ly
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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10
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Nygaard R, Romaniuk JAH, Rice DM, Cegelski L. Whole Ribosome NMR: Dipolar Couplings and Contributions to Whole Cells. J Phys Chem B 2017; 121:9331-9335. [PMID: 28901760 DOI: 10.1021/acs.jpcb.7b06736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solid-state NMR is a powerful tool for quantifying chemical composition and structure in complex assemblies and even whole cells. We employed N{P} REDOR NMR to obtain atomic-level distance propensities in intact 15N-labeled E. coli ribosomes. The experimental REDOR dephasing of shift-resolved lysyl amine nitrogens by phosphorus was comparable to that expected from a calculation of N-P distances involving the lysines included in the crystal structure coordinates. Among the nitrogen contributions to the REDOR spectra, the strongest dephasing emerged from the dipolar couplings to phosphorus involving nitrogen peaks ascribed primarily to rRNA, and the weakest dephasing arose from protein amide nitrogens. This approach is applicable to any macromolecular system and provides quantitative comparisons of distance proximities between shift-resolved nuclei of one type and heteronuclear dephasing spins. Enhanced molecular specificity could be achieved through the use of spectroscopic filters or specific labeling. Furthermore, ribosome 13C and 15N CPMAS spectra were compared with those of whole cells from which the ribosomes were isolated. Whole-cell signatures of ribosomes were identified and should be of value in comparing overall cellular ribosome content in whole-cell samples.
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Affiliation(s)
- Rie Nygaard
- Department of Chemistry, Stanford University , 380 Roth Way, Stanford California 94305, United States
| | - Joseph A H Romaniuk
- Department of Chemistry, Stanford University , 380 Roth Way, Stanford California 94305, United States
| | - David M Rice
- Department of Chemistry, Stanford University , 380 Roth Way, Stanford California 94305, United States
| | - Lynette Cegelski
- Department of Chemistry, Stanford University , 380 Roth Way, Stanford California 94305, United States
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11
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Identification of Mycobacterial RplJ/L10 and RpsA/S1 Proteins as Novel Targets for CD4 + T Cells. Infect Immun 2017; 85:IAI.01023-16. [PMID: 28115505 PMCID: PMC5364311 DOI: 10.1128/iai.01023-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/13/2017] [Indexed: 12/20/2022] Open
Abstract
Tuberculosis (TB) due to Mycobacterium tuberculosis remains a major global infectious disease problem, and a more efficacious vaccine is urgently needed for the control and prevention of disease caused by this organism. We previously reported that a genetically modified strain of Mycobacterium smegmatis called IKEPLUS is a promising TB vaccine candidate. Since protective immunity induced by IKEPLUS is dependent on antigen-specific CD4+ T cell memory, we hypothesized that the specificity of the CD4+ T cell response was a critical feature of this protection. Using in vitro assays of interferon gamma production (enzyme-linked immunosorbent spot [ELISPOT] assays) by splenocytes from IKEPLUS-immunized C57BL/6J mice, we identified an immunogenic peptide within the mycobacterial ribosomal large subunit protein RplJ, encoded by the Rv0651 gene. In a complementary approach, we generated major histocompatibility complex (MHC) class II-restricted T cell hybridomas from IKEPLUS-immunized mice. Screening of these T cell hybridomas against IKEPLUS and ribosomes enriched from IKEPLUS suggested that the CD4+ T cell response in IKEPLUS-immunized mice was dominated by the recognition of multiple components of the mycobacterial ribosome. Importantly, CD4+ T cells specific for mycobacterial ribosomes accumulate to significant levels in the lungs of IKEPLUS-immunized mice following aerosol challenge with virulent M. tuberculosis, consistent with a role for these T cells in protective host immunity in TB. The identification of CD4+ T cell responses to defined ribosomal protein epitopes expands the range of antigenic targets for adaptive immune responses to M. tuberculosis and may help to inform the design of more effective vaccines against tuberculosis.
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Munoz AM, Yourik P, Rajagopal V, Nanda JS, Lorsch JR, Walker SE. Active yeast ribosome preparation using monolithic anion exchange chromatography. RNA Biol 2016; 14:188-196. [PMID: 27981882 PMCID: PMC5324736 DOI: 10.1080/15476286.2016.1270004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In vitro studies of translation provide critical mechanistic details, yet purification of large amounts of highly active eukaryotic ribosomes remains a challenge for biochemists and structural biologists. Here, we present an optimized method for preparation of highly active yeast ribosomes that could easily be adapted for purification of ribosomes from other species. The use of a nitrogen mill for cell lysis coupled with chromatographic purification of the ribosomes results in 10-fold-increased yield and less variability compared with the traditional approach, which relies on sedimentation through sucrose cushions. We demonstrate that these ribosomes are equivalent to those made using the traditional method in a host of in vitro assays, and that utilization of this new method will consistently produce high yields of active yeast ribosomes.
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Affiliation(s)
- Antonio M Munoz
- a Laboratory on the Mechanism and Regulation of Protein Synthesis, The Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA
| | - Paul Yourik
- a Laboratory on the Mechanism and Regulation of Protein Synthesis, The Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA
| | | | - Jagpreet S Nanda
- a Laboratory on the Mechanism and Regulation of Protein Synthesis, The Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA
| | - Jon R Lorsch
- a Laboratory on the Mechanism and Regulation of Protein Synthesis, The Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA
| | - Sarah E Walker
- a Laboratory on the Mechanism and Regulation of Protein Synthesis, The Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA.,c Department of Biological Sciences , The State University of New York at Buffalo , Buffalo , NY , USA
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13
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Fan Y, Hoshino T, Nakamura A. Identification of a VapBC toxin-antitoxin system in a thermophilic bacterium Thermus thermophilus HB27. Extremophiles 2016; 21:153-161. [PMID: 27853887 DOI: 10.1007/s00792-016-0891-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/07/2016] [Indexed: 11/30/2022]
Abstract
There are 12 putative toxin-antitoxin (TA) loci in the Thermus thermophilus HB27 genome, including four VapBC and three HicBA families. Expression of these seven putative toxin genes in Escherichia coli demonstrated that one putative VapC toxin TTC0125 and two putative HicA toxins, TTC1395 and TTC1705, inhibited cell growth, and co-expression with cognate antitoxin genes rescued growth, indicating that these genes function as TA loci. In vitro analysis with the purified TTC0125 and total RNA/mRNA from E. coli and T. thermophilus showed that TTC0125 has RNase activity to rRNA and mRNA; this activity was inhibited by the addition of the purified TTC0126. Translation inhibition assays showed that TTC0125 inhibited protein synthesis by degrading mRNA but not by inactivating ribosomes. Amino acid substitutions of 14 predicted catalytic and conserved residues in VapC toxins to Ala or Asp in TTC0125 indicated that nine residues are important for its in vivo toxin activity and in vitro RNase activity. These data demonstrate that TTC0125-TTC0126 functions as a VapBC TA module and causes growth inhibition by degrading free RNA. This is the first study to identify the function of TA systems in T. thermophilus.
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Affiliation(s)
- Yuqi Fan
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Takayuki Hoshino
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Akira Nakamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
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14
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Gao C, Sun X, Wang H, Qiao W, Hu B. Affinity Monolith-Integrated Microchips for Protein Purification and Concentration. Methods Mol Biol 2016; 1466:85-92. [PMID: 27473483 DOI: 10.1007/978-1-4939-4014-1_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Affinity chromatography is a valuable method to purify and concentrate minute amount of proteins. Monoliths with epoxy groups for affinity immobilization were prepared by direct in-situ photopolymerization of glycidyl methacrylate and ethylene glycol dimethacrylate in porogenic solvents consisting of 1-dodecanol and cyclohexanol. By integrating affinity monoliths onto a microfluidic system, targeted biomolecules can be captured and retained on affinity column, while other biomolecules having no specific interactions toward the immobilized ligands flow through the microchannel. Therefore, proteins which remain on the affinity column are purified and concentrated, and then eluted by appropriate solutions and finally, separated by microchip capillary electrophoresis. This integrated microfluidic device has been applied to the purification and separation of specific proteins (FITC-labeled human serum albumin and IgG) in a mixture.
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Affiliation(s)
- Changlu Gao
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, 2 West Wenhua Road, Shandong, 264209, China.
| | - Xiuhua Sun
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, 2 West Wenhua Road, Shandong, 264209, China.
| | - Huaixin Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, 2 West Wenhua Road, Shandong, 264209, China
| | - Wei Qiao
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, 2 West Wenhua Road, Shandong, 264209, China
| | - Bo Hu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, 2 West Wenhua Road, Shandong, 264209, China
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15
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Prisic S, Hwang H, Dow A, Barnaby O, Pan TS, Lonzanida JA, Chazin WJ, Steen H, Husson RN. Zinc regulates a switch between primary and alternative S18 ribosomal proteins in Mycobacterium tuberculosis. Mol Microbiol 2015; 97:263-80. [PMID: 25858183 DOI: 10.1111/mmi.13022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2015] [Indexed: 12/21/2022]
Abstract
The Mycobacterium tuberculosis genome encodes five putative 'alternative' ribosomal proteins whose expression is repressed at high Zn(2+) concentration. Each alternative protein has a primary homologue that is predicted to bind Zn(2+). We hypothesized that zinc triggers a switch between these paired homologous proteins and therefore chose one of these pairs, S18-1/S18-2, to study mechanisms of the predicted competition for their incorporation into ribosomes. Our data show that Zn(2+)-depletion causes accumulation of both S18-2 mRNA and protein. In contrast, S18-1 mRNA levels are unchanged to slightly elevated under Zn(2+)-limited conditions. However, the amount of S18-1 protein is markedly decreased. We further demonstrate that both S18 proteins interact with ribosomal protein S6, a committed step in ribosome biogenesis. Zn(2+) is absolutely required for the S18-1/S6 interaction while it is dispensable for S18-2/S6 dimer formation. These data suggest a model in which S18-1 is the dominant ribosome constituent in high zinc conditions, e.g. inside of phagosomes, but that it can be replaced by S18-2 when zinc is deficient, e.g. in the extracellular milieu. Consequently, Zn(2+)-depletion may serve as a signal for building alternative ribosomes when M. tuberculosis is released from macrophages, to allow survival in the extracellular environment.
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Affiliation(s)
- Sladjana Prisic
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA.,Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI
| | - Hyonson Hwang
- Department of Pathology, Boston Children's Hospital/Harvard Medical School, Boston, MA
| | - Allexa Dow
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI
| | - Omar Barnaby
- Department of Pathology, Boston Children's Hospital/Harvard Medical School, Boston, MA
| | - Tenny S Pan
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI
| | | | - Walter J Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Hanno Steen
- Department of Pathology, Boston Children's Hospital/Harvard Medical School, Boston, MA
| | - Robert N Husson
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA
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16
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Yan G, Yan X. Ribosomal proteomics: Strategies, approaches, and perspectives. Biochimie 2015; 113:69-77. [PMID: 25869001 DOI: 10.1016/j.biochi.2015.03.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 12/20/2022]
Abstract
Over the past few decades, proteomic research has seen unprecedented development due to technological advancement. However, whole-cell proteomics still has limitations with respect to sample complexity and the accuracy of determining protein locations. To deal with these limitations, several subcellular proteomic studies have been initiated. Nevertheless, compared to other subcellular proteomic fields, such as mitochondrial proteomics, ribosomal proteomics has lagged behind due to the long-held idea that the ribosome is just a translation machine. Recently, with the proposed ribosome filter hypothesis and subsequent studies of ribosome-specific regulatory capacity, ribosomal proteomics has become a promising chapter for both proteomic and ribosomal research. In this review, we discuss the current strategies and approaches in ribosomal proteomics and the efficacies as well as disadvantages of individual approaches for further improvement.
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Affiliation(s)
- Guokai Yan
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Xianghua Yan
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
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Tuckey C, Asahara H, Zhou Y, Chong S. Protein synthesis using a reconstituted cell-free system. ACTA ACUST UNITED AC 2014; 108:16.31.1-16.31.22. [PMID: 25271715 DOI: 10.1002/0471142727.mb1631s108] [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: 01/23/2023]
Abstract
Most cell-free protein-synthesis systems are based on cell extracts, which often contain undesirable activities. Reconstituted systems, by contrast, are composed of a defined number of purified and recombinant components with minimal nuclease and protease activities. This unit describes the use of a particular commercial reconstituted system, PURExpress. This system allows in vitro synthesis of proteins from mRNA and circular and linear DNA templates, as well as co-translational labeling of proteins. Unique to this system, all recombinant protein components of the system are His-tagged, allowing purification of the synthesized untagged protein by removing the rest of the system's components. Newly synthesized proteins can often be visible on an SDS-PAGE gel and directly assayed for their functions without labeling and purification. Certain components of the system, such as ribosomes or release factors, can be omitted for specific applications. Such "delta" versions of the system are well suited for studies of bacterial translation, assays of ribosome function, incorporation of unnatural amino acids, and ribosome display of protein libraries.
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Spatially segregated transcription and translation in cells of the endomembrane-containing bacterium Gemmata obscuriglobus. Proc Natl Acad Sci U S A 2014; 111:11067-72. [PMID: 25024214 DOI: 10.1073/pnas.1409187111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dogma of coupled transcription and translation in bacteria has been challenged by recent reports of spatial segregation of these processes within the relatively simple cellular organization of the model organisms Escherichia coli and Bacillus subtilis. The bacterial species Gemmata obscuriglobus possesses an extensive endomembrane system. The membranes generate a very convoluted intracellular architecture in which some of the cell's ribosomes appear to have less direct access to the cell's nucleoid(s) than others. This observation prompted us to test the hypothesis that a substantial proportion of G. obscuriglobus translation may be spatially segregated from transcription. Using immunofluorescence and immunoelectron microscopy, we showed that translating ribosomes are localized throughout the cell, with a quantitatively greater proportion found in regions distal to nucleoid(s). Our results extend information about the phylogenetic and morphological diversity of bacteria in which the spatial organization of transcription and translation has been studied. These findings also suggest that endomembranes may provide an obstacle to colocated transcription and translation, a role for endomembranes that has not been reported previously for a prokaryotic organism. Our studies of G. obscuriglobus may provide a useful background for consideration of the evolutionary development of eukaryotic cellular complexity and how it led to decoupled processes of gene expression in eukaryotes.
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Lougheed KEA, Bennett MH, Williams HD. An in vivo crosslinking system for identifying mycobacterial protein-protein interactions. J Microbiol Methods 2014; 105:67-71. [PMID: 25034228 PMCID: PMC4169665 DOI: 10.1016/j.mimet.2014.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/03/2014] [Accepted: 07/07/2014] [Indexed: 11/29/2022]
Abstract
The analysis of protein-protein interactions in Mycobacterium tuberculosis has the potential to shed light on the functions of the large number of predicted open-reading frames annotated as conserved hypothetical proteins. We have developed a formaldehyde crosslinking system to detect in vivo interactions in mycobacteria. Our Gateway-adapted vector system uses three promoter strengths, including constitutive and regulatable versions, for the expression of target proteins with either an N- or C-terminal His-Strep-Strep tag. Tandem affinity purification using the His- and Strep-tags is well-suited to the isolation of protein complexes with a high purity and no detectable background. We have validated this approach using the well-described pyruvate dehydrogenase complex.
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Affiliation(s)
| | - Mark H Bennett
- Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom
| | - Huw D Williams
- Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom.
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Proteomic Analysis of theStreptomyces griseusRibosomal Fraction. Biosci Biotechnol Biochem 2014; 76:2267-74. [DOI: 10.1271/bbb.120556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Fast purification of the filamentous Potato virus Y using monolithic chromatographic supports. J Chromatogr A 2013; 1272:33-40. [DOI: 10.1016/j.chroma.2012.11.058] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 11/14/2012] [Accepted: 11/21/2012] [Indexed: 11/22/2022]
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22
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Podgornik A, Krajnc NL. Application of monoliths for bioparticle isolation. J Sep Sci 2012; 35:3059-72. [DOI: 10.1002/jssc.201200387] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 06/19/2012] [Accepted: 07/16/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Aleš Podgornik
- The Centre of Excellence for Biosensors, Instrumentation and Process Control - COBIK; Solkan Slovenia
- BIA Separations d.o.o.; Ajdovščina Slovenia
| | - Nika Lendero Krajnc
- BIA Separations d.o.o.; Ajdovščina Slovenia
- The Centre of Excellence for Biosensors, Instrumentation and Process Control - COBIK; Solkan Slovenia
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Monolithic ion exchange chromatographic methods for virus purification. Virology 2012; 434:271-7. [PMID: 23089255 DOI: 10.1016/j.virol.2012.09.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 09/19/2012] [Accepted: 09/21/2012] [Indexed: 11/23/2022]
Abstract
We report an ion exchange chromatographic purification method powerful for preparation of virus particles with ultrapure quality. The technology is based on large pore size monolithic anion exchangers, quaternary amine (QA) and diethyl aminoethyl (DEAE). These were applied to membrane-containing icosahedral bacteriophage PRD1, which bound specifically to both matrices. Virus particles eluted from the columns retained their infectivity, and were homogenous with high specific infectivity. The yields of infectious particles were up to 80%. Purified particles were recovered at high concentrations, approximately 5mg/ml, sufficient for virological, biochemical and structural analyses. We also tested the applicability of the monolithic anion exchange purification on a filamentous bacteriophage phi05_2302. Monolithic ion exchange chromatography is easily scalable and can be combined with other preparative virus purification methods.
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Trauner A, Lougheed KEA, Bennett MH, Hingley-Wilson SM, Williams HD. The dormancy regulator DosR controls ribosome stability in hypoxic mycobacteria. J Biol Chem 2012; 287:24053-63. [PMID: 22544737 PMCID: PMC3390679 DOI: 10.1074/jbc.m112.364851] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 04/27/2012] [Indexed: 01/01/2023] Open
Abstract
It is thought that during latent infection, Mycobacterium tuberculosis bacilli are retained within granulomas in a low-oxygen environment. The dormancy survival (Dos) regulon, regulated by the response regulator DosR, appears to be essential for hypoxic survival in M. tuberculosis, but it is not known how the regulon promotes survival. Here we report that mycobacteria, in contrast to enteric bacteria, do not form higher-order structures (e.g. ribosomal dimers) upon entry into stasis. Instead, ribosomes are stabilized in the associated form (70S). Using a strategy incorporating microfluidic, proteomic, and ribosomal profiling techniques to elucidate the fate of mycobacterial ribosomes during hypoxic stasis, we show that the dormancy regulator DosR is required for optimal ribosome stabilization. We present evidence that the majority of this effect is mediated by the DosR-regulated protein MSMEG_3935 (a S30AE domain protein), which is associated with the ribosome under hypoxic conditions. A Δ3935 mutant phenocopies the ΔdosR mutant during hypoxia, and complementation of ΔdosR with the MSMEG_3935 gene leads to complete recovery of dosR mutant phenotypes during hypoxia. We suggest that this protein is named ribosome-associated factor under hypoxia (RafH) and that it is the major factor responsible for DosR-mediated hypoxic survival in mycobacteria.
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Affiliation(s)
- Andrej Trauner
- From the Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kathryn E. A. Lougheed
- From the Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Mark H. Bennett
- From the Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Suzanne M. Hingley-Wilson
- From the Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Huw D. Williams
- From the Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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