51
|
Kelly CL, Harris AWK, Steel H, Hancock EJ, Heap JT, Papachristodoulou A. Synthetic negative feedback circuits using engineered small RNAs. Nucleic Acids Res 2019; 46:9875-9889. [PMID: 30212900 PMCID: PMC6182179 DOI: 10.1093/nar/gky828] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/06/2018] [Indexed: 12/13/2022] Open
Abstract
Negative feedback is known to enable biological and man-made systems to perform reliably in the face of uncertainties and disturbances. To date, synthetic biological feedback circuits have primarily relied upon protein-based, transcriptional regulation to control circuit output. Small RNAs (sRNAs) are non-coding RNA molecules that can inhibit translation of target messenger RNAs (mRNAs). In this work, we modelled, built and validated two synthetic negative feedback circuits that use rationally-designed sRNAs for the first time. The first circuit builds upon the well characterised tet-based autorepressor, incorporating an externally-inducible sRNA to tune the effective feedback strength. This allows more precise fine-tuning of the circuit output in contrast to the sigmoidal, steep input–output response of the autorepressor alone. In the second circuit, the output is a transcription factor that induces expression of an sRNA, which inhibits translation of the mRNA encoding the output, creating direct, closed-loop, negative feedback. Analysis of the noise profiles of both circuits showed that the use of sRNAs did not result in large increases in noise. Stochastic and deterministic modelling of both circuits agreed well with experimental data. Finally, simulations using fitted parameters allowed dynamic attributes of each circuit such as response time and disturbance rejection to be investigated.
Collapse
Affiliation(s)
- Ciarán L Kelly
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK.,Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Andreas W K Harris
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Edward J Hancock
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | | |
Collapse
|
52
|
Gottesman S. Trouble is coming: Signaling pathways that regulate general stress responses in bacteria. J Biol Chem 2019; 294:11685-11700. [PMID: 31197038 DOI: 10.1074/jbc.rev119.005593] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria can rapidly and reversibly respond to changing environments via complex transcriptional and post-transcriptional regulatory mechanisms. Many of these adaptations are specific, with the regulatory output tailored to the inducing signal (for instance, repairing damage to cell components or improving acquisition and use of growth-limiting nutrients). However, the general stress response, activated in bacterial cells entering stationary phase or subjected to nutrient depletion or cellular damage, is unique in that its common, broad output is induced in response to many different signals. In many different bacteria, the key regulator for the general stress response is a specialized sigma factor, the promoter specificity subunit of RNA polymerase. The availability or activity of the sigma factor is regulated by complex regulatory circuits, the majority of which are post-transcriptional. In Escherichia coli, multiple small regulatory RNAs, each made in response to a different signal, positively regulate translation of the general stress response sigma factor RpoS. Stability of RpoS is regulated by multiple anti-adaptor proteins that are also synthesized in response to different signals. In this review, the modes of signaling to and levels of regulation of the E. coli general stress response are discussed. They are also used as a basis for comparison with the general stress response in other bacteria with the aim of extracting key principles that are common among different species and highlighting important unanswered questions.
Collapse
Affiliation(s)
- Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| |
Collapse
|
53
|
Kim W, Choi JS, Kim D, Shin D, Suk S, Lee Y. Mechanisms for Hfq-Independent Activation of rpoS by DsrA, a Small RNA, in Escherichia coli. Mol Cells 2019; 42:426-439. [PMID: 31085808 PMCID: PMC6537650 DOI: 10.14348/molcells.2019.0040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Many small RNAs (sRNAs) regulate gene expression by base pairing to their target messenger RNAs (mRNAs) with the help of Hfq in Escherichia coli. The sRNA DsrA activates translation of the rpoS mRNA in an Hfq-dependent manner, but this activation ability was found to partially bypass Hfq when DsrA is overproduced. The precise mechanism by which DsrA bypasses Hfq is unknown. In this study, we constructed strains lacking all three rpoS-activating sRNAs (i.e., ArcZ, DsrA, and RprA) in hfq+ and Hfq- backgrounds, and then artificially regulated the cellular DsrA concentration in these strains by controlling its ectopic expression. We then examined how the expression level of rpoS was altered by a change in the concentration of DsrA. We found that the translation and stability of the rpoS mRNA are both enhanced by physiological concentrations of DsrA regardless of Hfq, but that depletion of Hfq causes a rapid degradation of DsrA and thereby decreases rpoS mRNA stability. These results suggest that the observed Hfq dependency of DsrA-mediated rpoS activation mainly results from the destabilization of DsrA in the absence of Hfq, and that DsrA itself contributes to the translational activation and stability of the rpoS mRNA in an Hfq-independent manner.
Collapse
Affiliation(s)
- Wonkyong Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Jee Soo Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Daun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Doohang Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Shinae Suk
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Younghoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| |
Collapse
|
54
|
Stojkova P, Spidlova P, Stulik J. Nucleoid-Associated Protein HU: A Lilliputian in Gene Regulation of Bacterial Virulence. Front Cell Infect Microbiol 2019; 9:159. [PMID: 31134164 PMCID: PMC6523023 DOI: 10.3389/fcimb.2019.00159] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/26/2019] [Indexed: 12/29/2022] Open
Abstract
Nucleoid-associated proteins belong to a group of small but abundant proteins in bacterial cells. These transcription regulators are responsible for many important cellular processes and also are involved in pathogenesis of bacteria. The best-known nucleoid-associated proteins, such as HU, FIS, H-NS, and IHF, are often discussed. The most important findings in research concerning HU protein are described in this mini review. Its roles in DNA compaction, shape modulation, and negative supercoiling induction have been studied intensively. HU protein regulates bacteria survival, growth, SOS response, virulence genes expression, cell division, and many other cell processes. Elucidating the mechanism of HU protein action has been the subject of many research projects. This mini review provides a comprehensive overview of the HU protein.
Collapse
Affiliation(s)
| | - Petra Spidlova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
| | | |
Collapse
|
55
|
Zhao S, Zhang K, Jiang S, Liu Z, Wang Z, Wang Y, Liu B. Resonance assignments of sigma factor S binding protein Crl from Escherichia coli. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:223-226. [PMID: 30806877 DOI: 10.1007/s12104-019-09881-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
During bacterial transcription, sigma (σ) factors reversibly bind to RNA polymerase (RNAP) and recognize specific promoter sequences to initiate the process. While different sigma factors are utilized under different external conditions, Sigma S (RpoS, σS), a stress-responding sigma factor, is activated when bacteria face external threats. σS, which has a much lower affinity to RNAP compared with sigma D (RpoD, σ70), is controlled by a very complex network of regulatory factors. Crl protein, a transcriptional factor from Escherichia coli (E. coli, Ec), stimulates σS-dependent transcription by promoting the association of σS with core RNA polymerase. As an important regulator for σS, Crl is induced by low temperature, leading to an increased transcription rate of a subset of genes of the rpoS regulon under stress conditions or in stationary phase of growth. However, the underlying molecular mechanism for Crl/σS remains elusive. Here we describe the complete 1H, 13C and 15N chemical shift assignments of Crl as the basis for NMR structure determination and interaction studies.
Collapse
Affiliation(s)
- Siyu Zhao
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Kaining Zhang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Songzi Jiang
- National Facility for Protein Science, Zhangjiang Laboratory, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Zhijun Liu
- National Facility for Protein Science, Zhangjiang Laboratory, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Zhihao Wang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Yawen Wang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China.
| | - Bing Liu
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China.
| |
Collapse
|
56
|
Schachterle JK, Zeng Q, Sundin GW. Three Hfq-dependent small RNAs regulate flagellar motility in the fire blight pathogen Erwinia amylovora. Mol Microbiol 2019; 111:1476-1492. [PMID: 30821016 DOI: 10.1111/mmi.14232] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 12/13/2022]
Abstract
Erwinia amylovora, the causative agent of fire blight disease of apple and pear trees, causes disease on flowers by invading natural openings at the base of the floral cup. To reach these openings, the bacteria use flagellar motility to swim from stigma tips to the hypanthium and through nectar. We have previously shown that the Hfq-dependent sRNAs ArcZ, OmrAB and RmaA regulate swimming motility in E. amylovora. Here, we tested these three sRNAs to determine at what regulatory level they exert their effects and to what extent they can complement each other. We found that ArcZ and OmrAB repress the flagellar master regulator flhD post-transcriptionally. We also found that ArcZ and RmaA positively regulate flhD at the transcriptional level. The role of ArcZ as an activator of flagellar motility appears to be unique to E. amylovora and may have recently evolved. Our results suggest that the Hfq-dependent sRNAs ArcZ, OmrAB and RmaA play an integral role in regulation of flagellar motility by acting primarily on the master regulator, FlhD, but also through additional factors.
Collapse
Affiliation(s)
- Jeffrey K Schachterle
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Quan Zeng
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA.,Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
57
|
Parmeciano Di Noto G, Molina MC, Quiroga C. Insights Into Non-coding RNAs as Novel Antimicrobial Drugs. Front Genet 2019; 10:57. [PMID: 30853970 PMCID: PMC6395445 DOI: 10.3389/fgene.2019.00057] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/24/2019] [Indexed: 12/21/2022] Open
Abstract
Multidrug resistant bacteria are a serious worldwide problem, especially carbapenem-resistant Enterobacteriaceae (such as Klebsiella pneumoniae and Escherichia coli), Acinetobacter baumannii and Pseudomonas aeruginosa. Since the emergence of extensive and pan-drug resistant bacteria there are few antibiotics left to treat patients, thus novel RNA-based strategies are being considered. Here, we examine the current situation of different non-coding RNAs found in bacteria as well as their function and potential application as antimicrobial agents. Furthermore, we discuss the factors that may contribute in the efficient development of RNA-based drugs, the limitations for their implementation and the use of nanocarriers for delivery.
Collapse
Affiliation(s)
- Gisela Parmeciano Di Noto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - María Carolina Molina
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| |
Collapse
|
58
|
Grüll MP, Massé E. Mimicry, deception and competition: The life of competing endogenous RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1525. [PMID: 30761752 DOI: 10.1002/wrna.1525] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 12/22/2022]
Abstract
Since their discovery, small regulatory RNAs (sRNAs) were thought to be regulated exclusively at the transcriptional level. However, accumulating data from recent reports indicate that posttranscriptional signals can also modulate the function and stability of sRNAs. One of these posttranscriptional signals are competing endogenous RNAs (ceRNAs). Commonly called RNA sponges, ceRNAs can effectively sequester sRNAs and prevent them from binding their cognate target messenger RNAs (mRNAs). Subsequently, they prevent sRNA-dependent regulation of translation and stability of mRNA targets. While some ceRNAs seem to be expressed constitutively, others are intricately regulated according to environmental conditions. The outcome of ceRNA binding to a sRNA reaches beyond simple sequestration. Various effects observed on sRNA functions extend from reducing transcriptional noise to promote RNA turnover. Here, we present a historical perspective of the discovery of ceRNAs in eukaryotic organisms and mainly focus on the synthesis and function of select, well-described, ceRNAs in bacterial cells. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions Translation > Translation Regulation RNA Turnover and Surveillance > Regulation of RNA Stability.
Collapse
Affiliation(s)
- Marc P Grüll
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Eric Massé
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| |
Collapse
|
59
|
SraL sRNA interaction regulates the terminator by preventing premature transcription termination of rho mRNA. Proc Natl Acad Sci U S A 2019; 116:3042-3051. [PMID: 30718400 DOI: 10.1073/pnas.1811589116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription termination is a critical step in the control of gene expression. One of the major termination mechanisms is mediated by Rho factor that dissociates the complex mRNA-DNA-RNA polymerase upon binding with RNA polymerase. Rho promotes termination at the end of operons, but it can also terminate transcription within leader regions, performing regulatory functions and avoiding pervasive transcription. Transcription of rho is autoregulated through a Rho-dependent attenuation in the leader region of the transcript. In this study, we have included an additional player in this pathway. By performing MS2-affinity purification coupled with RNA sequencing (MAPS), rho transcript was shown to directly interact with the small noncoding RNA SraL. Using bioinformatic in vivo and in vitro experimental analyses, SraL was shown to base pair with the 5'-UTR of rho mRNA upregulating its expression in several growth conditions. This base pairing was shown to prevent the action of Rho over its own message. Moreover, the results obtained indicate that both ProQ and Hfq are associated with this regulation. We propose a model that contemplates the action of Salmonella SraL sRNA in the protection of rho mRNA from premature transcription termination by Rho. Note that since the interaction region between both RNAs corresponds to a very-well-conserved sequence, it is plausible to admit that this regulation also occurs in other enterobacteria.
Collapse
|
60
|
Abstract
Small regulatory RNAs are now recognized as key regulators of gene expression in bacteria. They accumulate under specific conditions, most often because their synthesis is directly controlled by transcriptional regulators, including but not limited to alternative sigma factors and response regulators of two-component systems. In turn, small RNAs regulate, mostly at the posttranscriptional level, expression of multiple genes, among which are genes encoding transcriptional regulators. Small RNAs are thus embedded in mixed regulatory circuits combining transcriptional and posttranscriptional controls, and whose properties are discussed here.
Collapse
|
61
|
De Mets F, Van Melderen L, Gottesman S. Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA. Proc Natl Acad Sci U S A 2019; 116:1043-1052. [PMID: 30591570 PMCID: PMC6338826 DOI: 10.1073/pnas.1815288116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bacterial regulatory small RNAs act as crucial regulators in central carbon metabolism by modulating translation initiation and degradation of target mRNAs in metabolic pathways. Here, we demonstrate that a noncoding small RNA, SdhX, is produced by RNase E-dependent processing from the 3'UTR of the sdhCDAB-sucABCD operon, encoding enzymes of the tricarboxylic acid (TCA) cycle. In Escherichia coli, SdhX negatively regulates ackA, which encodes an enzyme critical for degradation of the signaling molecule acetyl phosphate, while the downstream pta gene, encoding the enzyme critical for acetyl phosphate synthesis, is not significantly affected. This discoordinate regulation of pta and ackA increases the accumulation of acetyl phosphate when SdhX is expressed. Mutations in sdhX that abolish regulation of ackA lead to more acetate in the medium (more overflow metabolism), as well as a strong growth defect in the presence of acetate as sole carbon source, when the AckA-Pta pathway runs in reverse. SdhX overproduction confers resistance to hydroxyurea, via regulation of ackA SdhX abundance is tightly coupled to the transcription signals of TCA cycle genes but escapes all known posttranscriptional regulation. Therefore, SdhX expression directly correlates with transcriptional input to the TCA cycle, providing an effective mechanism for the cell to link the TCA cycle with acetate metabolism pathways.
Collapse
Affiliation(s)
- François De Mets
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, B-6041 Gosselies, Belgium
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892-5430
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, B-6041 Gosselies, Belgium
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892-5430
| |
Collapse
|
62
|
Kim K, Golubeva YA, Vanderpool CK, Slauch JM. Oxygen-dependent regulation of SPI1 type three secretion system by small RNAs in Salmonella enterica serovar Typhimurium. Mol Microbiol 2018; 111:570-587. [PMID: 30484918 DOI: 10.1111/mmi.14174] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2018] [Indexed: 01/31/2023]
Abstract
Salmonella Typhimurium induces inflammatory diarrhea and uptake into intestinal epithelial cells using the Salmonella pathogenicity island 1 (SPI1) type III secretion system (T3SS). Three AraC-like regulators, HilD, HilC and RtsA, form a feed-forward regulatory loop that activates transcription of hilA, encoding the activator of the T3SS structural genes. Many environmental signals and regulatory systems are integrated into this circuit to precisely regulate SPI1 expression. A subset of these regulatory factors affects translation of hilD, but the mechanisms are poorly understood. Here, we identified two sRNAs, FnrS and ArcZ, which repress hilD translation, leading to decreased production of HilA. FnrS and ArcZ are oppositely regulated in response to oxygen, one of the key environmental signals affecting expression of SPI1. Mutational analysis demonstrates that FnrS and ArcZ bind to the hilD mRNA 5' UTR, resulting in translational repression. Deletion of fnrS led to increased HilD production under low-aeration conditions, whereas deletion of arcZ abolished the regulatory effect on hilD translation aerobically. The fnrS arcZ double mutant has phenotypes in a mouse oral infection model consistent with increased expression of SPI1. Together, these results suggest that coordinated regulation by these two sRNAs maximizes HilD production at an intermediate level of oxygen.
Collapse
Affiliation(s)
- Kyungsub Kim
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Yekaterina A Golubeva
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Carin K Vanderpool
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - James M Slauch
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| |
Collapse
|
63
|
Malabirade A, Partouche D, El Hamoui O, Turbant F, Geinguenaud F, Recouvreux P, Bizien T, Busi F, Wien F, Arluison V. Revised role for Hfq bacterial regulator on DNA topology. Sci Rep 2018; 8:16792. [PMID: 30429520 PMCID: PMC6235962 DOI: 10.1038/s41598-018-35060-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/26/2018] [Indexed: 12/11/2022] Open
Abstract
Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNA. Besides these RNA-related functions, Hfq has also been described as one of the nucleoid associated proteins shaping the bacterial chromosome. Therefore, Hfq appears as a versatile nucleic acid-binding protein, which functions are probably even more numerous than those initially suggested. For instance, E. coli Hfq, and more precisely its C-terminal region (CTR), has been shown to induce DNA compaction into a condensed form. In this paper, we establish that DNA induces Hfq-CTR amyloidogenesis, resulting in a change of DNA local conformation. Furthermore, we clarify the effect of Hfq on DNA topology. Our results evidence that, even if the protein has a strong propensity to compact DNA thanks to its amyloid region, it does not affect overall DNA topology. We confirm however that hfq gene disruption influences plasmid supercoiling in vivo, indicating that the effect on DNA topology in former reports was indirect. Most likely, this effect is related to small regulatory sRNA-Hfq-based regulation of another protein that influences DNA supercoiling, possibly a nucleoid associated protein such as H-NS or Dps. Finally, we hypothesise that this indirect effect on DNA topology explains, at least partially, the previously reported effect of Hfq on plasmid replication efficiency.
Collapse
Affiliation(s)
- Antoine Malabirade
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - David Partouche
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France.,Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Omar El Hamoui
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | | | | | - Thomas Bizien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Florent Busi
- Unité de Biologie Fonctionnelle et Adaptative, CNRS UMR8251, Université Paris Diderot, 75013, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France. .,Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France.
| |
Collapse
|
64
|
Thi Bach Nguyen H, Romero A D, Amman F, Sorger-Domenigg T, Tata M, Sonnleitner E, Bläsi U. Negative Control of RpoS Synthesis by the sRNA ReaL in Pseudomonas aeruginosa. Front Microbiol 2018; 9:2488. [PMID: 30420839 PMCID: PMC6215814 DOI: 10.3389/fmicb.2018.02488] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa (Pae) is an opportunistic human pathogen, able to resist host defense mechanisms and antibiotic treatment. In Pae, the master regulator of stress responses RpoS (σS) is involved in the regulation of quorum sensing and several virulence genes. Here, we report that the sRNA ReaL translationally silences rpoS mRNA, which results in a decrease of the RpoS levels. Our studies indicated that ReaL base-pairs with the Shine-Dalgarno region of rpoS mRNA. These studies are underlined by a highly similar transcription profile of a rpoS deletion mutant and a reaL over-expressing strain.
Collapse
Affiliation(s)
- Hue Thi Bach Nguyen
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna - Vienna Biocenter, Vienna, Austria
| | - David Romero A
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna - Vienna Biocenter, Vienna, Austria
| | - Fabian Amman
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Theresa Sorger-Domenigg
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna - Vienna Biocenter, Vienna, Austria
| | - Muralidhar Tata
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna - Vienna Biocenter, Vienna, Austria
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna - Vienna Biocenter, Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna - Vienna Biocenter, Vienna, Austria
| |
Collapse
|
65
|
Carrier MC, Morin C, Massé E. On the Prowl: An In Vivo Method to Identify RNA Partners of a sRNA. Methods Enzymol 2018; 612:251-268. [PMID: 30502945 DOI: 10.1016/bs.mie.2018.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial cells dispose of numerous strategies to regulate gene expression. Small regulatory RNAs (sRNA) are pervasive molecules that allow gene expression regulation with exquisite precision. These molecules can bind mRNAs and negatively or positively modify their stability and interfere with translation. However, many features of sRNAs render identification of new targets or RNA interacting partners increasingly complex. In this chapter, we present a detailed procedure of MAPS, an in vivo technique based on the copurification of any type of RNA bound to an MS2-tagged sRNA. By focusing on the interaction between two RNAs rather than the outcome of this interaction, MAPS has proven useful in identifying unprecedented sRNA-RNA interactions. Below, we describe how to prepare MAPS samples and how to analyze RNA sequencing data files to determine enrichment ratios of different RNAs in an experimental condition vs a control condition. MAPS can be applied to most sRNAs of Escherichia coli and Salmonella spp., and can be easily optimized to more distant bacterial species.
Collapse
Affiliation(s)
- Marie-Claude Carrier
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Claire Morin
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Eric Massé
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, QC, Canada.
| |
Collapse
|
66
|
Santiago-Frangos A, Woodson SA. Hfq chaperone brings speed dating to bacterial sRNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1475. [PMID: 29633565 PMCID: PMC6002925 DOI: 10.1002/wrna.1475] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/22/2018] [Accepted: 02/26/2018] [Indexed: 11/11/2022]
Abstract
Hfq is a ubiquitous, Sm-like RNA binding protein found in most bacteria and some archaea. Hfq binds small regulatory RNAs (sRNAs), facilitates base pairing between sRNAs and their mRNA targets, and directly binds and regulates translation of certain mRNAs. Because sRNAs regulate many stress response pathways in bacteria, Hfq is essential for adaptation to different environments and growth conditions. The chaperone activities of Hfq arise from multipronged RNA binding by three different surfaces of the Hfq hexamer. The manner in which the structured Sm core of Hfq binds RNA has been well studied, but recent work shows that the intrinsically disordered C-terminal domain of Hfq modulates sRNA binding, creating a kinetic hierarchy of RNA competition for Hfq and ensuring the release of double-stranded sRNA-mRNA complexes. A combination of structural, biophysical, and genetic experiments reveals how Hfq recognizes its RNA substrates and plays matchmaker for sRNAs and mRNAs in the cell. The interplay between structured and disordered domains of Hfq optimizes sRNA-mediated post-transcriptional regulation, and is a common theme in RNA chaperones. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry.
Collapse
Affiliation(s)
- Andrew Santiago-Frangos
- Program in Cellular, Molecular and Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| |
Collapse
|
67
|
Schwenk S, Arnvig KB. Regulatory RNA in Mycobacterium tuberculosis, back to basics. Pathog Dis 2018; 76:4966984. [PMID: 29796669 PMCID: PMC7615687 DOI: 10.1093/femspd/fty035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/09/2018] [Indexed: 01/17/2023] Open
Abstract
Since the turn of the millenium, RNA-based control of gene expression has added an extra dimension to the central dogma of molecular biology. Still, the roles of Mycobacterium tuberculosis regulatory RNAs and the proteins that facilitate their functions remain elusive, although there can be no doubt that RNA biology plays a central role in the baterium's adaptation to its many host environments. In this review, we have presented examples from model organisms and from M. tuberculosis to showcase the abundance and versatility of regulatory RNA, in order to emphasise the importance of these 'fine-tuners' of gene expression.
Collapse
MESH Headings
- Aconitate Hydratase/genetics
- Aconitate Hydratase/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Gene Expression Regulation, Bacterial
- Host-Pathogen Interactions
- Humans
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/metabolism
- Mycobacterium tuberculosis/pathogenicity
- Nucleic Acid Conformation
- RNA Stability
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Small Cytoplasmic/genetics
- RNA, Small Cytoplasmic/metabolism
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- Regulatory Sequences, Ribonucleic Acid
- Riboswitch
- Tuberculosis/microbiology
Collapse
Affiliation(s)
- Stefan Schwenk
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Kristine B Arnvig
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| |
Collapse
|
68
|
Stevens JT, Carothers JM. Programming Gene Expression by Engineering Transcript Stability Control and Processing in Bacteria. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jason T. Stevens
- University of Washington; Center for Synthetic Biology, Molecular Engineering and Sciences Institute, Departments of Chemical Engineering and Bioengineering; 4000 15th Ave NE, Seattle WA 98195-1654 USA
| | - James M. Carothers
- University of Washington; Center for Synthetic Biology, Molecular Engineering and Sciences Institute, Departments of Chemical Engineering and Bioengineering; 4000 15th Ave NE, Seattle WA 98195-1654 USA
| |
Collapse
|
69
|
Lu P, Wang Y, Hu Y, Chen S. RgsA, an RpoS-dependent sRNA, negatively regulates rpoS expression in Pseudomonas aeruginosa. MICROBIOLOGY-SGM 2018; 164:716-724. [PMID: 29473822 DOI: 10.1099/mic.0.000632] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
As a master regulator, the alternative sigma factor RpoS coordinates the transcription of genes associated with protection against environmental stresses in bacteria. In Pseudomonas aeruginosa, RpoS is also involved in quorum sensing and virulence. The cellular RpoS level is regulated at multiple levels, whereas the post-transcriptional regulation of rpoS in P. aeruginosa remains unclear. To identify and characterize small regulatory RNAs (sRNAs) regulating RpoS in P. aeruginosa, an sRNA library expressing a total of 263 sRNAs was constructed to examine their regulatory roles on rpoS expression. Our results demonstrate that rpoS expression is repressed by the RpoS-dependent sRNA RgsA at the post-transcriptional level. Unlike OxyS, an sRNA previously known to repress rpoS expression under oxidative stress in Escherichia coli, RgsA represses rpoS expression during the exponential phase. This repression requires the RNA chaperone Hfq. Furthermore, the 71-77 conserved region of RgsA is necessary for full repression of rpoS expression, and the -25 to +27 region of rpoS mRNA is sufficient for RgsA-mediated rpoS repression. Together, our results not only add RgsA to the RpoS regulatory circuits but also highlight the complexity of interplay between sRNAs and transcriptional regulators in bacteria.
Collapse
Affiliation(s)
- Pei Lu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Yifei Wang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Yangbo Hu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Shiyun Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| |
Collapse
|
70
|
Falcone M, Ferrara S, Rossi E, Johansen HK, Molin S, Bertoni G. The Small RNA ErsA of Pseudomonas aeruginosa Contributes to Biofilm Development and Motility through Post-transcriptional Modulation of AmrZ. Front Microbiol 2018; 9:238. [PMID: 29497413 PMCID: PMC5819304 DOI: 10.3389/fmicb.2018.00238] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/31/2018] [Indexed: 11/13/2022] Open
Abstract
The small RNA ErsA of Pseudomonas aeruginosa was previously suggested to be involved in biofilm formation via negative post-transcriptional regulation of the algC gene that encodes the virulence-associated enzyme AlgC, which provides sugar precursors for the synthesis of several polysaccharides. In this study, we show that a knock-out ersA mutant strain forms a flat and uniform biofilm, not characterized by mushroom-multicellular structures typical of a mature biofilm. Conversely, the knock-out mutant strain showed enhanced swarming and twitching motilities. To assess the influence of ErsA on the P. aeruginosa transcriptome, we performed RNA-seq experiments comparing the knock-out mutant with the wild-type. More than 160 genes were found differentially expressed in the knock-out mutant. Parts of these genes, important for biofilm formation and motility regulation, are known to belong also to the AmrZ transcriptional regulator regulon. Here, we show that ErsA binds in vitro and positively regulates amrZ mRNA at post-transcriptional level in vivo suggesting an interesting contribution of the ErsA-amrZ mRNA interaction in biofilm development at several regulatory levels.
Collapse
Affiliation(s)
- Marilena Falcone
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Silvia Ferrara
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Elio Rossi
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Helle K Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Giovanni Bertoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
71
|
DksA and ppGpp Regulate the σ S Stress Response by Activating Promoters for the Small RNA DsrA and the Anti-Adapter Protein IraP. J Bacteriol 2017; 200:JB.00463-17. [PMID: 29061665 DOI: 10.1128/jb.00463-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/17/2017] [Indexed: 01/01/2023] Open
Abstract
σS is an alternative sigma factor, encoded by the rpoS gene, that redirects cellular transcription to a large family of genes in response to stressful environmental signals. This so-called σS general stress response is necessary for survival in many bacterial species and is controlled by a complex, multifactorial pathway that regulates σS levels transcriptionally, translationally, and posttranslationally in Escherichia coli It was shown previously that the transcription factor DksA and its cofactor, ppGpp, are among the many factors governing σS synthesis, thus playing an important role in activation of the σS stress response. However, the mechanisms responsible for the effects of DksA and ppGpp have not been elucidated fully. We describe here how DksA and ppGpp directly activate the promoters for the anti-adaptor protein IraP and the small regulatory RNA DsrA, thereby indirectly influencing σS levels. In addition, based on effects of DksAN88I, a previously identified DksA variant with increased affinity for RNA polymerase (RNAP), we show that DksA can increase σS activity by another indirect mechanism. We propose that by reducing rRNA transcription, DksA and ppGpp increase the availability of core RNAP for binding to σS and also increase transcription from other promoters, including PdsrA and PiraP By improving the translation and stabilization of σS, as well as the ability of other promoters to compete for RNAP, DksA and ppGpp contribute to the switch in the transcription program needed for stress adaptation.IMPORTANCE Bacteria spend relatively little time in log phase outside the optimized environment found in a laboratory. They have evolved to make the most of alternating feast and famine conditions by seamlessly transitioning between rapid growth and stationary phase, a lower metabolic mode that is crucial for long-term survival. One of the key regulators of the switch in gene expression that characterizes stationary phase is the alternative sigma factor σS Understanding the factors governing σS activity is central to unraveling the complexities of growth, adaptation to stress, and pathogenesis. Here, we describe three mechanisms by which the RNA polymerase binding factor DksA and the second messenger ppGpp regulate σS levels.
Collapse
|
72
|
The Developmental Switch in Bacteriophage λ: A Critical Role of the Cro Protein. J Mol Biol 2017; 430:58-68. [PMID: 29158090 DOI: 10.1016/j.jmb.2017.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 11/21/2022]
Abstract
Bacteriophage λ of Escherichia coli has two alternative life cycles after infection-host survival with lysogen formation, or host lysis and phage production. In a lysogen, CI represses the two lytic promoters, pR and pL, and activates its own transcription from the auto-regulated pRM promoter. During induction from the lysogenic to lytic state, CI is inactivated, and the two lytic promoters are de-repressed allowing for expression of Cro from pR. Cro is known to repress transcription of CI from pRM to prevent lysogeny. We show here that when Cro and CI are both present but at low levels, the low level of Cro initially stimulates the lytic promoters while CI repressor is still present, stimulating the level of Cro to a concentration required for pRM repression. Cro has no stimulatory effect without the presence of CI. We propose that this early auto-activating role of Cro at lower concentrations is essential in the developmental switch to lytic growth, whereas pRM repression by Cro at relatively higher concentrations avoids restoring lysogeny.
Collapse
|
73
|
Negrete A, Shiloach J. Improving E. coli growth performance by manipulating small RNA expression. Microb Cell Fact 2017; 16:198. [PMID: 29137641 PMCID: PMC5686845 DOI: 10.1186/s12934-017-0810-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/02/2017] [Indexed: 12/17/2022] Open
Abstract
Efficient growth of E. coli, especially for production of recombinant proteins, has been a challenge for the biotechnological industry since the early 1970s. By employing multiple approaches, such as different media composition, various growth strategies and specific genetic manipulations, it is now possible to grow bacteria to concentrations exceeding 100 g/L and to achieve high concentrations of recombinant proteins. Although the growth conditions are carefully monitored and maintained, it is likely that during the growth process cells are exposed to periodic stress conditions, created by fluctuations in pH, dissolved oxygen, temperature, glucose, and salt concentration. These stress circumstances which can occur especially in large volume bioreactors, may affect the growth and production process. In the last several years, it has been recognized that small non-coding RNAs can act as regulators of bacterial gene expression. These molecules are found to be specifically involved in E. coli response to different environmental stress conditions; but so far, have not been used for improving production strains. The review provides summary of small RNAs identified on petri dish or in shake flask culture that can potentially affect growth characteristics of E. coli grown in bioreactor. Among them MicC and MicF that are involved in response to temperature changes, RyhB that responds to iron concentration, Gady which is associated with lower pH, Sgrs that is coupled with glucose transport and OxyS that responds to oxygen concentration. The manipulation of some of these small RNAs for improving growth of E. coli in Bioreactor is described in the last part of the review. Overexpression of SgrS was associated with improved growth and reduced acetate expression, over expression of GadY improved cell growth at acidic conditions and over expression of OxyS reduced the effect of oxidative stress. One of the possible advantages of manipulating sRNAs for improving cell growth is that the modifications occur at a post-translational level. Therefore, the use of sRNAs may exert minimal effect on the overall bacterial metabolism. The elucidation of the physiological role of newly discovered sRNAs will open new possibilities for creating strains with improved growth and production capabilities.
Collapse
Affiliation(s)
- Alejandro Negrete
- Biotechnology Core Laboratory, NIDDK, NIH, Bethesda, MD, 20892, USA.,MilliporeSigma, Carlsbad, CA, 92009, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory, NIDDK, NIH, Bethesda, MD, 20892, USA.
| |
Collapse
|
74
|
Yu YTN, Cooper E, Velicer GJ. A conserved stem of the Myxococcus xanthus sRNA Pxr controls sRNA accumulation and multicellular development. Sci Rep 2017; 7:15411. [PMID: 29133885 PMCID: PMC5684412 DOI: 10.1038/s41598-017-15439-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/26/2017] [Indexed: 11/11/2022] Open
Abstract
The small RNA (sRNA) Pxr negatively controls multicellular fruiting body formation in the bacterium Myxococcus xanthus, inhibiting the transition from growth to development when nutrients are abundant. Like many other prokaryotic sRNAs, Pxr is predicted to fold into three stem loops (SL1-SL3). SL1 and SL2 are highly conserved across the myxobacteria, whereas SL3 is much more variable. SL1 is necessary for the regulatory function of Pxr but the importance of SL3 in this regard is unknown. To test for cis genetic elements required for Pxr function, we deleted the entire pxr gene from a developmentally defective strain that fails to remove Pxr-mediated blockage of development and reintroduced variably truncated fragments of the pxr region to test for their ability to block development. These truncations demonstrated that SL3 is necessary for Pxr function in the defective strain. We further show that a highly conserved eight-base-pair segment of SL3 is not only necessary for Pxr to block development in the defective strain under starvation conditions, but is also required for Pxr to prevent fruiting body development by a developmentally proficient wild-type strain under high-nutrient conditions. This conserved segment of SL3 is also necessary for detectable levels of Pxr to accumulate, suggesting that this segment either stabilizes Pxr against premature degradation during vegetative growth or positively regulates its transcription.
Collapse
Affiliation(s)
- Yuen-Tsu N Yu
- Institute of Integrative Biology, ETH Zurich, Universitätstrasse 16, 8092, Zurich, Switzerland. .,Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
| | - Elizabeth Cooper
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Gregory J Velicer
- Institute of Integrative Biology, ETH Zurich, Universitätstrasse 16, 8092, Zurich, Switzerland. .,Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
| |
Collapse
|
75
|
Impact of bacterial sRNAs in stress responses. Biochem Soc Trans 2017; 45:1203-1212. [PMID: 29101308 PMCID: PMC5730939 DOI: 10.1042/bst20160363] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 12/11/2022]
Abstract
Bacterial life is harsh and involves numerous environmental and internal challenges that are perceived as stresses. Consequently, adequate responses to survive, cope with, and counteract stress conditions have evolved. In the last few decades, a class of small, non-coding RNAs (sRNAs) has been shown to be involved as key players in stress responses. This review will discuss — primarily from an enterobacterial perspective — selected stress response pathways that involve antisense-type sRNAs. These include themes of how bacteria deal with severe envelope stress, threats of DNA damage, problems with poisoning due to toxic sugar intermediates, issues of iron homeostasis, and nutrient limitation/starvation. The examples discussed highlight how stress relief can be achieved, and how sRNAs act mechanistically in regulatory circuits. For some cases, we will propose scenarios that may suggest why contributions from post-transcriptional control by sRNAs, rather than transcriptional control alone, appear to be a beneficial and universally selected feature.
Collapse
|
76
|
Wu P, Liu X, Yang L, Sun Y, Gong Q, Wu J, Shi Y. The important conformational plasticity of DsrA sRNA for adapting multiple target regulation. Nucleic Acids Res 2017; 45:9625-9639. [PMID: 28934467 PMCID: PMC5766208 DOI: 10.1093/nar/gkx570] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 06/22/2017] [Indexed: 01/08/2023] Open
Abstract
In bacteria, small non-coding RNAs (sRNAs) could function in gene regulations under variable stress responses. DsrA is an ∼90-nucleotide Hfq-dependent sRNA found in Escherichia coli. It regulates the translation and degradation of multiple mRNAs, such as rpoS, hns, mreB and rbsD mRNAs. However, its functional structure and particularly how it regulates multiple mRNAs remain obscure. Using NMR, we investigated the solution structures of the full-length and isolated stem-loops of DsrA. We first solved the NMR structure of the first stem-loop (SL1), and further studied the melting process of the SL1 induced by the base-pairing with the rpoS mRNA and the A-form duplex formation of the DsrA/rpoS complex. The secondary structure of the second stem-loop (SL2) was also determined, which contains a lower stem and an upper stem with distinctive stability. Interestingly, two conformational states of SL2 in dynamic equilibrium were observed in our NMR spectra, suggesting that the conformational selection may occur during the base-pairing between DsrA and mRNAs. In summary, our study suggests that the conformational plasticity of DsrA may represent a special mechanism sRNA employed to deal with its multiple regulatory targets of mRNA.
Collapse
Affiliation(s)
- Pengzhi Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Xiaodan Liu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Lingna Yang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Yitong Sun
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Qingguo Gong
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui 230027, China
| |
Collapse
|
77
|
Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing Conditions. mSystems 2017; 2:mSystems00024-17. [PMID: 28766584 PMCID: PMC5527300 DOI: 10.1128/msystems.00024-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/06/2017] [Indexed: 12/23/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) bacteria are a diverse group of pathogens that cause moderate to severe diarrhea in young children in developing countries. EPEC isolates can be further subclassified as typical EPEC (tEPEC) isolates that contain the bundle-forming pilus (BFP) or as atypical EPEC (aEPEC) isolates that do not contain BFP. Comparative genomics studies have recently highlighted the considerable genomic diversity among EPEC isolates. In the current study, we used RNA sequencing (RNA-Seq) to characterize the global transcriptomes of eight tEPEC isolates representing the identified genomic diversity, as well as one aEPEC isolate. The global transcriptomes were determined for the EPEC isolates under conditions of laboratory growth that are known to induce expression of virulence-associated genes. The findings demonstrate that unique genes of EPEC isolates from diverse phylogenomic lineages contribute to variation in their global transcriptomes. There were also phylogroup-specific differences in the global transcriptomes, including genes involved in iron acquisition, which had significant differential expression in the EPEC isolates belonging to phylogroup B2. Also, three EPEC isolates from the same phylogenomic lineage (EPEC8) had greater levels of similarity in their genomic content and exhibited greater similarities in their global transcriptomes than EPEC from other lineages; however, even among closely related isolates there were isolate-specific differences among their transcriptomes. These findings highlight the transcriptional variability that correlates with the previously unappreciated genomic diversity of EPEC. IMPORTANCE Recent studies have demonstrated that there is considerable genomic diversity among EPEC isolates; however, it is unknown if this genomic diversity leads to differences in their global transcription. This study used RNA-Seq to compare the global transcriptomes of EPEC isolates from diverse phylogenomic lineages. We demonstrate that there are lineage- and isolate-specific differences in the transcriptomes of genomically diverse EPEC isolates during growth under in vitro virulence-inducing conditions. This study addressed biological variation among isolates of a single pathovar in an effort to demonstrate that while each of these isolates is considered an EPEC isolate, there is significant transcriptional diversity among members of this pathovar. Future studies should consider whether this previously undescribed transcriptional variation may play a significant role in isolate-specific variability of EPEC clinical presentations.
Collapse
|
78
|
Ryan D, Mukherjee M, Suar M. The expanding targetome of small RNAs in Salmonella Typhimurium. Biochimie 2017; 137:69-77. [DOI: 10.1016/j.biochi.2017.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/10/2017] [Indexed: 10/20/2022]
|
79
|
Parker A, Cureoglu S, De Lay N, Majdalani N, Gottesman S. Alternative pathways for Escherichia coli biofilm formation revealed by sRNA overproduction. Mol Microbiol 2017; 105:309-325. [PMID: 28470798 DOI: 10.1111/mmi.13702] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2017] [Indexed: 01/06/2023]
Abstract
Small regulatory RNAs have major roles in many regulatory circuits in Escherichia coli and other bacteria, including the transition from planktonic to biofilm growth. We tested Hfq-dependent sRNAs in E. coli for their ability, when overproduced, to inhibit or stimulate biofilm formation, in two different growth media. We identify two mutually exclusive pathways for biofilm formation. In LB, PgaA, encoding an adhesion export protein, played a critical role; biofilm was independent of the general stress factor RpoS or CsgD, regulator of curli and other biofilm genes. The PgaA-dependent pathway was stimulated upon overproduction of DsrA, via negative regulation of H-NS, or of GadY, likely by titration of CsrA. In yeast extract casamino acids (YESCA) media, biofilm was dependent on RpoS and CsgD, but independent of PgaA; RpoS appears to indirectly negatively regulate the PgaA-dependent pathway in YESCA medium. Deletions of most sRNAs had very little effect on biofilm, although deletion of hfq, encoding an RNA chaperone, was defective in both LB and YESCA. Deletion of ArcZ, a small RNA activator of RpoS, decreased biofilm in YESCA; only a portion of this defect could be bypassed by overproduction of RpoS. Overall, sRNAs highlight different pathways to biofilm formation.
Collapse
Affiliation(s)
- Ashley Parker
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Suanur Cureoglu
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Nicholas De Lay
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Nadim Majdalani
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, 20892, USA
| |
Collapse
|
80
|
TrmL and TusA Are Necessary for rpoS and MiaA Is Required for hfq Expression in Escherichia coli. Biomolecules 2017; 7:biom7020039. [PMID: 28471404 PMCID: PMC5485728 DOI: 10.3390/biom7020039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 03/31/2017] [Accepted: 04/12/2017] [Indexed: 12/18/2022] Open
Abstract
Previous work demonstrated that efficient RNA Polymerase sigma S-subunit (RpoS) translation requires the N6-isopentenyladenosine i6A37 transfer RNA (tRNA) modification for UUX-Leu decoding. Here we investigate the effect of two additional tRNA modification systems on RpoS translation; the analysis was also extended to another High UUX-leucine codon (HULC) protein, Host Factor for phage Qβ (Hfq). One tRNA modification, the addition of the 2’-O-methylcytidine/uridine 34 (C/U34m) tRNA modification by tRNA (cytidine/uridine-2’O)-ribose methyltransferase L (TrmL), requires the presence of the N6-isopentenyladenosine 37 (i6A37) and therefore it seemed possible that the defect in RpoS translation in the absence of i6A37 prenyl transferase (MiaA) was in fact due to the inability to add the C/U34m modification to UUX-Leu tRNAs. The second modification, addition of 2-thiouridine (s2U), part of (mnm5s2U34), is dependent on tRNA 2-thiouridine synthesizing protein A (TusA), previously shown to affect RpoS levels. We compared expression of PBAD-rpoS990-lacZ translational fusions carrying wild-type UUX leucine codons with derivatives in which UUX codons were changed to CUX codons, in the presence and absence of TrmL or TusA. The absence of these proteins, and therefore presumably the modifications they catalyze, both abolished PBAD-rpoS990-lacZ translation activity. UUX-Leu to CUX-Leu codon mutations in rpoS suppressed the trmL requirement for PBAD-rpoS990-lacZ expression. Thus, it is likely that the C/U34m and s2U34 tRNA modifications are necessary for full rpoS translation. We also measured PBAD-hfq306-lacZ translational fusion activity in the absence of C/U34m (trmL) or i6A37 (miaA). The absence of i6A37 resulted in decreased PBAD-hfq306-lacZ expression, consistent with a role for i6A37 tRNA modification for hfq translation.
Collapse
|
81
|
Lahiry A, Stimple SD, Wood DW, Lease RA. Retargeting a Dual-Acting sRNA for Multiple mRNA Transcript Regulation. ACS Synth Biol 2017; 6:648-658. [PMID: 28067500 DOI: 10.1021/acssynbio.6b00261] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Multitargeting small regulatory RNAs (sRNAs) represent a potentially useful tool for metabolic engineering applications. Natural multitargeting sRNAs govern bacterial gene expression by binding to the translation initiation regions of protein-coding mRNAs through base pairing. We designed an Escherichia coli based genetic system to create and assay dual-acting retargeted-sRNA variants. The variants can be assayed for coordinate translational regulation of two alternate mRNA leaders fused to independent reporter genes. Accordingly, we began with the well-characterized E. coli native DsrA sRNA. The merits of using DsrA include its well-characterized separation of function into two independently folded stem-loop domains, wherein alterations at one stem do not necessarily abolish activity at the other stem. Expression of the sRNA and each reporter mRNA was independently controlled by small inducer molecules, allowing precise quantification of the regulatory effects of each sRNA:mRNA interaction in vivo with a microtiter plate assay. Using this system, we semirationally designed DsrA variants screened in E. coli for their ability to regulate key mRNA leader sequences from the Clostridium acetobutylicum n-butanol synthesis pathway. To coordinate intervention at two points in a metabolic pathway, we created bifunctional sRNA prototypes by combining sequences from two singly retargeted DsrA variants. This approach constitutes a platform for designing sRNAs to specifically target arbitrary mRNA transcript sequences, and thus provides a generalizable tool for retargeting and characterizing multitarget sRNAs for metabolic engineering.
Collapse
Affiliation(s)
- Ashwin Lahiry
- Department
of Microbiology, The Ohio State University, 484 W. 12th Avenue, Columbus, Ohio 43210, United States
| | - Samuel D. Stimple
- Department
of Chemical and Biomolecular Engineering, The Ohio State University, 151 W. Woodruff Avenue, Columbus, Ohio 43210, United States
| | - David W. Wood
- Department
of Chemical and Biomolecular Engineering, The Ohio State University, 151 W. Woodruff Avenue, Columbus, Ohio 43210, United States
- Department
of Microbiology, The Ohio State University, 484 W. 12th Avenue, Columbus, Ohio 43210, United States
| | - Richard A. Lease
- Department
of Chemical and Biomolecular Engineering, The Ohio State University, 151 W. Woodruff Avenue, Columbus, Ohio 43210, United States
| |
Collapse
|
82
|
Jeong Y, Shin H, Seo SW, Kim D, Cho S, Cho BK. Elucidation of bacterial translation regulatory networks. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
83
|
Han R, Xu L, Wang T, Liu B, Wang L. A Small Regulatory RNA Contributes to the Preferential Colonization of Escherichia coli O157:H7 in the Large Intestine in Response to a Low DNA Concentration. Front Microbiol 2017; 8:274. [PMID: 28289405 PMCID: PMC5326754 DOI: 10.3389/fmicb.2017.00274] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/09/2017] [Indexed: 11/13/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 (O157) is one of the most notorious human pathogens, causing severe disease in humans worldwide. O157 specifically colonizes the large intestine of mammals after passing through the small intestine, and this process is influenced by differential signals between the two regions. Small regulatory RNAs (sRNAs) are able to sense and respond to environmental changes and regulate diverse physiological processes in pathogenic bacteria. Although some sRNAs of O157 have been extensively investigated, whether these molecules can sense differences between the small and large intestine and influence the preferential colonization in the large intestine by O157 remains unknown. In this study, we identified a new sRNA, Esr055, in O157 which senses the low DNA concentration in the large intestine and contributes to the preferential colonization of the bacteria in this region. The number of O157 wild-type that adhered to the colon is 30.18 times higher than the number that adhered to the ileum of mice, while the number of the ΔEsr055 mutant that adhered to the colon decreased to 13.27 times higher than the number adhered to the ileum. Furthermore, we found that the expression of Esr055 is directly activated by the regulator, DeoR, and its expression is positively affected by DNA, which is significantly more abundant in the ileum than in the colon of mice. Additionally, combining the results of informatics predictions and transcriptomic analysis, we found that several virulence genes are up-regulated in the ΔEsr055 mutant and five candidate genes (z0568, z0974, z1356, z1926, and z5187) may be its direct targets.
Collapse
Affiliation(s)
- Runhua Han
- TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of EducationTianjin, China
| | - Letian Xu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of EducationTianjin, China; Tianjin Key Laboratory of Microbial Functional GenomicsTianjin, China
| | - Ting Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of EducationTianjin, China
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of EducationTianjin, China; Tianjin Key Laboratory of Microbial Functional GenomicsTianjin, China
| | - Lei Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of EducationTianjin, China; Tianjin Key Laboratory of Microbial Functional GenomicsTianjin, China; State Key Laboratory of Medicinal Chemical Biology, Nankai UniversityTianjin, China
| |
Collapse
|
84
|
Sedlyarova N, Shamovsky I, Bharati BK, Epshtein V, Chen J, Gottesman S, Schroeder R, Nudler E. sRNA-Mediated Control of Transcription Termination in E. coli. Cell 2016; 167:111-121.e13. [PMID: 27662085 DOI: 10.1016/j.cell.2016.09.004] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/12/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
Abstract
Bacterial small RNAs (sRNAs) have been implicated in various aspects of post-transcriptional gene regulation. Here, we demonstrate that sRNAs also act at the level of transcription termination. We use the rpoS gene, which encodes a general stress sigma factor σ(S), as a model system, and show that sRNAs DsrA, ArcZ, and RprA bind the rpoS 5'UTR to suppress premature Rho-dependent transcription termination, both in vitro and in vivo. sRNA-mediated antitermination markedly stimulates transcription of rpoS during the transition to the stationary phase of growth, thereby facilitating a rapid adjustment of bacteria to global metabolic changes. Next generation RNA sequencing and bioinformatic analysis indicate that Rho functions as a global "attenuator" of transcription, acting at the 5'UTR of hundreds of bacterial genes, and that its suppression by sRNAs is a widespread mode of bacterial gene regulation.
Collapse
Affiliation(s)
- Nadezda Sedlyarova
- Department of Biochemistry and Cellbiology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Binod K Bharati
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Jiandong Chen
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Renée Schroeder
- Department of Biochemistry and Cellbiology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
85
|
Hücker SM, Simon S, Scherer S, Neuhaus K. Transcriptional and translational regulation by RNA thermometers, riboswitches and the sRNA DsrA in Escherichia coli O157:H7 Sakai under combined cold and osmotic stress adaptation. FEMS Microbiol Lett 2016; 364:fnw262. [PMID: 27856567 DOI: 10.1093/femsle/fnw262] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/22/2016] [Accepted: 11/14/2016] [Indexed: 12/24/2022] Open
Abstract
The enteric pathogen Escherichia coli O157:H7 Sakai (EHEC) is able to grow at lower temperatures compared to commensal E. coli Growth at environmental conditions displays complex challenges different to those in a host. EHEC was grown at 37°C and at 14°C with 4% NaCl, a combination of cold and osmotic stress as present in the food chain. Comparison of RNAseq and RIBOseq data provided a snap shot of ongoing transcription and translation, differentiating transcriptional and post-transcriptional gene regulation, respectively. Indeed, cold and osmotic stress related genes are simultaneously regulated at both levels, but translational regulation clearly dominates. Special emphasis was given to genes regulated by RNA secondary structures in their 5'UTRs, such as RNA thermometers and riboswitches, or genes controlled by small RNAs encoded in trans The results reveal large differences in gene expression between short-time shock compared to adaptation in combined cold and osmotic stress. Whereas the majority of cold shock proteins, such as CspA, are translationally downregulated after adaptation, many osmotic stress genes are still significantly upregulated mainly translationally, but several also transcriptionally.
Collapse
Affiliation(s)
- Sarah Maria Hücker
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Svenja Simon
- Chair for Data Analysis and Visualization, Department of Computer and Information Science, University of Konstanz, Box 78, 78457 Konstanz, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| |
Collapse
|
86
|
Spot 42 sRNA regulates arabinose-inducible araBAD promoter activity by repressing synthesis of the high-affinity low-capacity arabinose transporter. J Bacteriol 2016; 199:e00691-16. [PMID: 27849174 DOI: 10.1128/jb.00691-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The L-arabinose-inducible araBAD promoter (PBAD) allows tightly controlled and tunable expression of genes of interest in a broad range of bacterial species. It has been successfully used to study bacterial sRNA regulation, where PBAD drives expression of target mRNA translational fusions. Here we report that in Escherichia coli, Spot 42 sRNA can regulate PBAD promoter activity by affecting arabinose uptake. We demonstrate that Spot 42 sRNA represses araF, a gene encoding the AraF subunit of the high-affinity low-capacity arabinose transporter AraFGH, through direct base pairing interactions. We further show that endogenous Spot 42 sRNA is sufficient to repress araF expression under various growth conditions. Finally, we demonstrate this posttranscriptional repression has a biological consequence, decreasing the induction of PBAD at low levels of arabinose. This problem can be circumvented using strategies reported previously for avoiding all-or-none induction behavior, that is through constitutive expression of the low-affinity high-capacity arabinose transporter AraE or induction with higher concentration of inducers. This work adds araF to the set of Spot 42-regulated genes, in agreement with previous studies suggesting that Spot 42, itself negatively regulated by cAMP-CRP complex, reinforces the catabolite repression network. IMPORTANCE The bacterial arabinose inducible system is widely used for titratable control of gene expression. We demonstrate here that a post-transcriptional mechanism mediated by the Spot 42 sRNA contributes to the functionality of the PBAD system at subsaturating inducer concentrations by affecting inducer uptake. Our finding extends the inputs into the known transcriptional control for the PBAD system, and has implications for improving its usage for tunable gene expression.
Collapse
|
87
|
Murina VN, Nikulin AD. Bacterial Small Regulatory RNAs and Hfq Protein. BIOCHEMISTRY (MOSCOW) 2016; 80:1647-54. [PMID: 26878571 DOI: 10.1134/s0006297915130027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Small regulatory RNA (sRNA) is a unique noncoding RNA involved in regulation of gene expression in both eukaryotic and bacterial cells. This short review discusses examples of positive and negative translation regulation by sRNAs in bacteria and participation of Hfq in these processes. The importance of structure investigation of nucleotide-protein and RNA-protein complexes for designing a model of Hfq interaction with both mRNA and sRNA simultaneously is demonstrated.
Collapse
Affiliation(s)
- V N Murina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | | |
Collapse
|
88
|
Woo JM, Kim JW, Song JW, Blank LM, Park JB. Activation of the Glutamic Acid-Dependent Acid Resistance System in Escherichia coli BL21(DE3) Leads to Increase of the Fatty Acid Biotransformation Activity. PLoS One 2016; 11:e0163265. [PMID: 27681369 PMCID: PMC5040553 DOI: 10.1371/journal.pone.0163265] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 09/05/2016] [Indexed: 01/29/2023] Open
Abstract
The biosynthesis of carboxylic acids including fatty acids from biomass is central in envisaged biorefinery concepts. The productivities are often, however, low due to product toxicity that hamper whole-cell biocatalyst performance. Here, we have investigated factors that influence the tolerance of Escherichia coli to medium chain carboxylic acid (i.e., n-heptanoic acid)-induced stress. The metabolic and genomic responses of E. coli BL21(DE3) and MG1655 grown in the presence of n-heptanoic acid indicated that the GadA/B-based glutamic acid-dependent acid resistance (GDAR) system might be critical for cellular tolerance. The GDAR system, which is responsible for scavenging intracellular protons by catalyzing decarboxylation of glutamic acid, was inactive in E. coli BL21(DE3). Activation of the GDAR system in this strain by overexpressing the rcsB and dsrA genes, of which the gene products are involved in the activation of GadE and RpoS, respectively, resulted in acid tolerance not only to HCl but also to n-heptanoic acid. Furthermore, activation of the GDAR system allowed the recombinant E. coli BL21(DE3) expressing the alcohol dehydrogenase of Micrococcus luteus and the Baeyer-Villiger monooxygenase of Pseudomonas putida to reach 60% greater product concentration in the biotransformation of ricinoleic acid (i.e., 12-hydroxyoctadec-9-enoic acid (1)) into n-heptanoic acid (5) and 11-hydroxyundec-9-enoic acid (4). This study may contribute to engineering E. coli-based biocatalysts for the production of carboxylic acids from renewable biomass.
Collapse
Affiliation(s)
- Ji-Min Woo
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Ji-Won Kim
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Ji-Won Song
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Jin-Byung Park
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
- * E-mail:
| |
Collapse
|
89
|
Mechanistic study of base-pairing small regulatory RNAs in bacteria. Methods 2016; 117:67-76. [PMID: 27693881 DOI: 10.1016/j.ymeth.2016.09.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/22/2016] [Indexed: 11/24/2022] Open
Abstract
In all three kingdoms of life, RNA is not only involved in the expression of genetic information, but also carries out extremely diverse cellular functions. This versatility is essentially due to the fact that RNA molecules can exploit the power of base pairing to allow them to fold into a wide variety of structures through which they can perform diverse roles, but also to selectively target and bind to other nucleic acids. This is true in particular for bacterial small regulatory RNAs that act by imperfect base-pairing with target mRNAs, and thereby control their expression through different mechanisms. Here we outline an overview of in vivo and in vitro approaches that are currently used to gain mechanistic insights into how these sRNAs control gene expression in bacteria.
Collapse
|
90
|
Fröhlich KS, Papenfort K. Interplay of regulatory RNAs and mobile genetic elements in enteric pathogens. Mol Microbiol 2016; 101:701-13. [DOI: 10.1111/mmi.13428] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Kathrin S. Fröhlich
- Department of Biology I, Microbiology; Ludwig-Maximilians-University Munich; 82152 Martinsried Germany
| | - Kai Papenfort
- Department of Biology I, Microbiology; Ludwig-Maximilians-University Munich; 82152 Martinsried Germany
| |
Collapse
|
91
|
Lee HJ, Gottesman S. sRNA roles in regulating transcriptional regulators: Lrp and SoxS regulation by sRNAs. Nucleic Acids Res 2016; 44:6907-23. [PMID: 27137887 PMCID: PMC5001588 DOI: 10.1093/nar/gkw358] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/21/2016] [Indexed: 11/13/2022] Open
Abstract
Post-transcriptional regulation of transcription factors contributes to regulatory circuits. We created translational reporter fusions for multiple central regulators in Escherichia coli and examined the effect of Hfq-dependent non-coding RNAs on these fusions. This approach yields an 'RNA landscape,' identifying Hfq-dependent sRNAs that regulate a given fusion. No significant sRNA regulation of crp or fnr was detected. hns was regulated only by DsrA, as previously reported. Lrp and SoxS were both found to be regulated post-transcriptionally. Lrp, ' L: eucine-responsive R: egulatory P: rotein,' regulates genes involved in amino acid biosynthesis and catabolism and other cellular functions. sRNAs DsrA, MicF and GcvB each independently downregulate the lrp translational fusion, confirming previous reports for MicF and GcvB. MicF and DsrA interact with an overlapping site early in the lrp ORF, while GcvB acts upstream at two independent sites in the long lrp leader. Surprisingly, GcvB was found to be responsible for significant downregulation of lrp after oxidative stress; MicF also contributed. SoxS, an activator of genes used to combat oxidative stress, is negatively regulated by sRNA MgrR. This study demonstrates that while not all global regulators are subject to sRNA regulation, post-transcriptional control by sRNAs allows multiple environmental signals to affect synthesis of the transcriptional regulator.
Collapse
Affiliation(s)
- Hyun-Jung Lee
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
92
|
Aubee JI, Olu M, Thompson KM. The i6A37 tRNA modification is essential for proper decoding of UUX-Leucine codons during rpoS and iraP translation. RNA (NEW YORK, N.Y.) 2016; 22:729-742. [PMID: 26979278 PMCID: PMC4836647 DOI: 10.1261/rna.053165.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
The translation of rpoS(σ(S)), the general stress/stationary phase sigma factor, is tightly regulated at the post-transcriptional level by several factors via mechanisms that are not clearly defined. One of these factors is MiaA, the enzyme necessary for the first step in theN(6)-isopentyl-2-thiomethyl adenosinemethyl adenosine 37 (ms(2)i(6)A37) tRNA modification. We tested the hypothesis that an elevated UUX-Leucine/total leucine codon ratio can be used to identify transcripts whose translation would be sensitive to loss of the MiaA-dependent modification. We identified iraPas another candidate MiaA-sensitive gene, based on the UUX-Leucine/total leucine codon ratio. AniraP-lacZ fusion was significantly decreased in the abse nce of MiaA, consistent with our predictive model. To determine the role of MiaA in UUX-Leucine decoding in rpoS and iraP, we measured β-galactosidase-specific activity of miaA(-)rpo Sandira P translational fusions upon overexpression of leucine tRNAs. We observed suppression of the MiaA effect on rpoS, and notira P, via overexpression of tRNA(LeuX)but not tRNA(LeuZ) We also tested the hypothesis that the MiaA requirement for rpoS and iraP translation is due to decoding of UUX-Leucine codons within the rpoS and iraP transcripts, respectively. We observed a partial suppression of the MiaA requirement for rpoS and iraP translational fusions containing one or both UUX-Leucine codons removed. Taken together, this suggests that MiaA is necessary for rpoS and iraP translation through proper decoding of UUX-Leucine codons and that rpoS and iraP mRNAs are both modification tunable transcripts (MoTTs) via the presence of the modification.
Collapse
Affiliation(s)
- Joseph I Aubee
- Department of Microbiology, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Morenike Olu
- Department of Microbiology, College of Medicine, Howard University, Washington, DC 20059, USA Department of Biology, Howard University, Washington, DC 20059, USA
| | - Karl M Thompson
- Department of Microbiology, College of Medicine, Howard University, Washington, DC 20059, USA
| |
Collapse
|
93
|
Ryan D, Ojha UK, Jaiswal S, Padhi C, Suar M. The Small RNA DsrA Influences the Acid Tolerance Response and Virulence of Salmonella enterica Serovar Typhimurium. Front Microbiol 2016; 7:599. [PMID: 27199929 PMCID: PMC4844625 DOI: 10.3389/fmicb.2016.00599] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/11/2016] [Indexed: 01/05/2023] Open
Abstract
The Gram-negative, enteropathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) is exposed to various stress conditions during pathogenesis, of which acid stress serves as a major defense mechanism in the host. Such environments are encountered in the stomach and Salmonella containing vacuole of phagocytic and non-phagocytic cells. It is only recently that small RNAs (sRNAs) have come to the forefront as major regulators of stress response networks. Consequently, the sRNA DsrA which regulates acid resistance in Escherichia coli, has not been characterized in the acid tolerance response (ATR) of Salmonella. In this study, we show dsrA to be induced two and threefold under adaptation and challenge phases of the ATR, respectively. Additionally, an isogenic mutant lacking dsrA (ΔDsrA) displayed lower viability under the ATR along with reduced motility, feeble adhesion and defective invasion efficacy in vitro. Expression analysis revealed down regulation of several Salmonella pathogenicity island-1 (SPI-1) effectors in ΔDsrA compared to the wild-type, under SPI-1 inducing conditions. Additionally, our in vivo data revealed ΔDsrA to be unable to cause gut inflammation in C57BL/6 mice at 72 h post infection, although intracellular survival and systemic dissemination remained unaffected. A possible explanation may be the significantly reduced expression of flagellin structural genes fliC and fljB in ΔDsrA, which have been implicated as major proinflammatory determinants. This study serves to highlight the role of sRNAs such as DsrA in both acid tolerance and virulence of S. Typhimurium. Additionally the robust phenotype of non-invasiveness could be exploited in developing SPI-I attenuated S. Typhimurium strains without disrupting SPI-I genes.
Collapse
Affiliation(s)
- Daniel Ryan
- Infection Biology Laboratory, School of Biotechnology, KIIT University Bhubaneswar, India
| | - Urmesh K Ojha
- Infection Biology Laboratory, School of Biotechnology, KIIT University Bhubaneswar, India
| | - Sangeeta Jaiswal
- Infection Biology Laboratory, School of Biotechnology, KIIT University Bhubaneswar, India
| | - Chandrashekhar Padhi
- Infection Biology Laboratory, School of Biotechnology, KIIT University Bhubaneswar, India
| | - Mrutyunjay Suar
- Infection Biology Laboratory, School of Biotechnology, KIIT University Bhubaneswar, India
| |
Collapse
|
94
|
Abstract
Over the last decade, small (often noncoding) RNA molecules have been discovered as important regulators influencing myriad aspects of bacterial physiology and virulence. In particular, small RNAs (sRNAs) have been implicated in control of both primary and secondary metabolic pathways in many bacterial species. This chapter describes characteristics of the major classes of sRNA regulators, and highlights what is known regarding their mechanisms of action. Specific examples of sRNAs that regulate metabolism in gram-negative bacteria are discussed, with a focus on those that regulate gene expression by base pairing with mRNA targets to control their translation and stability.
Collapse
|
95
|
Abstract
In the last few decades, small regulatory RNA (sRNA) molecules emerged as key regulators in every kingdom of life. Resolving the full targetome of sRNAs has however remained a challenge. To address this, we used an in vivo tagging MS2-affinity purification protocol coupled with RNA sequencing technology, namely MAPS, to assemble full bacterial small RNAs targetomes. The impressive potential of MAPS has been supported by a number of reports. Here, we concisely overview RNA-tagging history that preceded the development of the MAPS assay and expose the range of possible uses of this technology.
Collapse
Affiliation(s)
- Marie-Claude Carrier
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
| | - David Lalaouna
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
| | - Eric Massé
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
| |
Collapse
|
96
|
Lalaouna D, Massé E. The spectrum of activity of the small RNA DsrA: not so narrow after all. Curr Genet 2015; 62:261-4. [PMID: 26607444 DOI: 10.1007/s00294-015-0533-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 11/28/2022]
Abstract
For a long time, the small regulatory RNA DsrA has been considered as a regulator with a narrow spectrum of action due to its restricted targetome. Since the first reports on DsrA characterization, only two targets of DsrA have been described: rpoS and hns mRNAs, encoding the sigma factor σS and the nucleoid-associated protein H-NS, respectively. Recently, the scope of DsrA targetome has been expanded by the characterization of two negatively regulated mRNAs, mreB and rbsD, involved in cell wall biosynthesis and ribose metabolism, respectively. In this review, we summarize new insights in DsrA-mediated regulation and emphasize the versatility of DsrA modes of action.
Collapse
Affiliation(s)
- David Lalaouna
- RNA Group, Department of Biochemistry, Université de Sherbrooke, 3201 Jean Mignault Street, Sherbrooke, QC, J1E 4K8, Canada
| | - Eric Massé
- RNA Group, Department of Biochemistry, Université de Sherbrooke, 3201 Jean Mignault Street, Sherbrooke, QC, J1E 4K8, Canada.
| |
Collapse
|
97
|
Pletnev P, Osterman I, Sergiev P, Bogdanov A, Dontsova O. Survival guide: Escherichia coli in the stationary phase. Acta Naturae 2015; 7:22-33. [PMID: 26798489 PMCID: PMC4717247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
This review centers on the stationary phase of bacterial culture. The basic processes specific to the stationary phase, as well as the regulatory mechanisms that allow the bacteria to survive in conditions of stress, are described.
Collapse
Affiliation(s)
- P. Pletnev
- Moscow State University, Chemistry Department, Moscow, 119991, Russia
| | - I. Osterman
- Moscow State University, Chemistry Department, Moscow, 119991, Russia
| | - P. Sergiev
- Moscow State University, Chemistry Department, Moscow, 119991, Russia
| | - A. Bogdanov
- Moscow State University, Chemistry Department, Moscow, 119991, Russia
| | - O. Dontsova
- Moscow State University, Chemistry Department, Moscow, 119991, Russia
| |
Collapse
|
98
|
Cayrol B, Fortas E, Martret C, Cech G, Kloska A, Caulet S, Barbet M, Trépout S, Marco S, Taghbalout A, Busi F, Wegrzyn G, Arluison V. Riboregulation of the bacterial actin-homolog MreB by DsrA small noncoding RNA. Integr Biol (Camb) 2015; 7:128-41. [PMID: 25407044 DOI: 10.1039/c4ib00102h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The bacterial actin-homolog MreB is a key player in bacterial cell-wall biosynthesis and is required for the maintenance of the rod-like morphology of Escherichia coli. However, how MreB cellular levels are adjusted to growth conditions is poorly understood. Here, we show that DsrA, an E. coli small noncoding RNA (sRNA), is involved in the post-transcriptional regulation of mreB. DsrA is required for the downregulation of MreB cellular concentration during environmentally induced slow growth-rates, mainly growth at low temperature and during the stationary phase. DsrA interacts in an Hfq-dependent manner with the 5' region of mreB mRNA, which contains signals for translation initiation and thereby affects mreB translation and stability. Moreover, as DsrA is also involved in the regulation of two transcriptional regulators, σ(S) and the nucleoid associated protein H-NS, which negatively regulate mreB transcription, it also indirectly contributes to mreB transcriptional down-regulation. By using quantitative analyses, our results evidence the complexity of this regulation and the tangled interplay between transcriptional and post-transcriptional control. As transcription factors and sRNA-mediated post-transcriptional regulators use different timescales, we propose that the sRNA pathway helps to adapt to changes in temperature, but also indirectly mediates long-term regulation of MreB concentration. The tight regulation and fine-tuning of mreB gene expression in response to cellular stresses is discussed in regard to the effect of the MreB protein on cell elongation.
Collapse
Affiliation(s)
- Bastien Cayrol
- Laboratoire Léon Brillouin, CEA - Centre de Saclay, 91191 Gif-sur-Yvette, France.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
99
|
Lalaouna D, Morissette A, Carrier MC, Massé E. DsrA regulatory RNA represses bothhnsandrbsDmRNAs through distinct mechanisms inEscherichia coli. Mol Microbiol 2015; 98:357-69. [DOI: 10.1111/mmi.13129] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2015] [Indexed: 12/26/2022]
Affiliation(s)
- David Lalaouna
- Université de Sherbrooke; Faculty of Medicine and Health Sciences; Department of Biochemistry; RNA Group; Sherbrooke Québec Canada
| | - Audrey Morissette
- Université de Sherbrooke; Faculty of Medicine and Health Sciences; Department of Biochemistry; RNA Group; Sherbrooke Québec Canada
| | - Marie-Claude Carrier
- Université de Sherbrooke; Faculty of Medicine and Health Sciences; Department of Biochemistry; RNA Group; Sherbrooke Québec Canada
| | - Eric Massé
- Université de Sherbrooke; Faculty of Medicine and Health Sciences; Department of Biochemistry; RNA Group; Sherbrooke Québec Canada
| |
Collapse
|
100
|
Dexter J, Armshaw P, Sheahan C, Pembroke JT. The state of autotrophic ethanol production in Cyanobacteria. J Appl Microbiol 2015; 119:11-24. [PMID: 25865951 DOI: 10.1111/jam.12821] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 02/23/2015] [Accepted: 04/07/2015] [Indexed: 12/20/2022]
Abstract
Ethanol production directly from CO2 , utilizing genetically engineered photosynthetic cyanobacteria as a biocatalyst, offers significant potential as a renewable and sustainable source of biofuel. Despite the current absence of a commercially successful production system, significant resources have been deployed to realize this goal. Utilizing the pyruvate decarboxylase from Zymomonas species, metabolically derived pyruvate can be converted to ethanol. This review of both peer-reviewed and patent literature focuses on the genetic modifications utilized for metabolic engineering and the resultant effect on ethanol yield. Gene dosage, induced expression and cassette optimizat-ion have been analyzed to optimize production, with production rates of 0·1-0·5 g L(-1) day(-1) being achieved. The current 'toolbox' of molecular manipulations and future directions focusing on applicability, addressing the primary challenges facing commercialization of cyanobacterial technologies are discussed.
Collapse
Affiliation(s)
- J Dexter
- Molecular and Structural Biochemistry Laboratory, Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland.,Department of Design and Manufacturing Engineering, University of Limerick, Limerick, Ireland.,Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| | - P Armshaw
- Molecular and Structural Biochemistry Laboratory, Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland.,Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| | - C Sheahan
- Department of Design and Manufacturing Engineering, University of Limerick, Limerick, Ireland
| | - J T Pembroke
- Molecular and Structural Biochemistry Laboratory, Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland.,Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| |
Collapse
|