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Mo W, Yao C, Chen H, Nassor AK, Gui F, Hong C, Huang T, Guan X, Xu L, Pan X. Biosynthesis of high antibacterial silver chloride nanoparticles against Ralstonia solanacearum using spent mushroom substrate extract. NANO EXPRESS 2024; 5:015020. [DOI: 10.1088/2632-959x/ad2b81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2025]
Abstract
Abstract
In this study, a green and highly efficient method was proposed to synthesize nano-silver chloride (nano-AgCl) using spent mushroom substrate (SMS) extract as a cheap reactant. Nanoparticles were characterized by a series of techniques like x-ray diffraction (XRD), energy dispersive spectroscopy (EDS), scanning electron microscopy (SEM), and transmission electron microscopy (TEM), which showed the formation of near-spherical silver chloride nanoparticles with an average size of about 8.30 nm. Notably, the synthesized nano-silver chloride has a more prominent antibacterial effect against Ralstonia solanacearum (EC50 = 5.18 mg L−1) than non-nano-sized silver chloride particles, nano-silver chloride synthesized by chemical method, and commercial pesticides. In-depth, the study of the mechanism revealed that nano-silver chloride could cause cell membrane disruption, DNA damage and intracellular generation of reactive oxygen species (·OH, ·O2− and 1O2), leading to peroxidation damage in Ralstonia solanacearum (R. solanacearum). Moreover, the reaction between nano-silver chloride and bacteria could be driven by intermolecular forces instead of electrostatic interactions. Our study provides a new approach to synthesizing nano-silver chloride as a highly efficient antibacterial agent and broadens the utilization of agricultural waste spent mushroom substrate.
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Carpousis AJ, Campo N, Hadjeras L, Hamouche L. Compartmentalization of RNA Degradosomes in Bacteria Controls Accessibility to Substrates and Ensures Concerted Degradation of mRNA to Nucleotides. Annu Rev Microbiol 2022; 76:533-552. [PMID: 35671533 DOI: 10.1146/annurev-micro-041020-113308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA degradosomes are multienzyme complexes composed of ribonucleases, RNA helicases, and metabolic enzymes. RNase E-based degradosomes are widespread in Proteobacteria. The Escherichia coli RNA degradosome is sequestered from transcription in the nucleoid and translation in the cytoplasm by localization to the inner cytoplasmic membrane, where it forms short-lived clusters that are proposed to be sites of mRNA degradation. In Caulobacter crescentus, RNA degradosomes localize to ribonucleoprotein condensates in the interior of the cell [bacterial ribonucleoprotein-bodies (BR-bodies)], which have been proposed to drive the concerted degradation of mRNA to nucleotides. The turnover of mRNA in growing cells is important for maintaining pools of nucleotides for transcription and DNA replication. Membrane attachment of the E. coli RNA degradosome is necessary to avoid wasteful degradation of intermediates in ribosome assembly. Sequestering RNA degradosomes to C. crescentus BR-bodies, which exclude structured RNA, could have a similar role in protecting intermediates in ribosome assembly from degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Agamemnon J Carpousis
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , , .,TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nathalie Campo
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , ,
| | - Lydia Hadjeras
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , , .,Current affiliation: IMIB, University of Würzburg, Würzburg, Germany;
| | - Lina Hamouche
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , ,
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The context of the ribosome binding site in mRNAs defines specificity of action of kasugamycin, an inhibitor of translation initiation. Proc Natl Acad Sci U S A 2022; 119:2118553119. [PMID: 35064089 PMCID: PMC8794815 DOI: 10.1073/pnas.2118553119] [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] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
Several antibiotics targeting the large ribosomal subunit interfere with translation in a context-specific manner, preventing ribosomes from polymerizing specific amino acid sequences. Here, we reveal kasugamycin as a small ribosomal subunit-targeting antibiotic whose action depends on the sequence context of the untranslated messenger RNA (mRNA) segments. We show that kasugamycin-induced ribosomal arrest at the start codons of the genes and the resulting inhibition of gene expression depend on the nature of the mRNA nucleotide immediately preceding the start codon and on the proximity of the stop codon of the upstream cistron. Our findings underlie the importance of mRNA context for the action of protein synthesis inhibitors and might help to guide the development of better antibiotics. Kasugamycin (KSG) is an aminoglycoside antibiotic widely used in agriculture and exhibits considerable medical potential. Previous studies suggested that KSG interferes with translation by blocking binding of canonical messenger RNA (mRNA) and initiator transfer tRNA (tRNA) to the small ribosomal subunit, thereby preventing initiation of protein synthesis. Here, by using genome-wide approaches, we show that KSG can interfere with translation even after the formation of the 70S initiation complex on mRNA, as the extent of KSG-mediated translation inhibition correlates with increased occupancy of start codons by 70S ribosomes. Even at saturating concentrations, KSG does not completely abolish translation, allowing for continuing expression of some Escherichia coli proteins. Differential action of KSG significantly depends on the nature of the mRNA residue immediately preceding the start codon, with guanine in this position being the most conducive to inhibition by the drug. In addition, the activity of KSG is attenuated by translational coupling as genes whose start codons overlap with the coding regions or the stop codons of the upstream cistrons tend to be less susceptible to drug-mediated inhibition. Altogether, our findings reveal KSG as an example of a small ribosomal subunit-targeting antibiotic with a well-pronounced context specificity of action.
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Gemayel K, Lomsadze A, Borodovsky M. StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes. FRONTIERS IN BIOINFORMATICS 2021; 1:704157. [PMID: 36303749 PMCID: PMC9581028 DOI: 10.3389/fbinf.2021.704157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 11/04/2021] [Indexed: 12/31/2022] Open
Abstract
State-of-the-art algorithms of ab initio gene prediction for prokaryotic genomes were shown to be sufficiently accurate. A pair of algorithms would agree on predictions of gene 3'ends. Nonetheless, predictions of gene starts would not match for 15-25% of genes in a genome. This discrepancy is a serious issue that is difficult to be resolved due to the absence of sufficiently large sets of genes with experimentally verified starts. We have introduced StartLink that infers gene starts from conservation patterns revealed by multiple alignments of homologous nucleotide sequences. We also have introduced StartLink+ combining both ab initio and alignment-based methods. The ability of StartLink to predict the start of a given gene is restricted by the availability of homologs in a database. We observed that StartLink made predictions for 85% of genes per genome on average. The StartLink+ accuracy was shown to be 98-99% on the sets of genes with experimentally verified starts. In comparison with database annotations, we observed that the annotated gene starts deviated from the StartLink+ predictions for ∼5% of genes in AT-rich genomes and for 10-15% of genes in GC-rich genomes on average. The use of StartLink+ has a potential to significantly improve gene start annotation in genomic databases.
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Affiliation(s)
- Karl Gemayel
- School of Computational Science and Engineering, Georgia Tech, Atlanta, GA, United States
| | - Alexandre Lomsadze
- Wallace H Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, United States
| | - Mark Borodovsky
- School of Computational Science and Engineering, Georgia Tech, Atlanta, GA, United States
- Wallace H Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, United States
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
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Polyribosome-Dependent Clustering of Membrane-Anchored RNA Degradosomes To Form Sites of mRNA Degradation in Escherichia coli. mBio 2021; 12:e0193221. [PMID: 34488454 PMCID: PMC8546579 DOI: 10.1128/mbio.01932-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The essential endoribonuclease RNase E, which is a component of the Escherichia coli multienzyme RNA degradosome, has a global role in RNA processing and degradation. RNase E localizes to the inner cytoplasmic membrane in small, short-lived clusters (puncta). Rifampin, which arrests transcription, inhibits RNase E clustering and increases its rate of diffusion. Here, we show that inhibition of clustering is due to the arrest of transcription using a rifampin-resistant control strain. Two components of the RNA degradosome, the 3′ exoribonuclease polynucleotide phosphorylase (PNPase) and the DEAD box RNA helicase RhlB, colocalize with RNase E in puncta. Clustering of PNPase and RhlB is inhibited by rifampin, and their diffusion rates increase, as evidenced by in vivo photobleaching measurements. Results with rifampin treatment reported here show that RNA degradosome diffusion is constrained by interaction with RNA substrate. Kasugamycin, which arrests translation initiation, inhibits formation of puncta and increases RNA degradosome diffusion rates. Since kasugamycin treatment results in continued synthesis and turnover of ribosome-free mRNA but inhibits polyribosome formation, RNA degradosome clustering is therefore polyribosome dependent. Chloramphenicol, which arrests translation elongation, results in formation of large clusters (foci) of RNA degradosomes that are distinct from puncta. Since chloramphenicol-treated ribosomes are stable, the formation of RNA degradosome foci could be part of a stress response that protects inactive polyribosomes from degradation. Our results strongly suggest that puncta are sites where translationally active polyribosomes are captured by membrane-associated RNA degradosomes. These sites could be part of a scanning process that is an initial step in mRNA degradation.
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Hamouche L, Poljak L, Carpousis AJ. Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin. RNA (NEW YORK, N.Y.) 2021; 27:rna.078776.121. [PMID: 34099575 PMCID: PMC8284325 DOI: 10.1261/rna.078776.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/03/2021] [Indexed: 05/12/2023]
Abstract
Rifampicin, a broad-spectrum antibiotic, inhibits bacterial RNA polymerase. Here we show that rifampicin treatment of Escherichia coli results in a 50% decrease in cell size due to a terminal cell division. This decrease is a consequence of inhibition of transcription as evidenced by an isogenic rifampicin-resistant strain. There is also a 50% decrease in total RNA due mostly to a 90% decrease in 23S and 16S rRNA levels. Control experiments showed this decrease is not an artifact of our RNA purification protocol and therefore due to degradation in vivo. Since chromosome replication continues after rifampicin treatment, ribonucleotides from rRNA degradation could be recycled for DNA synthesis. Rifampicin-induced rRNA degradation occurs under different growth conditions and in different strain backgrounds. However, rRNA degradation is never complete thus permitting the re-initiation of growth after removal of rifampicin. The orderly shutdown of growth under conditions where the induction of stress genes is blocked by rifampicin is noteworthy. Inhibition of protein synthesis by chloramphenicol resulted in a partial decrease in 23S and 16S rRNA levels whereas kasugamycin treatment had no effect. Analysis of temperature-sensitive mutant strains implicate RNase E, PNPase and RNase R in rifampicin-induced rRNA degradation. We cannot distinguish between a direct role for RNase E in rRNA degradation versus an indirect role involving a slowdown of mRNA degradation. Since mRNA and rRNA appear to be degraded by the same ribonucleases, competition by rRNA is likely to result in slower mRNA degradation rates in the presence of rifampicin than under normal growth conditions.
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Affiliation(s)
- Lina Hamouche
- LMGM, CBI, Universite de Toulouse, CNRS, UPS, Toulouse, France
| | - Leonora Poljak
- LMGM, CBI, Universite de Toulouse, CNRS, UPS, Toulouse, France
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Chaudhuri S, Li L, Zimmerman M, Chen Y, Chen YX, Toosky MN, Gardner M, Pan M, Li YY, Kawaji Q, Zhu JH, Su HW, Martinot AJ, Rubin EJ, Dartois VA, Javid B. Kasugamycin potentiates rifampicin and limits emergence of resistance in Mycobacterium tuberculosis by specifically decreasing mycobacterial mistranslation. eLife 2018; 7:36782. [PMID: 30152756 PMCID: PMC6160228 DOI: 10.7554/elife.36782] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/27/2018] [Indexed: 12/23/2022] Open
Abstract
Most bacteria use an indirect pathway to generate aminoacylated glutamine and/or asparagine tRNAs. Clinical isolates of Mycobacterium tuberculosis with increased rates of error in gene translation (mistranslation) involving the indirect tRNA-aminoacylation pathway have increased tolerance to the first-line antibiotic rifampicin. Here, we identify that the aminoglycoside kasugamycin can specifically decrease mistranslation due to the indirect tRNA pathway. Kasugamycin but not the aminoglycoside streptomycin, can limit emergence of rifampicin resistance in vitro and increases mycobacterial susceptibility to rifampicin both in vitro and in a murine model of infection. Moreover, despite parenteral administration of kasugamycin being unable to achieve the in vitro minimum inhibitory concentration, kasugamycin alone was able to significantly restrict growth of Mycobacterium tuberculosis in mice. These data suggest that pharmacologically reducing mistranslation may be a novel mechanism for targeting bacterial adaptation. A bacterium called Mycobacterium tuberculosis is responsible for nearly 98% of cases of tuberculosis, which kills more people worldwide than any other infectious disease. This is due, in part, to the time it takes to cure individuals of the disease: patients have to take antibiotics continuously for at least six months to eradicate M. tuberculosis in the body. Bacteria, like all cells, make proteins using instructions contained within their genetic code. Cell components called ribosomes are responsible for translating these instructions and assembling the new proteins. Sometimes the ribosomes produce proteins that are slightly different to what the cell’s genetic code specified. These ‘incorrect proteins’ may not work properly so it is generally thought that cells try to prevent the mistakes from happening. However, scientists have recently found that the ribosomes in M. tuberculosis often assemble incorrect proteins. The more mistakes the ribosomes let happen, the more likely the bacteria are to survive when they are exposed to rifampicin, an antibiotic which is often used to treat tuberculosis infections. This suggests that it may be possible to make antibiotics more effective against M. tuberculosis by using them alongside a second drug that decreases the number of ribosome mistakes. Chaudhuri, Li et al. investigated the effect of a drug called kasugamycin on M. tuberculosis when the bacterium is cultured in the lab, and when it infects mice. The experiments found that Kasugamycin decreased the number of incorrect proteins assembled by the M. tuberculosis bacterium. When the drug was present, rifampicin also killed M. tuberculosis cells more efficiently. Furthermore, in the mice but not the cell cultures, kasugamycin alone was able to restrict the growth of the bacteria. This implies that M. tuberculosis cells may use ribosome mistakes as a strategy to survive in humans and other hosts. When it was given with rifampicin, kasugamycin caused several unwanted side effects in the mice, including weight loss; this may mean that the drug is currently not suitable to use in humans. Further studies may be able to find safer ways to decrease ribosome mistakes in M. tuberculosis, which could speed up the treatment of tuberculosis.
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Affiliation(s)
- Swarnava Chaudhuri
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Liping Li
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, United States
| | - Matthew Zimmerman
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, United States
| | - Yuemeng Chen
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Yu-Xiang Chen
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Melody N Toosky
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China.,Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| | - Michelle Gardner
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| | - Miaomiao Pan
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Yang-Yang Li
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Qingwen Kawaji
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Jun-Hao Zhu
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Hong-Wei Su
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Amanda J Martinot
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, United States
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| | - Veronique Anne Dartois
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, United States
| | - Babak Javid
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China.,Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
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Beck HJ, Moll I. Leaderless mRNAs in the Spotlight: Ancient but Not Outdated! Microbiol Spectr 2018; 6:10.1128/microbiolspec.rwr-0016-2017. [PMID: 30006995 PMCID: PMC11633608 DOI: 10.1128/microbiolspec.rwr-0016-2017] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Indexed: 02/07/2023] Open
Abstract
Previously, leaderless mRNAs (lmRNAs) were perceived to make up only a minor fraction of the transcriptome in bacteria. However, advancements in RNA sequencing technology are uncovering vast numbers of lmRNAs, particularly in archaea, Actinobacteria, and extremophiles and thus underline their significance in cellular physiology and regulation. Due to the absence of conventional ribosome binding signals, lmRNA translation initiation is distinct from canonical mRNAs and can therefore be differentially regulated. The ribosome's inherent ability to bind a 5'-terminal AUG can stabilize and protect the lmRNA from degradation or allow ribosomal loading for downstream initiation events. As a result, lmRNAs remain translationally competent during a variety of physiological conditions, allowing them to contribute to multiple regulatory mechanisms. Furthermore, the abundance of lmRNAs can increase during adverse conditions through the upregulation of lmRNA transcription from alternative promoters or by the generation of lmRNAs from canonical mRNAs cleaved by an endonucleolytic toxin. In these ways, lmRNA translation can continue during stress and contribute to regulation, illustrating their importance in the cell. Due to their presence in all domains of life and their ability to be translated by heterologous hosts, lmRNAs appear further to represent ancestral transcripts that might allow us to study the evolution of the ribosome and the translational process.
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Affiliation(s)
- Heather J Beck
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunology and Genetics, University of Vienna, Vienna Biocenter, A-1030 Vienna, Austria
| | - Isabella Moll
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunology and Genetics, University of Vienna, Vienna Biocenter, A-1030 Vienna, Austria
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Nikolic N, Didara Z, Moll I. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ 2017; 5:e3830. [PMID: 28948108 PMCID: PMC5610899 DOI: 10.7717/peerj.3830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/29/2017] [Indexed: 12/04/2022] Open
Abstract
Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein.
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Affiliation(s)
- Nela Nikolic
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
- Current affiliation: Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Zrinka Didara
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
- Current affiliation: Department of Life Sciences, IMC University of Applied Sciences Krems, Krems an der Donau, Austria
| | - Isabella Moll
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
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Benhalevy D, Biran I, Bochkareva ES, Sorek R, Bibi E. Evidence for a cytoplasmic pool of ribosome-free mRNAs encoding inner membrane proteins in Escherichia coli. PLoS One 2017; 12:e0183862. [PMID: 28841711 PMCID: PMC5571963 DOI: 10.1371/journal.pone.0183862] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Translation-independent mRNA localization represents an emerging concept in cell biology. In Escherichia coli, mRNAs encoding integral membrane proteins (MPRs) are targeted to the membrane where they are translated by membrane associated ribosomes and the produced proteins are inserted into the membrane co-translationally. In order to better understand aspects of the biogenesis and localization of MPRs, we investigated their subcellular distribution using cell fractionation, RNA-seq and qPCR. The results show that MPRs are overrepresented in the membrane fraction, as expected, and depletion of the signal recognition particle-receptor, FtsY reduced the amounts of all mRNAs on the membrane. Surprisingly, however, MPRs were also found relatively abundant in the soluble ribosome-free fraction and their amount in this fraction is increased upon overexpression of CspE, which was recently shown to interact with MPRs. CspE also conferred a positive effect on the membrane-expression of integral membrane proteins. We discuss the possibility that the effects of CspE overexpression may link the intriguing subcellular localization of MPRs to the cytosolic ribosome-free fraction with their translation into membrane proteins and that the ribosome-free pool of MPRs may represent a stage during their targeting to the membrane, which precedes translation.
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Affiliation(s)
- Daniel Benhalevy
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Biran
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Elena S. Bochkareva
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eitan Bibi
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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