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Vargas-Blanco DA, Shell SS. Regulation of mRNA Stability During Bacterial Stress Responses. Front Microbiol 2020; 11:2111. [PMID: 33013770 PMCID: PMC7509114 DOI: 10.3389/fmicb.2020.02111] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
Bacteria have a remarkable ability to sense environmental changes, swiftly regulating their transcriptional and posttranscriptional machinery as a response. Under conditions that cause growth to slow or stop, bacteria typically stabilize their transcriptomes in what has been shown to be a conserved stress response. In recent years, diverse studies have elucidated many of the mechanisms underlying mRNA degradation, yet an understanding of the regulation of mRNA degradation under stress conditions remains elusive. In this review we discuss the diverse mechanisms that have been shown to affect mRNA stability in bacteria. While many of these mechanisms are transcript-specific, they provide insight into possible mechanisms of global mRNA stabilization. To that end, we have compiled information on how mRNA fate is affected by RNA secondary structures; interaction with ribosomes, RNA binding proteins, and small RNAs; RNA base modifications; the chemical nature of 5' ends; activity and concentration of RNases and other degradation proteins; mRNA and RNase localization; and the stringent response. We also provide an analysis of reported relationships between mRNA abundance and mRNA stability, and discuss the importance of stress-associated mRNA stabilization as a potential target for therapeutic development.
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Affiliation(s)
- Diego A Vargas-Blanco
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States.,Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
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2
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Chancey ST, Bai X, Kumar N, Drabek EF, Daugherty SC, Colon T, Ott S, Sengamalay N, Sadzewicz L, Tallon LJ, Fraser CM, Tettelin H, Stephens DS. Transcriptional attenuation controls macrolide inducible efflux and resistance in Streptococcus pneumoniae and in other Gram-positive bacteria containing mef/mel(msr(D)) elements. PLoS One 2015; 10:e0116254. [PMID: 25695510 PMCID: PMC4335068 DOI: 10.1371/journal.pone.0116254] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/04/2014] [Indexed: 01/30/2023] Open
Abstract
Macrolide resistance, emerging in Streptococcus pneumoniae and other Gram-positive bacteria, is increasingly due to efflux pumps encoded by mef/mel(msr) operons found on discrete mobile genetic elements. The regulation of mef/mel(msr) in these elements is not well understood. We identified the mef(E)/mel transcriptional start, localized the mef(E)/mel promoter, and demonstrated attenuation of transcription as a mechanism of regulation of macrolide-inducible mef-mediated macrolide resistance in S. pneumoniae. The mef(E)/mel transcriptional start site was a guanine 327 bp upstream of mef(E). Consensus pneumococcal promoter -10 (5′-TATACT-3′) and -35 (5′-TTGAAC-3′) boxes separated by 17 bp were identified 7 bp upstream of the start site. Analysis of the predicted secondary structure of the 327 5’ region identified four pairs of inverted repeats R1-R8 predicted to fold into stem-loops, a small leader peptide [MTASMRLR, (Mef(E)L)] required for macrolide induction and a Rho-independent transcription terminator. RNA-seq analyses provided confirmation of transcriptional attenuation. In addition, expression of mef(E)L was also influenced by mef(E)L-dependent mRNA stability. The regulatory region 5’ of mef(E) was highly conserved in other mef/mel(msr)-containing elements including Tn1207.1 and the 5612IQ complex in pneumococci and Tn1207.3 in Group A streptococci, indicating a regulatory mechanism common to a wide variety of Gram-positive bacteria containing mef/mel(msr) elements.
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Affiliation(s)
- Scott T. Chancey
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center, Atlanta, Georgia, United States of America
| | - Xianhe Bai
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center, Atlanta, Georgia, United States of America
| | - Nikhil Kumar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Elliott F. Drabek
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Sean C. Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Thomas Colon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Sandra Ott
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Naomi Sengamalay
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Luke J. Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David S. Stephens
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center, Atlanta, Georgia, United States of America
- * E-mail:
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3
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Abstract
mRNA degradation is an important mechanism for controlling gene expression in bacterial cells. This process involves the orderly action of a battery of cellular endonucleases and exonucleases, some universal and others present only in certain species. These ribonucleases function with the assistance of ancillary enzymes that covalently modify the 5' or 3' end of RNA or unwind base-paired regions. Triggered by initiating events at either the 5' terminus or an internal site, mRNA decay occurs at diverse rates that are transcript specific and governed by RNA sequence and structure, translating ribosomes, and bound sRNAs or proteins. In response to environmental cues, bacteria are able to orchestrate widespread changes in mRNA lifetimes by modulating the concentration or specific activity of cellular ribonucleases or by unmasking the mRNA-degrading activity of cellular toxins.
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Affiliation(s)
- Monica P Hui
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016;
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Heß S, Gallert C. Demonstration of staphylococci with inducible macrolide-lincosamide-streptogramin B (MLSB) resistance in sewage and river water and of the capacity of anhydroerythromycin to induce MLSB. FEMS Microbiol Ecol 2013; 88:48-59. [DOI: 10.1111/1574-6941.12268] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 11/29/2013] [Accepted: 11/30/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Stefanie Heß
- Institute of Biology for Engineers and Biotechnology of Wastewater Treatment; Karlsruhe Institute of Technology; Karlsruhe Germany
| | - Claudia Gallert
- Department of Microbiology - Biotechnology; Faculty of Technology; University of Applied Science, Hochschule Emden/Leer; Emden Germany
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Initiation of mRNA decay in bacteria. Cell Mol Life Sci 2013; 71:1799-828. [PMID: 24064983 PMCID: PMC3997798 DOI: 10.1007/s00018-013-1472-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 09/01/2013] [Accepted: 09/03/2013] [Indexed: 12/24/2022]
Abstract
The instability of messenger RNA is fundamental to the control of gene expression. In bacteria, mRNA degradation generally follows an "all-or-none" pattern. This implies that if control is to be efficient, it must occur at the initiating (and presumably rate-limiting) step of the degradation process. Studies of E. coli and B. subtilis, species separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in this process in the two organisms. The early view that mRNA decay in these two model organisms is radically different has given way to new models that can be resumed by "different enzymes-similar strategies". The recent characterization of key ribonucleases sheds light on an impressive case of convergent evolution that illustrates that the surprisingly similar functions of these totally unrelated enzymes are of general importance to RNA metabolism in bacteria. We now know that the major mRNA decay pathways initiate with an endonucleolytic cleavage in E. coli and B. subtilis and probably in many of the currently known bacteria for which these organisms are considered representative. We will discuss here the different pathways of eubacterial mRNA decay, describe the major players and summarize the events that can precede and/or favor nucleolytic inactivation of a mRNA, notably the role of the 5' end and translation initiation. Finally, we will discuss the role of subcellular compartmentalization of transcription, translation, and the RNA degradation machinery.
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Divergent protein motifs direct elongation factor P-mediated translational regulation in Salmonella enterica and Escherichia coli. mBio 2013; 4:e00180-13. [PMID: 23611909 PMCID: PMC3638311 DOI: 10.1128/mbio.00180-13] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Elongation factor P (EF-P) is a universally conserved bacterial translation factor homologous to eukaryotic/archaeal initiation factor 5A. In Salmonella, deletion of the efp gene results in pleiotropic phenotypes, including increased susceptibility to numerous cellular stressors. Only a limited number of proteins are affected by the loss of EF-P, and it has recently been determined that EF-P plays a critical role in rescuing ribosomes stalled at PPP and PPG peptide sequences. Here we present an unbiased in vivo investigation of the specific targets of EF-P by employing stable isotope labeling of amino acids in cell culture (SILAC) to compare the proteomes of wild-type and efp mutant Salmonella. We found that metabolic and motility genes are prominent among the subset of proteins with decreased production in the Δefp mutant. Furthermore, particular tripeptide motifs are statistically overrepresented among the proteins downregulated in efp mutant strains. These include both PPP and PPG but also additional motifs, such as APP and YIRYIR, which were confirmed to induce EF-P dependence by a translational fusion assay. Notably, we found that many proteins containing polyproline motifs are not misregulated in an EF-P-deficient background, suggesting that the factors that govern EF-P-mediated regulation are complex. Finally, we analyzed the specific region of the PoxB protein that is modulated by EF-P and found that mutation of any residue within a specific GSCGPG sequence eliminates the requirement for EF-P. This work expands the known repertoire of EF-P target motifs and implicates factors beyond polyproline motifs that are required for EF-P-mediated regulation. Bacterial cells regulate gene expression at several points during and after transcription. During protein synthesis, for example, factors can interact with the ribosome to influence the production of specific proteins. Bacterial elongation factor P (EF-P) is a protein that facilitates the synthesis of proteins that contain polyproline motifs by preventing the ribosome from stalling. Bacterial cells that lack EF-P are viable but are sensitive to a large number of stress conditions. In this study, a global analysis of protein synthesis revealed that EF-P regulates many more proteins in the cell than predicted based solely on the prevalence of polyproline motifs. Several new EF-P-regulated motifs were uncovered, thereby providing a more complete picture of how this critical factor influences the cell’s response to stress at the level of protein synthesis.
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Dressaire C, Picard F, Redon E, Loubière P, Queinnec I, Girbal L, Cocaign-Bousquet M. Role of mRNA stability during bacterial adaptation. PLoS One 2013; 8:e59059. [PMID: 23516597 PMCID: PMC3596320 DOI: 10.1371/journal.pone.0059059] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 02/11/2013] [Indexed: 11/18/2022] Open
Abstract
Bacterial adaptation involves extensive cellular reorganization. In particular, growth rate adjustments are associated with substantial modifications of gene expression and mRNA abundance. In this work we aimed to assess the role of mRNA degradation during such variations. A genome-wide transcriptomic-based method was used to determine mRNA half-lives. The model bacterium Lactococcus lactis was used and different growth rates were studied in continuous cultures under isoleucine-limitation and in batch cultures during the adaptation to the isoleucine starvation. During continuous isoleucine-limited growth, the mRNAs of different genes had different half-lives. The stability of most of the transcripts was not constant, and increased as the growth rate decreased. This half-life diversity was analyzed to investigate determinants of mRNA stability. The concentration, length, codon adaptation index and secondary structures of mRNAs were found to contribute to the determination of mRNA stability in these conditions. However, the growth rate was, by far, the most influential determinant. The respective influences of mRNA degradation and transcription on the regulation of intra-cellular transcript concentration were estimated. The role of degradation on mRNA homeostasis was clearly evidenced: for more than 90% of the mRNAs studied during continuous isoleucine-limited growth of L. lactis, degradation was antagonistic to transcription. Although both transcription and degradation had, opposite effects, the mRNA changes in response to growth rate were driven by transcription. Interestingly, degradation control increased during the dynamic adaptation of bacteria as the growth rate reduced due to progressive isoleucine starvation in batch cultures. This work shows that mRNA decay differs between gene transcripts and according to the growth rate. It demonstrates that mRNA degradation is an important regulatory process involved in bacterial adaptation. However, its impact on the regulation of mRNA levels is smaller than that of transcription in the conditions studied.
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Affiliation(s)
- Clémentine Dressaire
- Université de Toulouse; The Institut National des Sciences Appliquées, UPS, INP, LISBP, Toulouse, France.
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8
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Laalami S, Putzer H. mRNA degradation and maturation in prokaryotes: the global players. Biomol Concepts 2011; 2:491-506. [DOI: 10.1515/bmc.2011.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/26/2011] [Indexed: 11/15/2022] Open
Abstract
AbstractThe degradation of messenger RNA is of universal importance for controlling gene expression. It directly affects protein synthesis by modulating the amount of mRNA available for translation. Regulation of mRNA decay provides an efficient means to produce just the proteins needed and to rapidly alter patterns of protein synthesis. In bacteria, the half-lives of individual mRNAs can differ by as much as two orders of magnitude, ranging from seconds to an hour. Most of what we know today about the diverse mechanisms of mRNA decay and maturation in prokaryotes comes from studies of the two model organisms Escherichia coli and Bacillus subtilis. Their evolutionary distance provided a large picture of potential pathways and enzymes involved in mRNA turnover. Among them are three ribonucleases, two of which have been discovered only recently, which have a truly general role in the initiating events of mRNA degradation: RNase E, RNase J and RNase Y. Their enzymatic characteristics probably determine the strategies of mRNA metabolism in the organism in which they are present. These ribonucleases are coded, alone or in various combinations, in all prokaryotic genomes, thus reflecting how mRNA turnover has been adapted to different ecological niches throughout evolution.
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Affiliation(s)
- Soumaya Laalami
- CNRS UPR 9073, affiliated with Univ Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Harald Putzer
- CNRS UPR 9073, affiliated with Univ Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France
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9
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Chancey ST, Zhou X, Zähner D, Stephens DS. Induction of efflux-mediated macrolide resistance in Streptococcus pneumoniae. Antimicrob Agents Chemother 2011; 55:3413-22. [PMID: 21537010 PMCID: PMC3122420 DOI: 10.1128/aac.00060-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Accepted: 04/25/2011] [Indexed: 01/17/2023] Open
Abstract
The antimicrobial efflux system encoded by the operon mef(E)-mel on the mobile genetic element MEGA in Streptococcus pneumoniae and other Gram-positive bacteria is inducible by macrolide antibiotics and antimicrobial peptides. Induction may affect the clinical response to the use of macrolides. We developed mef(E) reporter constructs and a disk diffusion induction and resistance assay to determine the kinetics and basis of mef(E)-mel induction. Induction occurred rapidly, with a >15-fold increase in transcription within 1 h of exposure to subinhibitory concentrations of erythromycin. A spectrum of environmental conditions, including competence and nonmacrolide antibiotics with distinct cellular targets, did not induce mef(E). Using 16 different structurally defined macrolides, induction was correlated with the amino sugar attached to C-5 of the macrolide lactone ring, not with the size (e.g., 14-, 15- or 16-member) of the ring or with the presence of the neutral sugar cladinose at C-3. Macrolides with a monosaccharide attached to C-5, known to block exit of the nascent peptide from the ribosome after the incorporation of up to eight amino acids, induced mef(E) expression. Macrolides with a C-5 disaccharide, which extends the macrolide into the ribosomal exit tunnel, disrupting peptidyl transferase activity, did not induce it. The induction of mef(E) did not require macrolide efflux, but the affinity of macrolides for the ribosome determined the availability for efflux and pneumococcal susceptibility. The induction of mef(E)-mel expression by inducing macrolides appears to be based on specific interactions of the macrolide C-5 saccharide with the ribosome that alleviate transcriptional attenuation of mef(E)-mel.
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Affiliation(s)
- Scott T. Chancey
- Division of Infectious Diseases, Department of Medicine
- Department of Veterans Affairs Medical Center, Atlanta, Georgia 30033
| | - Xiaoliu Zhou
- Division of Infectious Diseases, Department of Medicine
- Department of Veterans Affairs Medical Center, Atlanta, Georgia 30033
| | - Dorothea Zähner
- Division of Infectious Diseases, Department of Medicine
- Department of Veterans Affairs Medical Center, Atlanta, Georgia 30033
| | - David S. Stephens
- Division of Infectious Diseases, Department of Medicine
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322
- Department of Veterans Affairs Medical Center, Atlanta, Georgia 30033
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Romby P, Charpentier E. An overview of RNAs with regulatory functions in gram-positive bacteria. Cell Mol Life Sci 2010; 67:217-37. [PMID: 19859665 PMCID: PMC11115938 DOI: 10.1007/s00018-009-0162-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 09/07/2009] [Accepted: 09/23/2009] [Indexed: 11/26/2022]
Abstract
During the last decade, RNA molecules with regulatory functions on gene expression have benefited from a renewed interest. In bacteria, recent high throughput computational and experimental approaches have led to the discovery that 10-20% of all genes code for RNAs with critical regulatory roles in metabolic, physiological and pathogenic processes. The trans-acting RNAs comprise the noncoding RNAs, RNAs with a short open reading frame and antisense RNAs. Many of these RNAs act through binding to their target mRNAs while others modulate protein activity or target DNA. The cis-acting RNAs include regulatory regions of mRNAs that can respond to various signals. These RNAs often provide the missing link between sensing changing conditions in the environment and fine-tuning the subsequent biological responses. Information on their various functions and modes of action has been well documented for gram-negative bacteria. Here, we summarize the current knowledge of regulatory RNAs in gram-positive bacteria.
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Affiliation(s)
- Pascale Romby
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
| | - Emmanuelle Charpentier
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
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11
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Bechhofer DH. Messenger RNA decay and maturation in Bacillus subtilis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:231-73. [PMID: 19215774 DOI: 10.1016/s0079-6603(08)00806-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Our understanding of the ribonucleases that act to process and turn over RNA in Bacillus subtilis, a model Gram-positive organism, has increased greatly in recent years. This chapter discusses characteristics of B. subtilis ribonucleases that have been shown to participate in messenger RNA maturation and decay. Distinct features of a recently discovered ribonuclease, RNase J1, are reviewed, and are put in the context of a mechanism for the mRNA decay process in B. subtilis that differs greatly from the classical model developed for E. coli. This chapter is divided according to three parts of an mRNA-5' end, body, and 3' end-that could theoretically serve as sites for initiation of decay. How 5'-proximal elements affect mRNA half-life, and especially how these elements interface with RNase J1, forms the basis for a set of "rules" that may be useful in predicting mRNA stability.
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Affiliation(s)
- David H Bechhofer
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine of New York University, New York, NY 10029, USA
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12
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Daou-Chabo R, Mathy N, Bénard L, Condon C. Ribosomes initiating translation of thehbsmRNA protect it from 5′-to-3′ exoribonucleolytic degradation by RNase J1. Mol Microbiol 2009; 71:1538-50. [DOI: 10.1111/j.1365-2958.2009.06620.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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13
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Dreyfus M. Killer and protective ribosomes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:423-66. [PMID: 19215779 DOI: 10.1016/s0079-6603(08)00811-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In prokaryotes, translation influences mRNA decay. The breakdown of most Escherichia coli mRNAs is initiated by RNase E, a 5'-dependent endonuclease. Some mRNAs are protected by ribosomes even if these are located far upstream of cleavage sites ("protection at a distance"), whereas others require direct shielding of these sites. I argue that these situations reflect different modes of interaction of RNase E with mRNAs. Protection at a distance is most impressive in Bacilli, where ribosomes can protect kilobases of unstable downstream sequences. I propose that this protection reflects the role in mRNA decay of RNase J1, a 5'-->3' exonuclease with no E. coli equivalent. Finally, recent years have shown that besides their protective role, ribosomes can also cleave their mRNA under circumstances that cause ribosome stalling. The endonuclease associated with this "killing" activity, which has a eukaryotic counterpart ("no-go decay"), is not characterized; it may be borne by the distressed ribosome itself.
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14
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Mäder U, Zig L, Kretschmer J, Homuth G, Putzer H. mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol 2008; 70:183-96. [PMID: 18713320 DOI: 10.1111/j.1365-2958.2008.06400.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribonucleases J1 and J2 of Bacillus subtilis are evolutionarily conserved enzymes combining an endoribonucleolytic and a 5'-3' exoribonucleolytic activity in a single polypeptide. Their endoribonucleolytic cleavage specificity resembles that of RNase E, a key player in the processing and degradation of RNA in Escherichia coli. The biological significance of the paralogous RNases J1 and J2 in Bacillus subtilis is still unknown. Based on the premise that cleavage of an mRNA might alter its stability and hence its abundance, we have analysed the transcriptomes and proteomes of single and double mutant strains. The absence or decrease of both RNases J1 and J2 together profoundly alters the expression level of hundreds of genes. By contrast, the effect on global gene expression is minimal in single mutant strains, suggesting that the two nucleases have largely overlapping substrate specificities. Half-life measurements of individual mRNAs show that RNases J1/J2 can alter gene expression by modulating transcript stability. The absence/decrease of RNases J1 and J2 results in similar numbers of transcripts whose abundance is either increased or decreased, suggesting a complex role of these ribonucleases in both degradative and regulatory processing events that have an important impact on gene expression.
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Affiliation(s)
- Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, Department for Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Walther-Rathenau-Str. 49A, D-17489 Greifswald, Germany
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15
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Translational attenuation and mRNA stabilization as mechanisms of erm(B) induction by erythromycin. Antimicrob Agents Chemother 2008; 52:1782-9. [PMID: 18299414 DOI: 10.1128/aac.01376-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Translational attenuation has been proposed to be the mechanism by which the erm(B) gene is induced. Here, we report genetic and biochemical evidence, obtained by using erythromycin as the inducing antibiotic, that supports this hypothesis. We also show that erythromycin increases the level of the erm(B) transcript by stalling the ribosome on the leader mRNA and thereby facilitating the stabilization and processing of the mRNA. Erythromycin-induced mRNA stabilization and processing were observed with an ochre stop at codons 11 to 13 of the leader but not with an ochre stop at codon 10. This suggests that erythromycin does not stall the ribosome before codon 11 of the leader reaches the aminoacyl site. Secondary structure analyses of the erm(B) transcripts by in vitro and in vivo chemical probing techniques identified conformational changes in the transcripts that result from induction by erythromycin. These findings demonstrate that stalling of erythromycin-bound ribosomes at leader codon 11 causes the refolding of mRNA into a conformation in which the translational initiation site for the structural gene is unmasked and renders erm(B) translationally active.
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Abstract
The macrolides have evolved through four chemical generations since erythromycin became available for clinical use in 1952. The first generation, the 14-membered ring macrolide erythromycin, induced resistance and was replaced by the second generation 16-membered ring macrolides which did not. The inability to induce came at the price of mutation, in the pathogenic target strain, to constitutive expression of resistance. A third generation of macrolides improved the acid-stability, and therefore the pharmacokinetics of erythromycin, extending the clinical use of macrolides to Helicobacter pylori and Mycobacterium tuberculosis. Improved pharmacokinetics resulted in the selection of intrinsically resistant mutant strains with rRNA structural alterations. Expression of resistance in these strains was unexpected, explainable by low rRNA gene copy number which made resistance dominant. A fourth generation of macrolides, the 14-membered ring ketolides are the most recent development. Members of this generation are reported to be effective against inducibly resistant strains, and ketolide resistant strains have not yet been reported. In this review we discuss details of the ways in which bacteria have become resistant to the first three generations of macrolides, both with respect to their biochemistry, and the genetic mechanisms by which their expression is regulated.
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Affiliation(s)
- B Weisblum
- Department of Pharmacology, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA.
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17
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Depardieu F, Podglajen I, Leclercq R, Collatz E, Courvalin P. Modes and modulations of antibiotic resistance gene expression. Clin Microbiol Rev 2007; 20:79-114. [PMID: 17223624 PMCID: PMC1797629 DOI: 10.1128/cmr.00015-06] [Citation(s) in RCA: 246] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Since antibiotic resistance usually affords a gain of function, there is an associated biological cost resulting in a loss of fitness of the bacterial host. Considering that antibiotic resistance is most often only transiently advantageous to bacteria, an efficient and elegant way for them to escape the lethal action of drugs is the alteration of resistance gene expression. It appears that expression of bacterial resistance to antibiotics is frequently regulated, which indicates that modulation of gene expression probably reflects a good compromise between energy saving and adjustment to a rapidly evolving environment. Modulation of gene expression can occur at the transcriptional or translational level following mutations or the movement of mobile genetic elements and may involve induction by the antibiotic. In the latter case, the antibiotic can have a triple activity: as an antibacterial agent, as an inducer of resistance to itself, and as an inducer of the dissemination of resistance determinants. We will review certain mechanisms, all reversible, that bacteria have elaborated to achieve antibiotic resistance by the fine-tuning of the expression of genetic information.
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Affiliation(s)
- Florence Depardieu
- Unité des Agents Antibactériens, Institut Pasteur, 75724 Paris Cedex 15, France
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18
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Schumann W. Production of Recombinant Proteins in Bacillus subtilis. ADVANCES IN APPLIED MICROBIOLOGY 2007; 62:137-89. [PMID: 17869605 DOI: 10.1016/s0065-2164(07)62006-1] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wolfgang Schumann
- Institute of Genetics, University of Bayreuth, Bayreuth D-95440, Germany
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19
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Petersen C. Control of functional mRNA stability in bacteria: multiple mechanisms of nucleolytic and non-nucleolytic inactivation. Mol Microbiol 2006; 6:277-82. [PMID: 1372674 DOI: 10.1111/j.1365-2958.1992.tb01469.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Messenger RNA in bacteria may be inactivated by several parallel mechanisms acting independently on different target sites. For any species of mRNA the overall rate of inactivation is determined by the sum of the contributions from the different mechanisms. Transcripts may be inactivated directly by endonucleolytic attack or by processive nucleolytic degradation, which may proceed in the 3'-5' direction and probably also in the 5'-3' direction. Moreover, the functional lifetime of many mRNAs may be determined by processes that are not nucleolytic, such as the binding of translational repressors or the formation of secondary structures which prevent initiation of translation. These non-nucleolytic processes may also determine the chemical stability as chemical degradation frequently appears to be closely coupled to functional inactivation. The relative importance of the different mechanisms in the inactivation of bulk cellular mRNA, as well as the general prospects for engineering of stable mRNAs are discussed.
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Affiliation(s)
- C Petersen
- University Institute of Microbiology, University of Copenhagen, Denmark
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20
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Abstract
The lifetimes of bacterial mRNAs are strongly affected by their association with ribosomes. Events occurring at any stage during translation, including ribosome binding, polypeptide elongation, or translation termination, can influence the susceptibility of mRNA to ribonuclease attack. Ribosomes usually act as protective barriers that impede mRNA cleavage, but in some instances they can instead trigger the decay of the mRNA to which they are bound or send a signal that leads to widespread mRNA destabilization within a cell. The influence of translation on mRNA decay provides a quality-control mechanism for minimizing the use of poorly or improperly translated mRNAs as templates for the production of abnormal proteins that might be toxic to bacteria.
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Affiliation(s)
- Atilio Deana
- Skirball Institute of Biomolecular Medicine and Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
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21
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Abstract
Previous work showed that a 42-nucleotide sequence from an SP82 bacteriophage early RNA functions as a 5' mRNA stabilizer in Bacillus subtilis. Real-time reverse transcriptase polymerase chain reaction (RT-PCR) analysis of decay of a model mRNA with alterations at the 5'-end was used to elucidate the mechanism of SP82-mediated stability. A predicted 5'-terminal stem-loop structure was essential for stabilization. Increasing the strength of the 5'-terminal structure above a minimum level did not result in increased stability. A thorough analysis of the context in which the stabilizing structure occurred included the effects of distance from 5'-end, translation of downstream coding sequence, and distance between the secondary structure and the ribosome binding site. Our data are consistent with the dominant mRNA decay pathway in B. subtilis being 5'-end dependent.
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Affiliation(s)
- Josh S Sharp
- Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine of New York University, Box 1603, 1 Gustave L. Levy Place, New York, NY 10029-6754, USA
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22
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Daguer JP, Chambert R, Petit-Glatron MF. Increasing the stability of sacB transcript improves levansucrase production in Bacillus subtilis. Lett Appl Microbiol 2005; 41:221-6. [PMID: 16033525 DOI: 10.1111/j.1472-765x.2005.01729.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To develop a strategy to increase the stability of transcripts of structural genes expressed under the control of sacR, the leader region of Bacillus subtilis levansucrase gene. METHODS AND RESULTS Insertion of Shine Dalgarno like sequences in the 5'-untranslated sacR region controlling the expression of sacB. Depending on the number of stabilizing sequences inserted and the position of these sequences with respect to the translation start codon, it was observed that the mRNA stability and the final protein production could be increased or decreased. CONCLUSIONS This mRNA stabilization can be used to increase exocellular protein production in the degU32 (Hy) mutant. SIGNIFICANCE AND IMPACT OF THE STUDY This approach can be applied to the expression of heterologous genes of biotechnological interest.
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Affiliation(s)
- J P Daguer
- Laboratoire Génétique et Membranes, Institut Jacques Monod, CNRS-Universités Paris VI et Paris VII, Paris, France
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23
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Power PM, Jones RA, Beacham IR, Bucholtz C, Jennings MP. Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli. Biochem Biophys Res Commun 2004; 322:1038-44. [PMID: 15336569 DOI: 10.1016/j.bbrc.2004.08.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2004] [Indexed: 11/21/2022]
Abstract
Translational pausing may occur due to a number of mechanisms, including the presence of non-optimal codons, and it is thought to play a role in the folding of specific polypeptide domains during translation and in the facilitation of signal peptide recognition during sec-dependent protein targeting. In this whole genome analysis of Escherichia coli we have found that non-optimal codons in the signal peptide-encoding sequences of secretory genes are overrepresented relative to the "mature" portions of these genes; this is in addition to their overrepresentation in the 5'-regions of genes encoding non-secretory proteins. We also find increased non-optimal codon usage at the 3' ends of most E. coli genes, in both non-secretory and secretory sequences. Whereas presumptive translational pausing at the 5' and 3' ends of E. coli messenger RNAs may clearly have a general role in translation, we suggest that it also has a specific role in sec-dependent protein export, possibly in facilitating signal peptide recognition. This finding may have important implications for our understanding of how the majority of non-cytoplasmic proteins are targeted, a process that is essential to all biological cells.
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Affiliation(s)
- Peter M Power
- School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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24
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Abstract
A 254-nucleotide model mRNA, designated deltaermC mRNA, was used to study the effects of translational signals and ribosome transit on mRNA decay in Bacillus subtilis. DeltaermC mRNA features a strong ribosome-binding site (RBS) and a 62-amino-acid-encoding open reading frame, followed by a transcription terminator structure. Inactivation of the RBS or the start codon resulted in a fourfold decrease in the mRNA half-life, demonstrating the importance of ternary complex formation for mRNA stability. Data for the decay of deltaermC mRNAs with stop codons at positions increasingly proximal to the translational start site showed that actual translation--even the formation of the first peptide bond--was not important for stability. The half-life of an untranslated 3.2-kb deltaermC-lacZ fusion RNA was similar to that of a translated deltaermC-lacZ mRNA, indicating that the translation of even a longer RNA was not required for wild-type stability. The data are consistent with a model in which ribosome binding and the formation of the ternary complex interfere with a 5'-end-dependent activity, possibly a 5'-binding endonuclease, which is required for the initiation of mRNA decay. This model is supported by the finding that increasing the distance from the 5' end to the start codon resulted in a 2.5-fold decrease in the mRNA half-life. These results underscore the importance of the 5' end to mRNA stability in B. subtilis.
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Affiliation(s)
- Josh S Sharp
- Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York University, New York, New York 10029, USA
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25
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Hambraeus G, von Wachenfeldt C, Hederstedt L. Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs. Mol Genet Genomics 2003; 269:706-14. [PMID: 12884008 DOI: 10.1007/s00438-003-0883-6] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2003] [Accepted: 06/08/2003] [Indexed: 10/26/2022]
Abstract
We have used DNA microarrays to survey rates of mRNA decay on a genomic scale in early stationary-phase cultures of Bacillus subtilis. The decay rates for mRNAs corresponding to about 1500 genes could be estimated. About 80% of these mRNAs had a half-life of less than 7 min. More than 30 mRNAs, including both mono- and polycistronic transcripts, were found to be extremely stable, i.e. to have a half-life of > or =15 min. Only two such transcripts were known previously in B. subtilis. The results provide the first overview of mRNA decay rates in a gram-positive bacterium and help to identify polycistronic operons. We could find no obvious correlation between the stability of an mRNA and the function of the encoded protein. We have also not found any general features in the 5' regions of mRNAs that distinguish stable from unstable transcripts. The identified set of extremely stable mRNAs may be useful in the construction of stable recombinant genes for the overproduction of biomolecules in Bacillus species.
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Affiliation(s)
- G Hambraeus
- Department of Cell and Organism Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
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26
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Abstract
This review focuses on the enzymes and pathways of RNA processing and degradation in Bacillus subtilis, and compares them to those of its gram-negative counterpart, Escherichia coli. A comparison of the genomes from the two organisms reveals that B. subtilis has a very different selection of RNases available for RNA maturation. Of 17 characterized ribonuclease activities thus far identified in E. coli and B. subtilis, only 6 are shared, 3 exoribonucleases and 3 endoribonucleases. Some enzymes essential for cell viability in E. coli, such as RNase E and oligoribonuclease, do not have homologs in B. subtilis, and of those enzymes in common, some combinations are essential in one organism but not in the other. The degradation pathways and transcript half-lives have been examined to various degrees for a dozen or so B. subtilis mRNAs. The determinants of mRNA stability have been characterized for a number of these and point to a fundamentally different process in the initiation of mRNA decay. While RNase E binds to the 5' end and catalyzes the rate-limiting cleavage of the majority of E. coli RNAs by looping to internal sites, the equivalent nuclease in B. subtilis, although not yet identified, is predicted to scan or track from the 5' end. RNase E can also access cleavage sites directly, albeit less efficiently, while the enzyme responsible for initiating the decay of B. subtilis mRNAs appears incapable of direct entry. Thus, unlike E. coli, RNAs possessing stable secondary structures or sites for protein or ribosome binding near the 5' end can have very long half-lives even if the RNA is not protected by translation.
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Affiliation(s)
- Ciarán Condon
- UPR 9073, Institut de Biologie Physico-Chimique, 75005 Paris, France.
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27
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Hambraeus G, Karhumaa K, Rutberg B. A 5' stem-loop and ribosome binding but not translation are important for the stability of Bacillus subtilis aprE leader mRNA. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1795-1803. [PMID: 12055299 DOI: 10.1099/00221287-148-6-1795] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Bacillus subtilis aprE leader is a determinant of extreme mRNA stability. The authors examined what properties of the aprE leader confer stability on an mRNA. The secondary structure of the aprE leader mRNA was analysed in vitro and in vivo, and mutations were introduced into different domains of an aprE leader-lacZ fusion. The half-lives of the corresponding transcripts were determined and beta-galactosidase activities were measured. Removal of a stem-loop structure at the 5' end or diminishing the strength of the RBS reduced the half-lives from more than 25 min to about 5 min. Interfering with translation by abolishing the start codon or creating an early stop codon had no or little effect on mRNA stability. The authors conclude that a 5' stem-loop and binding of ribosomes are necessary for the stability of aprE leader mRNA. The present results, together with a number of other data, suggest that translation of a B. subtilis mRNA is generally not important for its stability; the situation seems different in Escherichia coli. It is further concluded that the calculated strength of a B. subtilis RBS cannot be used to predict the stability of the corresponding transcript.
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Affiliation(s)
- Gustav Hambraeus
- Department of Microbiology, Lund University, Sölvegatan 12, SE-223 62 Lund, Sweden1
| | - Kaisa Karhumaa
- Department of Microbiology, Lund University, Sölvegatan 12, SE-223 62 Lund, Sweden1
| | - Blanka Rutberg
- Department of Microbiology, Lund University, Sölvegatan 12, SE-223 62 Lund, Sweden1
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28
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Drider D, DiChiara JM, Wei J, Sharp JS, Bechhofer DH. Endonuclease cleavage of messenger RNA in Bacillus subtilis. Mol Microbiol 2002; 43:1319-29. [PMID: 11918816 DOI: 10.1046/j.1365-2958.2002.02830.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A deletion derivative of the ermC gene was constructed that expresses a 254-nucleotide mRNA. The small size of this mRNA facilitated the detection of processing products that did not differ greatly in size from the full-length transcript. In the presence of erythromycin, which induces ribosome stalling near the 5' end of ermC mRNA, the 254-nucleotide mRNA was cleaved endonucleolytically at the site of ribosome stalling. Only the downstream product of this cleavage was detectable; the upstream product was apparently too unstable to be detected. The downstream cleavage product accumulated at times after rifampicin addition, suggesting that the stalled ribosome at the 5' end conferred stability to this RNA fragment. Neither Bs-RNase III nor RNase M5, the two known narrow-specificity endoribonucleases of Bacillus subtilis, was responsible for this cleavage. These results indicate the presence in B. subtilis of another specific endoribonuclease, which may be ribosome associated.
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Affiliation(s)
- Djamel Drider
- Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, Box 1603, 1 Gustave Levy Place, New York, NY 10029, USA
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29
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Grunberg-Manago M. Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annu Rev Genet 2000; 33:193-227. [PMID: 10690408 DOI: 10.1146/annurev.genet.33.1.193] [Citation(s) in RCA: 237] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The stability of mRNA in prokaryotes depends on multiple factors and it has not yet been possible to describe the process of mRNA degradation in terms of a unique pathway. However, important advances have been made in the past 10 years with the characterization of the cis-acting RNA elements and the trans-acting cellular proteins that control mRNA decay. The trans-acting proteins are mainly four nucleases, two endo- (RNase E and RNase III) and two exonucleases (PNPase and RNase II), and poly(A) polymerase. RNase E and PNPase are found in a multienzyme complex called the degradosome. In addition to the host nucleases, phage T4 encodes a specific endonuclease called RegB. The cis-acting elements that protect mRNA from degradation are stable stem-loops at the 5' end of the transcript and terminators or REP sequences at their 3' end. The rate-limiting step in mRNA decay is usually an initial endonucleolytic cleavage that often occurs at the 5' extremity. This initial step is followed by directional 3' to 5' degradation by the two exonucleases. Several examples, reviewed here, indicate that mRNA degradation is an important step at which gene expression can be controlled. This regulation can be either global, as in the case of growth rate-dependent control, or specific, in response to changes in the environmental conditions.
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30
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Abstract
Messenger RNAs in prokaryotes exhibit short half-lives when compared with eukaryotic mRNAs. Considerable progress has been made during recent years in our understanding of mRNA degradation in bacteria. Two major aspects determine the life span of a messenger in the bacterial cell. On the side of the substrate, the structural features of mRNA have a profound influence on the stability of the molecule. On the other hand, there is the degradative machinery. Progress in the biochemical characterization of proteins involved in mRNA degradation has made clear that RNA degradation is a highly organized cellular process in which several protein components, and not only nucleases, are involved. In Escherichia coli, these proteins are organized in a high molecular mass complex, the degradosome. The key enzyme for initial events in mRNA degradation and for the assembly of the degradosome is endoribonuclease E. We discuss the identified components of the degradosome and its mode of action. Since research in mRNA degradation suffers from dominance of E. coli-related observations we also look to other organisms to ask whether they could possibly follow the E. coli standard model.
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Affiliation(s)
- R Rauhut
- Institut für Mikro- und Molekularbiologie der Justus-Liebig-Universität Giessen, Germany.
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31
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Joyce SA, Dreyfus M. In the absence of translation, RNase E can bypass 5' mRNA stabilizers in Escherichia coli. J Mol Biol 1998; 282:241-54. [PMID: 9735284 DOI: 10.1006/jmbi.1998.2027] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Bacilli, ribosomes or 30 S ribosomal subunits that are stalled or bound on mRNAs can stabilize downstream regions, hence the view that the degradation machinery scans mRNAs from their 5' end. In E. coli, several mRNAs can also be stabilized by secondary structures involving their 5' end. To test whether a bound 30 S subunit can act as a 5' stabilizer in E. coli, we compare here the stabilities of two untranslated variants of the lacZ mRNA, the decay of which is controlled by RNase E. In the first variant, a 35 nt region including the Ribosome Binding Site (RBS) is deleted, whereas in the second it is replaced by an 11 nt-long Shine-Dalgarno (SD) sequence lacking an associated start codon. In the latter variant, an 80 nt fragment encompassing the SD and extending up to the mRNA 5' end was stable in vivo (t1/2>one hour), reflecting 30 S binding. Yet, the full-length message was not more stable than when the SD was absent, although two small decay intermediates retaining the 5' end appear somewhat stabilized. A third variant was constructed in which the RBS is replaced by an insert which can fold back onto the lac leader, creating a putative hairpin involving the mRNA 5' end. The fragment corresponding to this hairpin was stable but, again, the full-length message was not stabilized. Thus, the untranslated lacZ mRNA cannot be protected against RNase E by 5' stabilizers, suggesting that mRNA scanning is not an obligate feature of RNase E-controlled degradation. Altogether, these results suggest important differences in mRNA degradation between E. coli and B. subtilis. In addition, we show that mRNA regions involved in stable hairpins or Shine-Dalgarno pairings can be metabolically stable in E. coli.
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Affiliation(s)
- S A Joyce
- Laboratoire de Génétique Moléculaire, CNRS URA 1302, Ecole Normale Supérieure, 46 rue d'Ulm, Paris, 75230, France
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32
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Abstract
We undertook the study of the decay process of the cry1Aa mRNA of Bacillus thuringiensis expressed in B. subtilis. The cry1Aa transcript is a 3.7-kb mRNA expressed during sporulation whose transcriptional control has previously been studied in both B. subtilis and B. thuringiensis. We found that the cry1Aa mRNA has a half-life of around 9 min and that its decay occurs through endoribonucleolytic cleavages which result in three groups of high-molecular-weight mRNA intermediates ranging in size from 2.7 to 0.5 kb. A comparative study carried out with Escherichia coli showed a similar pattern of degradation intermediates. Primer extension analysis carried out on RNA from B. subtilis revealed that most cleavages occur within two regions located toward the 5' and 3' ends of the mRNA. The most prominent processing site observed for the cry1Aa mRNA isolated from B. subtilis is only two bases away from that occurring on RNA isolated from E. coli. Most cleavage sites occur at seemingly single-stranded RNA segments rich in A and U nucleotides, suggesting that a common and conserved mechanism may process the cry1Aa mRNA.
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MESH Headings
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Bacillus thuringiensis/genetics
- Bacillus thuringiensis/metabolism
- Bacillus thuringiensis Toxins
- Bacterial Proteins/genetics
- Bacterial Toxins
- Base Composition
- Blotting, Northern
- Cloning, Molecular
- Endoribonucleases/metabolism
- Endotoxins/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Hemolysin Proteins
- Nucleic Acid Conformation
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Spores, Bacterial
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Affiliation(s)
- C Vázquez-Cruz
- Departamento de Ingeniería Genética, CINVESTAV IPN, Unidad Irapuato, Guanajuato, México
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33
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Abstract
To study the role of mRNA termination in the regulation of ermK, we introduced mismatches into terminators by in vitro mutagenesis. In wild-type ermK, only truncated transcription products were detected in the absence of induction. In contrast, only the full-length transcript was synthesized in the terminator 1 and terminator 2 double mutants, even in the absence of erythromycin. These results indicate that the expression of ermK is primarily regulated by transcriptional attenuation rather than translational attenuation. We also tested the possible contribution of translational attenuation control to the regulation of ermK by constructing a triple mutant (terminator 1 plus terminator 2 plus the methylase Shine-Dalgarno region). A higher level of beta-galactosidase synthesis was seen in the triple mutant. Therefore, unlike with previously described attenuators, it can be concluded that both transcriptional and translational attenuation contribute to the regulation of ermK, although transcriptional attenuation plays a larger role.
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Affiliation(s)
- S S Choi
- College of Pharmacy, Seoul National University, Korea
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34
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Abstract
Progress in our understanding of several biological processes promises to broaden the usefulness of Escherichia coli as a tool for gene expression. There is an expanding choice of tightly regulated prokaryotic promoters suitable for achieving high-level gene expression. New host strains facilitate the formation of disulfide bonds in the reducing environment of the cytoplasm and offer higher protein yields by minimizing proteolytic degradation. Insights into the process of protein translocation across the bacterial membranes may eventually make it possible to achieve robust secretion of specific proteins into the culture medium. Studies involving molecular chaperones have shown that in specific cases, chaperones can be very effective for improved protein folding, solubility, and membrane transport. Negative results derived from such studies are also instructive in formulating different strategies. The remarkable increase in the availability of fusion partners offers a wide range of tools for improved protein folding, solubility, protection from proteases, yield, and secretion into the culture medium, as well as for detection and purification of recombinant proteins. Codon usage is known to present a potential impediment to high-level gene expression in E. coli. Although we still do not understand all the rules governing this phenomenon, it is apparent that "rare" codons, depending on their frequency and context, can have an adverse effect on protein levels. Usually, this problem can be alleviated by modification of the relevant codons or by coexpression of the cognate tRNA genes. Finally, the elucidation of specific determinants of protein degradation, a plethora of protease-deficient host strains, and methods to stabilize proteins afford new strategies to minimize proteolytic susceptibility of recombinant proteins in E. coli.
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Affiliation(s)
- S C Makrides
- Department of Molecular Biology, T Cell Sciences, Inc., Needham, Massachusetts 02194, USA
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35
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Le Chatelier E, Ehrlich SD, Jannière L. Countertranscript-driven attenuation system of the pAM beta 1 repE gene. Mol Microbiol 1996; 20:1099-112. [PMID: 8809762 DOI: 10.1111/j.1365-2958.1996.tb02550.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The plasmid-encoded RepE protein is absolutely essential and rate-limiting for replication of the promiscuous plasmid pAM beta 1 originating from Enterococcus faecalis. We previously showed that the rep gene is transcribed from a promoter that is negatively regulated (approximately 10-fold reduction) by the CopF repressor. In this report, we show that this transcription is decreased a further approximately 10-times by a countertranscript-driven transcriptional attenuation system. Extensive mutagenesis revealed that this system operates by a mechanism similar to that previously described for the unrelated repC gene of plasmid pT181.
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Affiliation(s)
- E Le Chatelier
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
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36
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Nierlich DP, Murakawa GJ. The decay of bacterial messenger RNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 52:153-216. [PMID: 8821261 DOI: 10.1016/s0079-6603(08)60967-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- D P Nierlich
- Department of Microbiology and Molecular Genetics, University of California, Los Angeles 90024, USA
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37
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Weisblum B. Insights into erythromycin action from studies of its activity as inducer of resistance. Antimicrob Agents Chemother 1995; 39:797-805. [PMID: 7785974 PMCID: PMC162632 DOI: 10.1128/aac.39.4.797] [Citation(s) in RCA: 179] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- B Weisblum
- Department of Pharmacology, University of Wisconsin Medical School, Madison 53706, USA
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38
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Abstract
Post-transcriptional mechanisms operate in regulation of gene expression in bacteria, the amount of a given gene product being also dependent on the inactivation rate of its own message. Moreover, segmental differences in mRNA stability of polycistronic transcripts may be responsible for differential expression of genes clustered in operons. Given the absence of 5' to 3' exoribonucleolytic activities in prokaryotes, both endoribonucleases and 3' to 5' exoribonucleases are involved in chemical decay of mRNA. As the 3' to 5' exoribonucleolytic activities are readily blocked by stem-loop structures which are usual at the 3' ends of bacterial messages, the rate of decay is primarily determined by the rate of the first endonucleolytic cleavage within the transcripts, after which the resulting mRNA intermediates are degraded by the 3' to 5' exoribonucleases. Consequently, the stability of a given transcript is determined by the accessibility of suitable target sites to endonucleolytic activities. A considerable number of bacterial messages decay with a net 5' to 3' directionality. Two different alternative models have been proposed to explain such a finding, the first invoking the presence of functional coupling between degradation and the movement of the ribosomes along the transcripts, the second one implying the existence of a 5' to 3' processive '5' binding nuclease'. The different systems by which these two current models of mRNA decay have been tested will be presented with particular emphasis on polycistronic transcripts.
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Affiliation(s)
- P Alifano
- Dipartimento di Biologia e Patologia Cellulare e Molecolare L. Califano, Università di Napoli Federico II, Italy
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39
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Abstract
Ribosome stalling in the leader region of ermC mRNA results in a 10-15-fold increase in ermC mRNA half-life in Bacillus subtilis. Fusion of the ermC 5' regulatory region to several B. subtilis coding sequences resulted in induced stability of the fusion RNAs, showing that the ermC 5' region acts as a general '5' stabilizer'. RNA products of an ermC-lacZ transcriptional fusion were inducibly stable in the complete absence of translation and included a small RNA that is likely to be a decay product arising by blockage of a 3'-to-5' exoribonuclease activity. Insertion of sequences that encode endonucleolytic cleavage sites into the ermC coding sequence resulted in cleavage products whose stability depended on the nature of their 5' and 3' ends. It can be concluded from this study that initiation of mRNA decay in B. subtilis generally occurs at or near the 5' terminus.
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Affiliation(s)
- J F DiMari
- Department of Biochemistry, Mount Sinai School of Medicine, New York, New York 10029
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40
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Bouvet P, Belasco JG. Control of RNase E-mediated RNA degradation by 5'-terminal base pairing in E. coli. Nature 1992; 360:488-91. [PMID: 1280335 DOI: 10.1038/360488a0] [Citation(s) in RCA: 189] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Despite the variety of messenger RNA half-lives in bacteria (0.5-30 min in Escherichia coli) and their importance in controlling gene expression, their molecular basis remains obscure. The lifetime of an entire mRNA molecule can be determined by features near its 5' end, but no 5' exoribonuclease has been identified in any prokaryotic organism. A mutation that inactivates E. coli RNase E also increases the average lifetime of bulk E. coli mRNA and of many individual messages, suggesting that cleavage by this endonuclease may be the rate-determining step in the degradation of most mRNAs in E. coli. We have investigated the substrate preference of RNase E in E. coli by using variants of RNA I, a small untranslated RNA whose swift degradation in vivo is initiated by RNase E cleavage at an internal site. We report here that RNase E has an unprecedented substrate specificity for an endoribonuclease, as it preferentially cleaves RNAs that have several unpaired nucleotides at the 5' end. The sensitivity of RNase E to 5'-terminal base pairing may explain how determinants near the 5' end can control rates of mRNA decay in bacteria.
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Affiliation(s)
- P Bouvet
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
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41
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Abstract
The expression of the chloramphenicol-inducible chloramphenicol-acetyltransferase gene (cat), encoded on Staphylococcus aureus plasmid pUB112, is regulated via a translational attenuation mechanism. Ribosomes, which are arrested by chloramphenicol during synthesis of a short leader peptide, activate catmRNA translation by opening a 5'-located stem-loop structure, thus setting free the cat ribosome-binding site. We have determined the 5' and 3' ends of catmRNA and analysed its stability in Bacillus subtilis. In the absence of the antibiotic, the half-life of catmRNA is shorter than 0.5 min; it is enhanced to about 8 min by sub-inhibitory concentrations of the drug. No decay intermediates of catmRNA could be detected, indicating a very fast degradation after an initial rate-limiting step. ochre nonsense mutations in the 5' region of the cat structural gene, which eliminate catmRNA translation, did not affect its chloramphenicol-induced stabilization. Mutations in the leader-peptide coding region, which abolish ribosome stalling and, therefore, cat gene induction, also eliminate catmRNA stabilization. We conclude that catmRNA is stabilized on induction by a chloramphenicol-arrested ribosome, which physically protects a nuclease-sensitive target site in the 5' region of catmRNA against exo- or endonucleolytic initiation of degradation. This protection is analogous to ermA and ermC mRNA and seems to reflect a general mechanism for stabilization of mRNA derived from inducible antibiotic resistance genes in B. subtilis.
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Affiliation(s)
- J Dreher
- Molekulare Genetik der Universität, Heidelberg, Germany
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42
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Kwak JH, Choi EC, Weisblum B. Transcriptional attenuation control of ermK, a macrolide-lincosamide-streptogramin B resistance determinant from Bacillus licheniformis. J Bacteriol 1991; 173:4725-35. [PMID: 1713206 PMCID: PMC208150 DOI: 10.1128/jb.173.15.4725-4735.1991] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
ermK instructs bacteria to synthesize an erythromycin-inducible 23S rRNA methylase that confers resistance to the macrolide, lincosamide, and streptogramin B antibiotics. Expression of ermK is regulated by transcriptional attenuation, in contrast to other inducible erm genes, previously described, which are regulated translationally. The ermK mRNA leader sequence has a total length of 357 nucleotides and encodes a 14-amino-acid leader peptide together with its ribosome binding site. Additionally, the mRNA leader sequence can fold in either of two mutually exclusive conformations, one of which is postulated to form in the absence of induction and to contain two rho factor-independent terminators. Truncated transcription products ca. 210 and 333 nucleotides long were synthesized in the absence of induction, both in vivo and in vitro, as predicted by the transcriptional attenuation model; run-off transcription in vitro with rITP favored the synthesis of the full-length run-off transcript over that of the 210- and 333-nucleotide truncated products. Northern (RNA) blot analysis of transcripts synthesized in vivo in the absence of erythromycin indicated that transcription terminated at either of the two inverted complementary repeat sequences in the leader that were postulated to serve as rho factor-independent terminators; moreover, no full-length transcripts were detectable in the uninduced samples. In contrast, full-length (ca. 1,200-nucleotide) transcripts were only detected in RNA samples synthesized in vivo in the presence of erythromycin. Full-length transcripts formed in the absence of induction from transcriptional readthrough past the two proposed transcription terminators would fold in a way that would sequester the ribosome binding site together with the first two codons of the ErmK methylase, reducing its efficiency in translation. This feature could therefore provide additional control of expression in the absence of induction; however, such regulation, if operative, would act only secondarily, both in time and place, relative to transcriptional control. Analysis by reverse transcriptase mapping of in vivo transcripts from two primers that bracket the transcription terminator responsible for the 210-nucleotide truncated fragment supports the transcriptional attenuation model proposed and suggests further that the synthesis of the ermK message is initiated constitutively upstream of the proposed terminator but completed inductively downstream of this site.
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Affiliation(s)
- J H Kwak
- College of Pharmacy, Seoul National University, Korea
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43
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Leclercq R, Courvalin P. Bacterial resistance to macrolide, lincosamide, and streptogramin antibiotics by target modification. Antimicrob Agents Chemother 1991; 35:1267-72. [PMID: 1929280 PMCID: PMC245156 DOI: 10.1128/aac.35.7.1267] [Citation(s) in RCA: 419] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- R Leclercq
- Service de Bactériologie-Virologie-Hygiène, Hôpital Henri Mondor, Université Paris XII, Créteil, France
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44
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Abstract
Induction of translation of the ermC gene product in Bacillus subtilis occurs upon exposure to erythromycin and is a result of ribosome stalling in the ermC leader peptide coding sequence. Another result of ribosome stalling is stabilization of ermC mRNA. The effect of leader RNA secondary structure, methylase translation, and leader peptide translation on induced ermC mRNA stability was examined by constructing various mutations in the ermC leader region. Analysis of deletion mutations showed that ribosome stalling causes induction of ermC mRNA stability in the absence of methylase translation and ermC leader RNA secondary structure. Furthermore, deletions that removed much of the leader peptide coding sequence had no effect on induced ermC mRNA stability. A leader region mutation was constructed such that ribosome stalling occurred in a position upstream of the natural stall site, resulting in induced mRNA stability without induction of translation. This mutation was used to measure the effect of mRNA stabilization on ermC gene expression.
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Affiliation(s)
- K K Hue
- Department of Biochemistry, Mount Sinai School of Medicine, New York, New York 10029-6574
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45
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Beattie DT, Knapp S, Mekalanos JJ. Evidence that modulation requires sequences downstream of the promoters of two vir-repressed genes of Bordetella pertussis. J Bacteriol 1990; 172:6997-7004. [PMID: 2174866 PMCID: PMC210820 DOI: 10.1128/jb.172.12.6997-7004.1990] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Gene expression in Bordetella pertussis is altered by environmental signals in a process called antigenic modulation. In the presence of modulating signals, expression of several known virulence factors and outer membrane proteins is coordinately reduced. From a bank of TnphoA fusions, we have identified five genes whose expression profiles are reciprocal of those of the major virulence determinants; that is, alkaline phosphatase activity is maximal during growth in the presence of the modulators nicotinic acid and MgSO4 (S. Knapp and J. J. Mekalanos, J. Bacteriol. 170:5059-5066, 1988). We have called these loci vir-repressed genes (vrg). Two of these gene fusions (vrg-6 and vrg-18) have been cloned in Escherichia coli, returned on low-copy-number plasmids to several strains of B. pertussis, and found to be regulated similarly to the fusions harbored on the chromosome. Deletions of the two vrg promoters were constructed and returned to B. pertussis. Regulation was maintained even when all but 24 nucleotides upstream of the vrg-18 initiation codon and 60 nucleotides upstream of the vrg-6 initiation codon were deleted, suggesting that cis-acting regulatory elements of these genes lie very near or within the coding region. We observed a 21-base palindromic sequence overlapping an 8-base direct repeat within the signal sequence coding region of vrg-6; insertion of a 6-bp linker in this region abolished regulation. These repetitive sequences are also at the site of greatest primary sequence identify between vrg-6 and vrg-18 and correspond to the signal sequence coding region. We propose models that involve recognition of this region by a vir-regulated gene product.
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Affiliation(s)
- D T Beattie
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
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46
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Régnier P, Grunberg-Manago M. RNase III cleavages in non-coding leaders of Escherichia coli transcripts control mRNA stability and genetic expression. Biochimie 1990; 72:825-34. [PMID: 2085545 DOI: 10.1016/0300-9084(90)90192-j] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The primary transcripts of the rpsO-pnp, rnc-era-recO and metY-nusA-infB operons of E coli are each processed by RNase III, upstream of the first translated gene, in hair-pin structures formed by the 5' non-coding leader. The mRNAs of the 3 operons, of which the 5' terminal motifs have been removed by RNase III, decay significantly more rapidly than the uncut transcripts which accumulate in the RNase III deficient strain. The rapid decay of a primary transcript of the metY-nusA-infB operon, initiated at a secondary promoter in the vicinity of the RNase III sites, suggests that the 5' features upstream of the RNase III cutting sites are responsible for the stability of the uncut RNAs. RNase III autocontrols its own expression by removing the 5' motif which stabilizes its mRNA. Similarly, the synthesis of polynucleotide phosphorylase and of protein Era are also controlled by RNase III cleavages which trigger the degradation of their messengers. The role of RNase III in the regulation of gene expression and the possible mechanisms of mRNA stabilization and of 5' to 3' decay initiated by RNase III processing are discussed.
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47
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Abstract
The ermC gene confers resistance to MLS antibiotics in a Bacillus subtilis host. Synthesis of the ermC gene product, a ribosomal RNA methylase, is inducible by the addition of subinhibitory concentrations of erythromycin. Regulation of ermC gene expression occurs at the post-transcriptional level in three ways: translational attenuation, translational autoregulation, and messenger RNA stabilization.
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Affiliation(s)
- D H Bechhofer
- Department of Biochemistry, Mount Sinai School of Medicine, New York, New York 10029
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48
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Rogers EJ, Lovett PS. Erythromycin induces expression of the chloramphenicol acetyltransferase gene cat-86. J Bacteriol 1990; 172:4694-5. [PMID: 2115875 PMCID: PMC213306 DOI: 10.1128/jb.172.8.4694-4695.1990] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The plasmid gene cat-86 specifies chloramphenicol-inducible chloramphenicol acetyltransferase in Bacillus subtilis. This gene, like the erythromycin-inducible erm genes, is regulated by translational attenuation. Here we show that cat-86 is also inducibly regulated by erythromycin. cat-86 does not confer resistance to erythromycin.
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Affiliation(s)
- E J Rogers
- Department of Biological Sciences, University of Maryland Baltimore County, Catonsville 21228
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49
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Mayford M, Weisblum B. The ermC leader peptide: amino acid alterations leading to differential efficiency of induction by macrolide-lincosamide-streptogramin B antibiotics. J Bacteriol 1990; 172:3772-9. [PMID: 2113911 PMCID: PMC213355 DOI: 10.1128/jb.172.7.3772-3779.1990] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The inducibility of ermC by erythromycin, megalomicin, and celesticetin was tested with both wild-type ermC and several regulatory mutants altered in the 19-amino-acid-residue leader peptide, MGIFSIFVISTVHYQP NKK. In the model test system that was used, the ErmC methylase was translationally fused to beta-galactosidase. Mutational alterations that mapped in the interval encoding Phe-4 through Ile-9 of the leader peptide not only affected induction by individual antibiotics, but did so differentially. The subset of mutations that affected inducibility by the two macrolides erythromycin and megalomicin overlapped and were distinct from the subset of mutations that affected induction by celesticetin. These studies provide a model system for experimentally varying the relative efficiencies with which different antibiotics induce the expression of ermC. The possibility that antibiotics with inducing activity interact directly with the nascent leader peptide was tested by using a chemically synthesized decapeptide, MGIFSIFVIS--, attached at its C-terminus to a solid-phase support. This peptide, however, failed to bind erythromycin in vitro.
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Affiliation(s)
- M Mayford
- Department of Molecular Biology, University of Wisconsin, Madison
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