101
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Burbank LP, Stenger DC. A Temperature-Independent Cold-Shock Protein Homolog Acts as a Virulence Factor in Xylella fastidiosa. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:335-344. [PMID: 26808446 DOI: 10.1094/mpmi-11-15-0260-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Xylella fastidiosa, causal agent of Pierce's disease (PD) of grapevine, is a fastidious organism that requires very specific conditions for replication and plant colonization. Cold temperatures reduce growth and survival of X. fastidiosa both in vitro and in planta. However, little is known regarding physiological responses of X. fastidiosa to temperature changes. Cold-shock proteins (CSP), a family of nucleic acid-binding proteins, act as chaperones facilitating translation at low temperatures. Bacterial genomes often encode multiple CSP, some of which are strongly induced following exposure to cold. Additionally, CSP contribute to the general stress response through mRNA stabilization and posttranscriptional regulation. A putative CSP homolog (Csp1) with RNA-binding activity was identified in X. fastidiosa Stag's Leap. The csp1 gene lacked the long 5' untranslated region characteristic of cold-inducible genes and was expressed in a temperature-independent manner. As compared with the wild type, a deletion mutant of csp1 (∆csp1) had decreased survival rates following cold exposure and salt stress in vitro. The deletion mutant also was significantly less virulent in grapevine, as compared with the wild type, in the absence of cold stress. These results suggest an important function of X. fastidiosa Csp1 in response to cellular stress and during plant colonization.
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Affiliation(s)
- Lindsey P Burbank
- Agricultural Research Service, United States Department of Agriculture, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave, Parlier, CA 93648-9757, U.S.A
| | - Drake C Stenger
- Agricultural Research Service, United States Department of Agriculture, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave, Parlier, CA 93648-9757, U.S.A
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102
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Su Z, Zhu J, Xu Z, Xiao R, Zhou R, Li L, Chen H. A Transcriptome Map of Actinobacillus pleuropneumoniae at Single-Nucleotide Resolution Using Deep RNA-Seq. PLoS One 2016; 11:e0152363. [PMID: 27018591 PMCID: PMC4809551 DOI: 10.1371/journal.pone.0152363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/13/2016] [Indexed: 12/21/2022] Open
Abstract
Actinobacillus pleuropneumoniae is the pathogen of porcine contagious pleuropneumoniae, a highly contagious respiratory disease of swine. Although the genome of A. pleuropneumoniae was sequenced several years ago, limited information is available on the genome-wide transcriptional analysis to accurately annotate the gene structures and regulatory elements. High-throughput RNA sequencing (RNA-seq) has been applied to study the transcriptional landscape of bacteria, which can efficiently and accurately identify gene expression regions and unknown transcriptional units, especially small non-coding RNAs (sRNAs), UTRs and regulatory regions. The aim of this study is to comprehensively analyze the transcriptome of A. pleuropneumoniae by RNA-seq in order to improve the existing genome annotation and promote our understanding of A. pleuropneumoniae gene structures and RNA-based regulation. In this study, we utilized RNA-seq to construct a single nucleotide resolution transcriptome map of A. pleuropneumoniae. More than 3.8 million high-quality reads (average length ~90 bp) from a cDNA library were generated and aligned to the reference genome. We identified 32 open reading frames encoding novel proteins that were mis-annotated in the previous genome annotations. The start sites for 35 genes based on the current genome annotation were corrected. Furthermore, 51 sRNAs in the A. pleuropneumoniae genome were discovered, of which 40 sRNAs were never reported in previous studies. The transcriptome map also enabled visualization of 5'- and 3'-UTR regions, in which contained 11 sRNAs. In addition, 351 operons covering 1230 genes throughout the whole genome were identified. The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures). The transcriptional units described in this study provide a foundation for future studies concerning the gene functions and the transcriptional regulatory architectures of this pathogen.
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Affiliation(s)
- Zhipeng Su
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiawen Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhuofei Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ran Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
- * E-mail: (HC); (LL)
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, Wuhan 430070, China
- * E-mail: (HC); (LL)
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103
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Piersimoni L, Giangrossi M, Marchi P, Brandi A, Gualerzi CO, Pon CL. De novo Synthesis and Assembly of rRNA into Ribosomal Subunits during Cold Acclimation in Escherichia coli. J Mol Biol 2016; 428:1558-73. [PMID: 26953262 DOI: 10.1016/j.jmb.2016.02.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 10/22/2022]
Abstract
During the cold adaptation that follows a cold stress, bacterial cells undergo many physiological changes and extensive reprogramming of their gene expression pattern. Bulk gene expression is drastically reduced, while a set of cold shock genes is selectively and transiently expressed. The initial stage of cold acclimation is characterized by the establishment of a stoichiometric imbalance of the translation initiation factors (IFs)/ribosomes ratio that contributes to the preferential translation of cold shock transcripts. Whereas de novo synthesis of the IFs following cold stress has been documented, nothing was known concerning the activity of the rrn operons during the cold acclimation period. In this work, we focus on the expression of the rrn operons and the fate of rRNA after temperature downshift. We demonstrate that in Escherichia coli, rRNA synthesis does not stop during the cold acclimation phase, but continues with greater contribution of the P2 compared to the P1 promoter and all seven rrn operons are active, although their expression levels change with respect to pre-stress conditions. Eight hours after the 37°→10 °C temperature downshift, the newly transcribed rRNA represents up to 20% of total rRNA and is preferentially found in the polysomes. However, with respect to the de novo synthesis of the IFs, both rRNA transcription and maturation are slowed down drastically by cold stress, thereby accounting in part for the stoichiometric imbalance of the IFs/ribosomes. Overall, our data indicate that new ribosomes, which are possibly suitable to function at low temperature, are slowly assembled during cold acclimation.
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Affiliation(s)
- Lolita Piersimoni
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, 62032 Camerino, Italy
| | - Mara Giangrossi
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, 62032 Camerino, Italy
| | - Paolo Marchi
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, 62032 Camerino, Italy
| | - Anna Brandi
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, 62032 Camerino, Italy
| | - Claudio O Gualerzi
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, 62032 Camerino, Italy.
| | - Cynthia L Pon
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, 62032 Camerino, Italy
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104
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Jahn N, Brantl S. Heat-shock-induced refolding entails rapid degradation of bsrG toxin mRNA by RNases Y and J1. Microbiology (Reading) 2016; 162:590-599. [DOI: 10.1099/mic.0.000247] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Natalie Jahn
- Friedrich-Schiller-Universität Jena, Lehrstuhl für Genetik, AG Bakteriengenetik, Philosophenweg 12, 07743 Jena, Germany
| | - Sabine Brantl
- Friedrich-Schiller-Universität Jena, Lehrstuhl für Genetik, AG Bakteriengenetik, Philosophenweg 12, 07743 Jena, Germany
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105
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Jian H, Xiong L, Xu G, Xiao X, Wang F. Long 5' untranslated regions regulate the RNA stability of the deep-sea filamentous phage SW1. Sci Rep 2016; 6:21908. [PMID: 26898180 PMCID: PMC4762005 DOI: 10.1038/srep21908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/01/2016] [Indexed: 01/01/2023] Open
Abstract
Virus production in the deep-sea environment has been found to be high, and viruses have been suggested to play significant roles in the overall functioning of this ecosystem. Nevertheless, little is known about these viruses, including the mechanisms that control their production, which makes them one of the least understood biological entities on Earth. Previously, we isolated the filamentous phage SW1, whose virus production and gene transcription were found to be active at low temperatures, from a deep-sea bacterium, Shewanella piezotolerans WP3. In this study, the operon structure of phage SW1 is presented, which shows two operons with exceptionally long 5′ and 3′ untranslated regions (UTRs). In addition, the 5′UTR was confirmed to significantly influence the RNA stability of the SW1 transcripts. Our study revealed novel regulation of the operon and led us to propose a unique regulatory mechanism for Inoviruses. This type of RNA-based regulation may represent a mechanism for significant viral production in the cold deep biosphere.
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Affiliation(s)
- Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Lei Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Guanpeng Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, PR China
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106
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Audas TE, Lee S. Stressing out over long noncoding RNA. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:184-91. [PMID: 26142536 PMCID: PMC9479161 DOI: 10.1016/j.bbagrm.2015.06.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 12/26/2022]
Abstract
Genomic studies have revealed that humans possess far fewer protein-encoding genes than originally predicted. These over-estimates were drawn from the inherent developmental and stimuli-responsive complexity found in humans and other mammals, when compared to lower eukaryotic organisms. This left a conceptual void in many cellular networks, as a new class of functional molecules was necessary for "fine-tuning" the basic proteomic machinery. Transcriptomics analyses have determined that the vast majority of the genetic material is transcribed as noncoding RNA, suggesting that these molecules could provide the functional diversity initially sought from proteins. Indeed, as discussed in this review, long noncoding RNAs (lncRNAs), the largest family of noncoding transcripts, have emerged as common regulators of many cellular stressors; including heat shock, metabolic deprivation and DNA damage. These stimuli, while divergent in nature, share some common stress-responsive pathways, notably inhibition of cell proliferation. This role intrinsically makes stress-responsive lncRNA regulators potential tumor suppressor or proto-oncogenic genes. As the list of functional RNA molecules continues to rapidly expand it is becoming increasingly clear that the significance and functionality of this family may someday rival that of proteins. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Timothy E Audas
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Stephen Lee
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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107
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Fechter P, Parmentier D, Wu Z, Fuchsbauer O, Romby P, Marzi S. Traditional Chemical Mapping of RNA Structure In Vitro and In Vivo. Methods Mol Biol 2016; 1490:83-103. [PMID: 27665595 DOI: 10.1007/978-1-4939-6433-8_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chemical probing is often used to gain knowledge on the secondary and tertiary structures of RNA molecules either free or engaged in complexes with ligands. The method monitors the reactivity of each nucleotide towards chemicals of various specificities reflecting the hydrogen bonding environment of each nucleotide within the RNA molecule. In addition, information can be obtained on the binding site of a ligand (noncoding RNAs, protein, metabolites), and on RNA conformational changes that accompanied ligand binding or perturbation of the environmental cues. The detection of the modifications can be obtained either by using end-labeled RNA molecules or by primer extension using reverse transcriptase. The goal of this chapter is to provide the reader with an experimental guide to probe the structure of RNA in vitro and in vivo with the most suitable chemical probes.
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Affiliation(s)
- Pierre Fechter
- Biotechnologie et Signalisation Cellulaire, CNRS-INSERM, ESBS, Université de Strasbourg, 300 boulevard Sebastien Brant, Illkirch, 67412, France
| | - Delphine Parmentier
- Architecture et Réactivité de l'ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France
| | - ZongFu Wu
- College of Veterinary Medicine, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Olivier Fuchsbauer
- Architecture et Réactivité de l'ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France.
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France
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108
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Abstract
Pathogenic bacteria sense environmental cues, including the local temperature, to control the production of key virulence factors. Thermal regulation can be achieved at the level of DNA, RNA or protein and although many virulence factors are subject to thermal regulation, the exact mechanisms of control are yet to be elucidated in many instances. Understanding how virulence factors are regulated by temperature presents a significant challenge, as gene expression and protein production are often influenced by complex regulatory networks involving multiple transcription factors in bacteria. Here we highlight some recent insights into thermal regulation of virulence in pathogenic bacteria. We focus on bacteria which cause disease in mammalian hosts, which are at a significantly higher temperature than the outside environment. We outline the mechanisms of thermal regulation and how understanding this fundamental aspect of the biology of bacteria has implications for pathogenesis and human health.
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Affiliation(s)
- Oliver Lam
- a The Sir William Dunn School of Pathology ; University of Oxford ; Oxford , UK
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109
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Holder IT, Hartig JS. A matter of location: influence of G-quadruplexes on Escherichia coli gene expression. ACTA ACUST UNITED AC 2015; 21:1511-21. [PMID: 25459072 DOI: 10.1016/j.chembiol.2014.09.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/13/2014] [Accepted: 09/17/2014] [Indexed: 01/01/2023]
Abstract
We provide important insights into secondary-structure-mediated regulation of gene expression in Escherichia coli. In a comprehensive survey, we show that the strand orientation and the exact position of a G-quadruplex sequence strongly influence its effect on transcription and translation. We generated a series of reporter gene constructs that contained systematically varied positions of quadruplexes and respective control sequences inserted into several positions within the promoter, 50-UTR, and 30-UTR regions. G-rich sequences at specific locations in the promoter and also in proximity to the ribosome-binding site (RBS) showed pronounced inhibitory effects. Additionally, we rationally designed a system where quadruplex formation showed a gene-activating behavior. Moreover, we characterized quadruplexes in proximity to the RBS that occur naturally in E. coli genes, demonstrating that some of these quadruplexes exert significant modulation of gene expression. Taken together, our data show strong position-dependent effects of quadruplex secondary structures on bacterial gene expression.
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110
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Guijarro JA, Cascales D, García-Torrico AI, García-Domínguez M, Méndez J. Temperature-dependent expression of virulence genes in fish-pathogenic bacteria. Front Microbiol 2015. [PMID: 26217329 PMCID: PMC4496569 DOI: 10.3389/fmicb.2015.00700] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Virulence gene expression in pathogenic bacteria is modulated by environmental parameters. A key factor in this expression is temperature. Its effect on virulence gene expression in bacteria infecting warm-blooded hosts is well documented. Transcription of virulence genes in these bacteria is induced upon a shift from low environmental to a higher host temperature (37°C). Interestingly, host temperatures usually correspond to the optimum for growth of these pathogenic bacteria. On the contrary, in ectothermic hosts such as fish, molluscs, and amphibians, infection processes generally occur at a temperature lower than that for the optimal growth of the bacteria. Therefore, regulation of virulence gene expression in response to temperature shift has to be modulated in a different way to that which is found in bacteria infecting warm-blooded hosts. The current understanding of virulence gene expression and its regulation in response to temperature in fish-pathogenic bacteria is limited, but constant extension of our knowledge base is essential to enable a rational approach to the problem of the bacterial fish diseases affecting the aquaculture industry. This is an interesting issue and progress needs to be made in order to diminish the economic losses caused by these diseases. The intention of this review is, for the first time, to compile the scattered results existing in the field in order to lay the groundwork for future research. This article is an overview of those relevant virulence genes that are expressed at temperatures lower than that for optimal bacterial growth in different fish-pathogenic bacteria as well as the principal mechanisms that could be involved in their regulation.
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Affiliation(s)
- José A. Guijarro
- *Correspondence: José A. Guijarro, Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Instituto de Biotecnología de Asturias, Universidad de Oviedo, C/Julían Clavería 6, 33006 Oviedo, Spain,
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111
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Kang N, Choi E, Kim SG, Hwang J. Inhibitory effect of UvrD and DinG on the replication of ColE1-derived plasmids in Escherichia coli. Plasmid 2015; 81:32-41. [PMID: 26143370 DOI: 10.1016/j.plasmid.2015.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/20/2015] [Accepted: 06/25/2015] [Indexed: 11/18/2022]
Abstract
CspA has been identified as a major cold-shock protein in Escherichia coli. CspA binds to RNAs which are abnormally folded at low temperature and then acts as an RNA chaperone unfolding those RNAs. The dramatic expression of cspA at low temperature is contributed by posttranscriptional stability and robust translatability. Interestingly, when cspA mRNA encoding a premature nonsense codon was overexpressed at low temperature, cell growth was completely inhibited. This phenotype was termed LACE (the low temperature-dependent antibiotic effect of truncated cspA expression), and this lethality resulted from exclusive stalling of most ribosomes on mutant cspA mRNAs. In a previous study, we demonstrated that overexpression of the ATP-dependent DNA helicases, UvrD and DinG, suppressed the lethality and ribosome stalling caused by mutant cspA mRNA. In the present study, we attempted to elucidate how these two DNA helicases help recover normal growth under LACE condition. Interestingly, we found that UvrD and DinG appeared to have an ability to down-regulate the replication of pUC-based high copy plasmid. In plasmid copy number tests, the amount of pUC-based plasmid encoding mutant cspA was reduced by 3-10-fold when either UvrD or DinG was expressed. Through a β-galactosidase activity assay, we also confirmed that expression of the lacZα gene inserted into the pUC-based plasmid was significantly reduced due to down-regulation of plasmid replication. Our findings imply that UvrD and DinG, known as non-replicative helicases, play a novel role in the regulation of ColE1-like plasmid replication.
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Affiliation(s)
- Nalae Kang
- Department of Microbiology, Pusan National University, Busan, Republic of Korea
| | - Eunsil Choi
- Department of Microbiology, Pusan National University, Busan, Republic of Korea
| | - Sung-Gun Kim
- Department of Biomedical Science, Youngdong University, Chungbuk, Republic of Korea.
| | - Jihwan Hwang
- Department of Microbiology, Pusan National University, Busan, Republic of Korea.
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112
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Wang C, Jin C, Zhang J, Bao Q, Liu B, Tan H. Transcriptomic analysis of Thermoanaerobacter tengcongensis grown at different temperatures by RNA sequencing. J Genet Genomics 2015; 42:335-8. [PMID: 26165500 DOI: 10.1016/j.jgg.2015.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/26/2015] [Accepted: 03/03/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Chuan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunlei Jin
- School of Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiyu Bao
- School of Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Bo Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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113
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Hoynes-O'Connor A, Hinman K, Kirchner L, Moon TS. De novo design of heat-repressible RNA thermosensors in E. coli. Nucleic Acids Res 2015; 43:6166-79. [PMID: 25979263 PMCID: PMC4499127 DOI: 10.1093/nar/gkv499] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/04/2015] [Indexed: 11/15/2022] Open
Abstract
RNA-based temperature sensing is common in bacteria that live in fluctuating environments. Most naturally-occurring RNA thermosensors are heat-inducible, have long sequences, and function by sequestering the ribosome binding site in a hairpin structure at lower temperatures. Here, we demonstrate the de novo design of short, heat-repressible RNA thermosensors. These thermosensors contain a cleavage site for RNase E, an enzyme native to Escherichia coli and many other organisms, in the 5′ untranslated region of the target gene. At low temperatures, the cleavage site is sequestered in a stem–loop, and gene expression is unobstructed. At high temperatures, the stem–loop unfolds, allowing for mRNA degradation and turning off expression. We demonstrated that these thermosensors respond specifically to temperature and provided experimental support for the central role of RNase E in the mechanism. We also demonstrated the modularity of these RNA thermosensors by constructing a three-input composite circuit that utilizes transcriptional, post-transcriptional, and post-translational regulation. A thorough analysis of the 24 thermosensors allowed for the development of design guidelines for systematic construction of similar thermosensors in future applications. These short, modular RNA thermosensors can be applied to the construction of complex genetic circuits, facilitating rational reprogramming of cellular processes for synthetic biology applications.
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Affiliation(s)
- Allison Hoynes-O'Connor
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kristina Hinman
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lukas Kirchner
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tae Seok Moon
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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114
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Wagner D, Rinnenthal J, Narberhaus F, Schwalbe H. Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution. Nucleic Acids Res 2015; 43:5572-85. [PMID: 25940621 PMCID: PMC4477652 DOI: 10.1093/nar/gkv414] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/08/2015] [Indexed: 12/16/2022] Open
Abstract
The cyanobacterial hsp17 ribonucleicacid thermometer (RNAT) is one of the smallest naturally occurring RNAT. It forms a single hairpin with an internal 1×3-bulge separating the start codon in stem I from the ribosome binding site (RBS) in stem II. We investigated the temperature-dependent regulation of hsp17 by mapping individual base-pair stabilities from solvent exchange nuclear magnetic resonance (NMR) spectroscopy. The wild-type RNAT was found to be stabilized by two critical CG base pairs (C14-G27 and C13-G28). Replacing the internal 1×3 bulge by a stable CG base pair in hsp17rep significantly increased the global stability and unfolding cooperativity as evidenced by circular dichroism spectroscopy. From the NMR analysis, remote stabilization and non-nearest neighbour effects exist at the base-pair level, in particular for nucleotide G28 (five nucleotides apart from the side of mutation). Individual base-pair stabilities are coupled to the stability of the entire thermometer within both the natural and the stabilized RNATs by enthalpy–entropy compensation presumably mediated by the hydration shell. At the melting point the Gibbs energies of the individual nucleobases are equalized suggesting a consecutive zipper-type unfolding mechanism of the RBS leading to a dimmer-like function of hsp17 and switch-like regulation behaviour of hsp17rep. The data show how minor changes in the nucleotide sequence not only offset the melting temperature but also alter the mode of temperature sensing. The cyanobacterial thermosensor demonstrates the remarkable adjustment of natural RNATs to execute precise temperature control.
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Affiliation(s)
- Dominic Wagner
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | - Jörg Rinnenthal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr University, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
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Li J, Qi L, Guo Y, Yue L, Li Y, Ge W, Wu J, Shi W, Dong X. Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus. Sci Rep 2015; 5:9209. [PMID: 25784521 PMCID: PMC5378194 DOI: 10.1038/srep09209] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/23/2015] [Indexed: 11/12/2022] Open
Abstract
Psychrophilic methanogenic Archaea contribute significantly to global methane emissions, but archaeal cold adaptation mechanisms remain poorly understood. Hinted by that mRNA architecture determined secondary structure respond to cold more promptly than proteins, differential RNA-seq was used in this work to examine the genome-wide transcription start sites (TSSs) of the psychrophilic methanogen Methanolobus psychrophilus R15 and its response to cold. Unlike most prokaryotic mRNAs with short 5' untranslated regions (5' UTR, median lengths of 20-40 nt), 51% mRNAs of this methanogen have large 5' UTR (>50 nt). For 24% of the mRNAs, the 5' UTR is >150 nt. This implies that post-transcriptional regulation may be significance in the psychrophile. Remarkably, 219 (14%) genes possessed multiple gene TSSs (gTSSs), and 84 genes exhibited temperature-regulated gTSS selection to express alternative 5' UTR. Primer extension studies confirmed the temperature-dependent TSS selection and a stem-loop masking of ribosome binding sites was predicted from the longer 5' UTRs, suggesting alternative 5' UTRs-mediated translation regulation in the cold adaptation as well. In addition, 195 small RNAs (sRNAs) were detected, and Northern blots confirmed that many sRNAs were induced by cold. Thus, this study revealed an integrated transcriptional and post-transcriptional regulation for cold adaptation in a psychrophilic methanogen.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
| | - Yang Guo
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
| | - Yanping Li
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Weizhen Ge
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Jun Wu
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Wenyuan Shi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 10833 Le Conte Avenue, Los Angeles, CA90095, USA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
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116
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Duval M, Simonetti A, Caldelari I, Marzi S. Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics. Biochimie 2015; 114:18-29. [PMID: 25792421 DOI: 10.1016/j.biochi.2015.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/08/2015] [Indexed: 11/15/2022]
Abstract
To adapt their metabolism rapidly and constantly in response to environmental variations, bacteria often target the translation initiation process, during which the ribosome assembles on the mRNA. Here, we review different mechanisms of regulation mediated by cis-acting elements, sRNAs and proteins, showing, when possible, their intimate connection with the translational apparatus. Indeed the ribosome itself could play a direct role in several regulatory mechanisms. Different features of the regulatory signals (sequences, structures and their positions on the mRNA) are contributing to the large variety of regulatory mechanisms. Ribosome heterogeneity, variation of individual cells responses and the spatial and temporal organization of the translation process add more layers of complexity. This hampers to define manageable set of rules for bacterial translation initiation control.
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Affiliation(s)
- Mélodie Duval
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Angelita Simonetti
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
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117
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118
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Hansen AK, Degnan PH. Widespread expression of conserved small RNAs in small symbiont genomes. THE ISME JOURNAL 2014; 8:2490-502. [PMID: 25012903 PMCID: PMC4260695 DOI: 10.1038/ismej.2014.121] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 06/02/2014] [Accepted: 06/05/2014] [Indexed: 12/17/2022]
Abstract
Genome architecture of a microbe markedly changes when it transitions from a free-living lifestyle to an obligate symbiotic association within eukaryotic cells. These symbiont genomes experience numerous rearrangements and massive gene loss, which is expected to radically alter gene regulatory networks compared with those of free-living relatives. As such, it remains unclear whether and how these small symbiont genomes regulate gene expression. Here, using a label-free mass-spec quantification approach we found that differential protein regulation occurs in Buchnera, a model symbiont with a reduced genome, when it transitions between two distinct life stages. However, differential mRNA expression could not be detected between Buchnera life stages, despite the presence of a small number of putative transcriptional regulators. Instead a comparative analysis of small RNA expression profiles among five divergent Buchnera lineages, spanning a variety of Buchnera life stages, reveals 140 novel intergenic and antisense small RNAs and 517 untranslated regions that were significantly expressed, some of which have been conserved for ∼65 million years. In addition, the majority of these small RNAs exhibit both sequence covariation and thermodynamic stability, indicators of a potential structural RNA role. Together, these data suggest that gene regulation at the post-transcriptional level may be important in Buchnera. This is the first study to empirically identify Buchnera small RNAs, and we propose that these novel small RNAs may facilitate post-transcriptional regulation through translational inhibition/activation, and/or transcript stability. Ultimately, post-transcriptional regulation may shape metabolic complementation between Buchnera and its aphid host, thus impacting the animal's ecology and evolution.
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Affiliation(s)
- Allison K Hansen
- Department of Entomology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Ecology and Evolutionary Biology, Microbial Diversity Institute, Yale University, New Haven, CT, USA
| | - Patrick H Degnan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Microbial Pathogenesis, Microbial Diversity Institute, Yale University, New Haven, CT, USA
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119
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Delvillani F, Sciandrone B, Peano C, Petiti L, Berens C, Georgi C, Ferrara S, Bertoni G, Pasini ME, Dehò G, Briani F. Tet-Trap, a genetic approach to the identification of bacterial RNA thermometers: application to Pseudomonas aeruginosa. RNA (NEW YORK, N.Y.) 2014; 20:1963-1976. [PMID: 25336583 PMCID: PMC4238360 DOI: 10.1261/rna.044354.114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 09/10/2014] [Indexed: 06/04/2023]
Abstract
Modulation of mRNA translatability either by trans-acting factors (proteins or sRNAs) or by in cis-acting riboregulators is widespread in bacteria and controls relevant phenotypic traits. Unfortunately, global identification of post-transcriptionally regulated genes is complicated by poor structural and functional conservation of regulatory elements and by the limitations of proteomic approaches in protein quantification. We devised a genetic system for the identification of post-transcriptionally regulated genes and we applied this system to search for Pseudomonas aeruginosa RNA thermometers, a class of regulatory RNA that modulates gene translation in response to temperature changes. As P. aeruginosa is able to thrive in a broad range of environmental conditions, genes differentially expressed at 37 °C versus lower temperatures may be involved in infection and survival in the human host. We prepared a plasmid vector library with translational fusions of P. aeruginosa DNA fragments (PaDNA) inserted upstream of TIP2, a short peptide able to inactivate the Tet repressor (TetR) upon expression. The library was assayed in a streptomycin-resistant merodiploid rpsL(+)/rpsL31 Escherichia coli strain in which the dominant rpsL(+) allele, which confers streptomycin sensitivity, was repressed by TetR. PaDNA fragments conferring thermosensitive streptomycin resistance (i.e., expressing PaDNA-TIP2 fusions at 37°C, but not at 28°C) were sequenced. We identified four new putative thermosensors. Two of them were validated with conventional reporter systems in E. coli and P. aeruginosa. Interestingly, one regulates the expression of ptxS, a gene implicated in P. aeruginosa pathogenesis.
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Affiliation(s)
- Francesco Delvillani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Barbara Sciandrone
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Clelia Peano
- Istituto di Tecnologie Biomediche, CNR, 20090 Segrate, Italy
| | - Luca Petiti
- Istituto di Tecnologie Biomediche, CNR, 20090 Segrate, Italy Doctoral Program of Molecular and Translational Medicine, Università degli Studi di Milano, 20133 Milano, Italy
| | - Christian Berens
- Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Christiane Georgi
- Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Silvia Ferrara
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Giovanni Bertoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Maria Enrica Pasini
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Gianni Dehò
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
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120
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Righetti F, Narberhaus F. How to find RNA thermometers. Front Cell Infect Microbiol 2014; 4:132. [PMID: 25279353 PMCID: PMC4166951 DOI: 10.3389/fcimb.2014.00132] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/02/2014] [Indexed: 11/27/2022] Open
Abstract
Temperature is one of the decisive signals that a mammalian pathogen has entered its warm-blooded host. Among the many ways to register temperature changes, bacteria often use temperature-modulated structures in the untranslated region of mRNAs. In this article, we describe how such RNA thermometers (RNATs) have been discovered one by one upstream of heat shock and virulence genes in the past, and how next-generation sequencing approaches are able to reveal novel temperature-responsive RNA structures on a global scale.
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121
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Dorman CJ. H-NS-like nucleoid-associated proteins, mobile genetic elements and horizontal gene transfer in bacteria. Plasmid 2014; 75:1-11. [DOI: 10.1016/j.plasmid.2014.06.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 11/29/2022]
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Czapski TR, Trun N. Expression of csp genes in E. coli K-12 in defined rich and defined minimal media during normal growth, and after cold-shock. Gene 2014; 547:91-7. [PMID: 24952137 DOI: 10.1016/j.gene.2014.06.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/11/2014] [Accepted: 06/17/2014] [Indexed: 11/25/2022]
Abstract
Cold-shock proteins (Csps) are a family of small nucleic acid-binding proteins found in 72% of sequenced bacterial genomes. Where it has been examined, at least one csp gene is required for cell viability. In Escherichia coli K-12, there are nine homologous csp genes named A-I. Regulation studies performed on individual members of this family have suggested that cspA, cspB, cspG, and cspI are cold-induced, cspC and cspE are constitutively expressed, cspD is stationary phase induced, and the induction patterns for cspF and cspH have yet to be determined. Aside from microarray studies, transcript levels from all nine csp genes have never been assayed using the same technique or in the same cells. The purpose of this study was to use quantitative RT-PCR to establish csp expression patterns for all nine csp genes at 37°C in defined rich and defined minimal media, and after a shift to 15°C for either 1h or 4h. We found that transcript levels for each of the csp genes changed throughout the growth curve. Transcripts for cspA, -B, and -E were more abundant than those detected for the other csp genes in defined rich medium. cspE mRNA levels in defined minimal medium were drastically higher than mRNA for the other csp genes. Of the nine csp genes, only cspI showed a significant increase in mRNA accumulation after cold-shock in defined rich medium. When mRNA accumulation was compared across the nine csp genes, there were more cspE transcripts in the cell than cspA, -B, -G, or -I transcripts after 1h cold-shock in either defined rich or defined minimal media. In defined minimal medium, transcription of cspA, -B, -G, and -I was induced after cold-shock.
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Affiliation(s)
- Tiffaney R Czapski
- Dept. Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Nancy Trun
- Dept. Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA.
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123
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Sahukhal GS, Elasri MO. Identification and characterization of an operon, msaABCR, that controls virulence and biofilm development in Staphylococcus aureus. BMC Microbiol 2014; 14:154. [PMID: 24915884 PMCID: PMC4229872 DOI: 10.1186/1471-2180-14-154] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 06/05/2014] [Indexed: 12/02/2022] Open
Abstract
Background Community-acquired, methicillin-resistant Staphylococcus aureus strains often cause localized infections in immunocompromised hosts, but some strains show enhanced virulence leading to severe infections even among healthy individuals with no predisposing risk factors. The genetic basis for this enhanced virulence has yet to be determined. S. aureus possesses a wide variety of virulence factors, the expression of which is carefully coordinated by a variety of regulators. Several virulence regulators have been well characterized, but others have yet to be thoroughly investigated. Previously, we identified the msa gene as a regulator of several virulence genes, biofilm development, and antibiotic resistance. We also found evidence of the involvement of upstream genes in msa function. Results To investigate the mechanism of regulation of the msa gene (renamed msaC), we examined the upstream genes whose expression was affected by its deletion. We showed that msaC is part of a newly defined four-gene operon (msaABCR), in which msaC is a non-protein-coding RNA that is essential for the function of the operon. Furthermore, we found that an antisense RNA (msaR) is complementary to the 5′ end of the msaB gene and is expressed in a growth phase-dependent manner suggesting that it is involved in regulation of the operon. Conclusion These findings allow us to define a new operon that regulates fundamental phenotypes in S. aureus such as biofilm development and virulence. Characterization of the msaABCR operon will allow us to investigate the mechanism of function of this operon and the role of the individual genes in regulation and interaction with its targets. This study identifies a new element in the complex regulatory circuits in S. aureus, and our findings may be therapeutically relevant.
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Affiliation(s)
- Gyan S Sahukhal
- Department of Biological Sciences, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-0001, USA.
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124
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Wachter A. Gene regulation by structured mRNA elements. Trends Genet 2014; 30:172-81. [PMID: 24780087 DOI: 10.1016/j.tig.2014.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/20/2014] [Indexed: 01/19/2023]
Abstract
The precise temporal and spatial coordination of gene activity, based on the integration of internal and external signals, is crucial for the accurate functioning of all biological processes. Although the basic principles of gene expression were established some 60 years ago, recent research has revealed a surprising complexity in the control of gene activity. Many of these gene regulatory mechanisms occur at the level of the mRNA, including sophisticated gene control tasks mediated by structured mRNA elements. We now know that mRNA folds can serve as highly specific receptors for various types of molecules, as exemplified by metabolite-binding riboswitches, and interfere with pro- and eukaryotic gene expression at the level of transcription, translation, and RNA processing. Gene regulation by structured mRNA elements comprises versatile strategies including self-cleaving ribozymes, RNA-folding-mediated occlusion or presentation of cis-regulatory sequences, and sequestration of trans-acting factors including other RNAs and proteins.
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Affiliation(s)
- Andreas Wachter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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125
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Churkin A, Avihoo A, Shapira M, Barash D. RNAthermsw: direct temperature simulations for predicting the location of RNA thermometers. PLoS One 2014; 9:e94340. [PMID: 24718440 PMCID: PMC3981793 DOI: 10.1371/journal.pone.0094340] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 03/14/2014] [Indexed: 11/18/2022] Open
Abstract
The mechanism of RNA thermometers is a subject of growing interest. Also known as RNA thermosensors, these temperature-sensitive segments of the mRNA regulate gene expression by changing their secondary structure in response to temperature fluctuations. The detection of RNA thermometers in various genes of interest is valuable as it could lead to the discovery of new thermometers participating in fundamental processes such as preferential translation during heat-shock. RNAthermsw is a user-friendly webserver for predicting the location of RNA thermometers using direct temperature simulations. It operates by analyzing dotted figures generated as a result of a moving window that performs successive energy minimization folding predictions. Inputs include the RNA sequence, window size, and desired temperature change. RNAthermsw can be freely accessed at http://www.cs.bgu.ac.il/~rnathemsw/RNAthemsw/ (with the slash sign at the end). The website contains a help page with explanations regarding the exact usage.
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Affiliation(s)
- Alexander Churkin
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
| | | | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
- * E-mail:
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126
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Abstract
RNA dynamics play a fundamental role in many cellular functions. However, there is no general framework to describe these complex processes, which typically consist of many structural maneuvers that occur over timescales ranging from picoseconds to seconds. Here, we classify RNA dynamics into distinct modes representing transitions between basins on a hierarchical free-energy landscape. These transitions include large-scale secondary-structural transitions at >0.1-s timescales, base-pair/tertiary dynamics at microsecond-to-millisecond timescales, stacking dynamics at timescales ranging from nanoseconds to microseconds, and other "jittering" motions at timescales ranging from picoseconds to nanoseconds. We review various modes within these three different tiers, the different mechanisms by which they are used to regulate function, and how they can be coupled together to achieve greater functional complexity.
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127
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Cao Y, Li J, Jiang N, Dong X. Mechanism for stabilizing mRNAs involved in methanol-dependent methanogenesis of cold-adaptive Methanosarcina mazei zm-15. Appl Environ Microbiol 2014; 80:1291-8. [PMID: 24317083 PMCID: PMC3911069 DOI: 10.1128/aem.03495-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/02/2013] [Indexed: 11/20/2022] Open
Abstract
Methylotrophic methanogenesis predominates at low temperatures in the cold Zoige wetland in Tibet. To elucidate the basis of cold-adapted methanogenesis in these habitats, Methanosarcina mazei zm-15 was isolated, and the molecular basis of its cold activity was studied. For this strain, aceticlastic methanogenesis was reduced 7.7-fold during growth at 15°C versus 30°C. Methanol-derived methanogenesis decreased only 3-fold under the same conditions, suggesting that it is more cold adaptive. Reverse transcription-quantitative PCR (RT-qPCR) detected <2-fold difference in the transcript abundances of mtaA1, mtaB1, and mtaC1, the methanol methyltransferase (Mta) genes, in 30°C versus 15°C culture, while ackA and pta mRNAs, encoding acetate kinase (Ack) and phosphotransacetylase (Pta) in aceticlastic methanogenesis, were 4.5- and 6.8-fold higher in 30°C culture than in 15°C culture. The in vivo half-lives of mtaA1 and mtaC1B1 mRNAs were similar in 30°C and 15°C cultures. However, the pta-ackA mRNA half-life was significantly reduced in 15°C culture compared to 30°C culture. Using circularized RNA RT-PCR, large 5' untranslated regions (UTRs) (270 nucleotides [nt] and 238 nt) were identified for mtaA1 and mtaC1B1 mRNAs, while only a 27-nt 5' UTR was present in the pta-ackA transcript. Removal of the 5' UTRs significantly reduced the in vitro half-lives of mtaA1 and mtaC1B1 mRNAs. Remarkably, fusion of the mtaA1 or mtaC1B1 5' UTRs to pta-ackA mRNA increased its in vitro half-life at both 30°C and 15°C. These results demonstrate that the large 5' UTRs significantly enhance the stability of the mRNAs involved in methanol-derived methanogenesis in the cold-adaptive M. mazei zm-15.
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Affiliation(s)
- Yi Cao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
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128
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Pfeifer-Sancar K, Mentz A, Rückert C, Kalinowski J. Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique. BMC Genomics 2013; 14:888. [PMID: 24341750 PMCID: PMC3890552 DOI: 10.1186/1471-2164-14-888] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/03/2013] [Indexed: 01/16/2023] Open
Abstract
Background The use of RNAseq to resolve the transcriptional organization of an organism was established in recent years and also showed the complexity and dynamics of bacterial transcriptomes. The aim of this study was to comprehensively investigate the transcriptome of the industrially relevant amino acid producer and model organism Corynebacterium glutamicum by RNAseq in order to improve its genome annotation and to describe important features for transcription and translation. Results RNAseq data sets were obtained by two methods, one that focuses on 5′-ends of primary transcripts and another that provides the overall transcriptome with an improved resolution of 3′-ends of transcripts. Subsequent data analysis led to the identification of more than 2,000 transcription start sites (TSSs), the definition of 5′-UTRs (untranslated regions) for annotated protein-coding genes, operon structures and many novel transcripts located between or in antisense orientation to protein-coding regions. Interestingly, a high number of mRNAs (33%) is transcribed as leaderless transcripts. From the data, consensus promoter and ribosome binding site (RBS) motifs were identified and it was shown that the majority of genes in C. glutamicum are transcribed monocistronically, but operons containing up to 16 genes are also present. Conclusions The comprehensive transcriptome map of C. glutamicum established in this study represents a major step forward towards a complete definition of genetic elements (e.g. promoter regions, gene starts and stops, 5′-UTRs, RBSs, transcript starts and ends) and provides the ideal basis for further analyses on transcriptional regulatory networks in this organism. The methods developed are easily applicable for other bacteria and have the potential to be used also for quantification of transcriptomes, replacing microarrays in the near future.
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Affiliation(s)
| | | | | | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany.
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129
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Lai D, Proctor JR, Meyer IM. On the importance of cotranscriptional RNA structure formation. RNA (NEW YORK, N.Y.) 2013; 19:1461-1473. [PMID: 24131802 PMCID: PMC3851714 DOI: 10.1261/rna.037390.112] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation.
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130
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Barria C, Malecki M, Arraiano CM. Bacterial adaptation to cold. MICROBIOLOGY-SGM 2013; 159:2437-2443. [PMID: 24068238 DOI: 10.1099/mic.0.052209-0] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Micro-organisms react to a rapid temperature downshift by triggering a physiological response to ensure survival in unfavourable conditions. Adaptation includes changes in membrane composition and in the translation and transcription machineries. The cold shock response leads to a growth block and overall repression of translation; however, there is the induction of a set of specific proteins that help to tune cell metabolism and readjust it to the new conditions. For a mesophile like E. coli, the adaptation process takes about 4 h. Although the bacterial cold shock response was discovered over two decades ago we are still far from understanding this process. In this review, we aim to describe current knowledge, focusing on the functions of RNA-interacting proteins and RNases involved in cold shock adaptation.
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Affiliation(s)
- C Barria
- Instituto de Tecnologia Quimica e Biologica (ITQB), Oeiras, Portugal
| | - M Malecki
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland.,Instituto de Tecnologia Quimica e Biologica (ITQB), Oeiras, Portugal
| | - C M Arraiano
- Instituto de Tecnologia Quimica e Biologica (ITQB), Oeiras, Portugal
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131
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Lee K, Huang X, Yang C, Lee D, Ho V, Nobuta K, Fan JB, Wang K. A genome-wide survey of highly expressed non-coding RNAs and biological validation of selected candidates in Agrobacterium tumefaciens. PLoS One 2013; 8:e70720. [PMID: 23950988 PMCID: PMC3738593 DOI: 10.1371/journal.pone.0070720] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 06/26/2013] [Indexed: 12/31/2022] Open
Abstract
Agrobacterium tumefaciens is a plant pathogen that has the natural ability of delivering and integrating a piece of its own DNA into plant genome. Although bacterial non-coding RNAs (ncRNAs) have been shown to regulate various biological processes including virulence, we have limited knowledge of how Agrobacterium ncRNAs regulate this unique inter-Kingdom gene transfer. Using whole transcriptome sequencing and an ncRNA search algorithm developed for this work, we identified 475 highly expressed candidate ncRNAs from A. tumefaciens C58, including 101 trans-encoded small RNAs (sRNAs), 354 antisense RNAs (asRNAs), 20 5' untranslated region (UTR) leaders including a RNA thermosensor and 6 riboswitches. Moreover, transcription start site (TSS) mapping analysis revealed that about 51% of the mapped mRNAs have 5' UTRs longer than 60 nt, suggesting that numerous cis-acting regulatory elements might be encoded in the A. tumefaciens genome. Eighteen asRNAs were found on the complementary strands of virA, virB, virC, virD, and virE operons. Fifteen ncRNAs were induced and 7 were suppressed by the Agrobacterium virulence (vir) gene inducer acetosyringone (AS), a phenolic compound secreted by the plants. Interestingly, fourteen of the AS-induced ncRNAs have putative vir box sequences in the upstream regions. We experimentally validated expression of 36 ncRNAs using Northern blot and Rapid Amplification of cDNA Ends analyses. We show functional relevance of two 5' UTR elements: a RNA thermonsensor (C1_109596F) that may regulate translation of the major cold shock protein cspA, and a thi-box riboswitch (C1_2541934R) that may transcriptionally regulate a thiamine biosynthesis operon, thiCOGG. Further studies on ncRNAs functions in this bacterium may provide insights and strategies that can be used to better manage pathogenic bacteria for plants and to improve Agrobacterum-mediated plant transformation.
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Affiliation(s)
- Keunsub Lee
- Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, Iowa, United States of America
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Xiaoqiu Huang
- Department of Computer Science, Iowa State University, Ames, Iowa, United States of America
| | - Chichun Yang
- Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, Iowa, United States of America
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Danny Lee
- Scientific Research, Illumina Inc., San Diego, California, United States of America
| | - Vincent Ho
- Scientific Research, Illumina Inc., San Diego, California, United States of America
| | - Kan Nobuta
- Scientific Research, Illumina Inc., San Diego, California, United States of America
| | - Jian-Bing Fan
- Scientific Research, Illumina Inc., San Diego, California, United States of America
| | - Kan Wang
- Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, Iowa, United States of America
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
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132
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Ivancic T, Jamnik P, Stopar D. Cold shock CspA and CspB protein production during periodic temperature cycling in Escherichia coli. BMC Res Notes 2013; 6:248. [PMID: 23815967 PMCID: PMC3704898 DOI: 10.1186/1756-0500-6-248] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 06/25/2013] [Indexed: 11/30/2022] Open
Abstract
Background Temperature is an important environmental factor which can dramatically affect biochemical processes in bacteria. Temperatures above optimal cause heat shock, while low temperatures induce cold shock. Since the physiological response of the bacterium Escherichia coli to slow temperature fluctuation is not well known, we investigated the effect of periodic temperature cycling between 37° and 8°C with a period of 2 h on proteome profile, cold shock CspA and CspB protein and gene production. Results Several proteins (i.e. succinyl-CoA synthetase subunit alpha, periplasmic oligopeptide-binding protein, maltose-binding periplasmic protein, outer membrane porin protein, flavodoxin-1, phosphoserine aminotransferase) were up or down regulated during temperature cycling, in addition to CspA and CspB production. The results indicate that transcription of cspA and cspB increased during each temperature downshift and consistently decreased after each temperature upshift. In sharp contrast CspA-FLAG and CspB-FLAG protein concentrations in the cell increased during the first temperature down-shift and remained unresponsive to further temperature fluctuations. The proteins CspA-FLAG and CspB-FLAG were not significantly degraded during the temperature cycling. Conclusion The study demonstrated that slow periodic temperature cycling affected protein production compared to cells constantly incubated at 37°C or during classical cold shock. Bacterial cspA and cspB mRNA transcript levels fluctuated in synchrony with the temperature fluctuations. There was no corresponding pattern of CspA and CspB protein production during temperature cycling.
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Affiliation(s)
- Tina Ivancic
- Laboratory of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Večna Pot 111, 1000 Ljubljana, Slovenia
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133
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Steinmann R, Dersch P. Thermosensing to adjust bacterial virulence in a fluctuating environment. Future Microbiol 2013; 8:85-105. [PMID: 23252495 DOI: 10.2217/fmb.12.129] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The lifecycle of most microbial pathogens can be divided into two states: existence outside and inside their hosts. The sudden temperature upshift experienced upon entry from environmental or vector reservoirs into a warm-blooded host is one of the most crucial signals informing the pathogens to adjust virulence gene expression and their host-stress survival program. This article reviews the plethora of sophisticated strategies that bacteria have evolved to sense temperature, and outlines the molecular signal transduction mechanisms used to modulate synthesis of crucial virulence determinants. The molecular details of thermal control through conformational changes of DNA, RNA and proteins are summarized, complex and diverse thermosensing principles are introduced and their potential as drug targets or synthetic tools are discussed.
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Affiliation(s)
- Rebekka Steinmann
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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134
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Zhu JYA, Steif A, Proctor JR, Meyer IM. Transient RNA structure features are evolutionarily conserved and can be computationally predicted. Nucleic Acids Res 2013; 41:6273-85. [PMID: 23625966 PMCID: PMC3695514 DOI: 10.1093/nar/gkt319] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Functional RNA structures tend to be conserved during evolution. This finding is, for example, exploited by comparative methods for RNA secondary structure prediction that currently provide the state-of-art in terms of prediction accuracy. We here provide strong evidence that homologous RNA genes not only fold into similar final RNA structures, but that their folding pathways also share common transient structural features that have been evolutionarily conserved. For this, we compile and investigate a non-redundant data set of 32 sequences with known transient and final RNA secondary structures and devise a dedicated computational analysis pipeline.
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Affiliation(s)
- Jing Yun A Zhu
- Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
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135
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Structural requirement in Clostridium perfringens collagenase mRNA 5' leader sequence for translational induction through small RNA-mRNA base pairing. J Bacteriol 2013; 195:2937-46. [PMID: 23585542 DOI: 10.1128/jb.00148-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Gram-positive anaerobic bacterium Clostridium perfringens is pathogenic to humans and animals, and the production of its toxins is strictly regulated during the exponential phase. We recently found that the 5' leader sequence of the colA transcript encoding collagenase, which is a major toxin of this organism, is processed and stabilized in the presence of the small RNA VR-RNA. The primary colA 5'-untranslated region (5'UTR) forms a long stem-loop structure containing an internal bulge and masks its own ribosomal binding site. Here we found that VR-RNA directly regulates colA expression through base pairing with colA mRNA in vivo. However, when the internal bulge structure was closed by point mutations in colA mRNA, translation ceased despite the presence of VR-RNA. In addition, a mutation disrupting the colA stem-loop structure induced mRNA processing and ColA-FLAG translational activation in the absence of VR-RNA, indicating that the stem-loop and internal bulge structure of the colA 5' leader sequence is important for regulation by VR-RNA. On the other hand, processing was required for maximal ColA expression but was not essential for VR-RNA-dependent colA regulation. Finally, colA processing and translational activation were induced at a high temperature without VR-RNA. These results suggest that inhibition of the colA 5' leader structure through base pairing is the primary role of VR-RNA in colA regulation and that the colA 5' leader structure is a possible thermosensor.
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136
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Hoe CH, Raabe CA, Rozhdestvensky TS, Tang TH. Bacterial sRNAs: regulation in stress. Int J Med Microbiol 2013; 303:217-29. [PMID: 23660175 DOI: 10.1016/j.ijmm.2013.04.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/26/2013] [Accepted: 04/07/2013] [Indexed: 11/28/2022] Open
Abstract
Bacteria are often exposed to a hostile environment and have developed a plethora of cellular processes in order to survive. A burgeoning list of small non-coding RNAs (sRNAs) has been identified and reported to orchestrate crucial stress responses in bacteria. Among them, cis-encoded sRNA, trans-encoded sRNA, and 5'-untranslated regions (UTRs) of the protein coding sequence are influential in the bacterial response to environmental cues, such as fluctuation of temperature and pH as well as other stress conditions. This review summarizes the role of bacterial sRNAs in modulating selected stress conditions and highlights the alliance between stress response and clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial defense.
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Affiliation(s)
- Chee-Hock Hoe
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Kepala Batas, 13200 Penang, Malaysia.
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137
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Di Pietro F, Brandi A, Dzeladini N, Fabbretti A, Carzaniga T, Piersimoni L, Pon CL, Giuliodori AM. Role of the ribosome-associated protein PY in the cold-shock response of Escherichia coli. Microbiologyopen 2013; 2:293-307. [PMID: 23420694 PMCID: PMC3633353 DOI: 10.1002/mbo3.68] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/18/2012] [Accepted: 12/28/2012] [Indexed: 11/25/2022] Open
Abstract
Protein Y (PY) is an Escherichia coli cold-shock protein which has been proposed to be responsible for the repression of bulk protein synthesis during cold adaptation. Here, we present in vivo and in vitro data which clarify the role of PY and its mechanism of action. Deletion of yfiA, the gene encoding protein PY, demonstrates that this protein is dispensable for cold adaptation and is not responsible for the shutdown of bulk protein synthesis at the onset of the stress, although it is able to partially inhibit translation. In vitro assays reveal that the extent of PY inhibition changes with different mRNAs and that this inhibition is related to the capacity of PY of binding 30S subunits with a fairly strong association constant, thus stimulating the formation of 70S monomers. Furthermore, our data provide evidence that PY competes with the other ribosomal ligands for the binding to the 30S subunits. Overall these results suggest an alternative model to explain PY function during cold shock and to reconcile the inhibition caused by PY with the active translation observed for some mRNAs during cold shock.
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Affiliation(s)
- Fabio Di Pietro
- Laboratory of Molecular Biology and Biotechnology, School of Biosciences and Biotechnology, University of Camerino, 62032 Camerino, MC, Italy
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138
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Lehti TA, Bauchart P, Kukkonen M, Dobrindt U, Korhonen TK, Westerlund-Wikström B. Phylogenetic group-associated differences in regulation of the common colonization factor Mat fimbria in Escherichia coli. Mol Microbiol 2013; 87:1200-22. [PMID: 23347101 DOI: 10.1111/mmi.12161] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2013] [Indexed: 11/28/2022]
Abstract
Heterogeneity of cell population is a key component behind the evolutionary success of Escherichia coli. The heterogeneity supports species adaptation and mainly results from lateral gene transfer. Adaptation may also involve genomic alterations that affect regulation of conserved genes. Here we analysed regulation of the mat (or ecp) genes that encode a conserved fimbrial adhesin of E. coli. We found that the differential and temperature-sensitive expression control of the mat operon is dependent on mat promoter polymorphism and closely linked to phylogenetic grouping of E. coli. In the mat promoter lineage favouring fimbriae expression, the mat operon-encoded regulator MatA forms a positive feedback loop that overcomes the repression by H-NS and stabilizes the fimbrillin mRNA under low growth temperature, acidic pH or elevated levels of acetate. The study exemplifies phylogenetic group-associated expression of a highly common surface organelle in E. coli.
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Affiliation(s)
- Timo A Lehti
- Division of General Microbiology, Department of Biosciences, FI-00014 University of Helsinki, Helsinki, Finland
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139
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Enhanced in vitro translation at reduced temperatures using a cold-shock RNA motif. Biotechnol Lett 2012; 35:389-95. [DOI: 10.1007/s10529-012-1091-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
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140
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Gerarden KP, Fuchs AM, Koch JM, Mueller MM, Graupner DR, O'Rorke JT, Frost CD, Heinen HA, Lackner ER, Schoeller SJ, House PG, Peterson FC, Veldkamp CT. Solution structure of the cold-shock-like protein from Rickettsia rickettsii. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1284-8. [PMID: 23143233 PMCID: PMC3515365 DOI: 10.1107/s174430911203881x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 09/10/2012] [Indexed: 11/25/2022]
Abstract
The solution structure of the cold-shock-like protein from R. rickettsii, the causative agent of Rocky Mountain spotted fever, is reported. Rocky Mountain spotted fever is caused by Rickettsia rickettsii infection. R. rickettsii can be transmitted to mammals, including humans, through the bite of an infected hard-bodied tick of the family Ixodidae. Since the R. rickettsii genome contains only one cold-shock-like protein and given the essential nature of cold-shock proteins in other bacteria, the structure of the cold-shock-like protein from R. rickettsii was investigated. With the exception of a short α-helix found between β-strands 3 and 4, the solution structure of the R. rickettsii cold-shock-like protein has the typical Greek-key five-stranded β-barrel structure found in most cold-shock domains. Additionally, the R. rickettsii cold-shock-like protein, with a ΔG of unfolding of 18.4 kJ mol−1, has a similar stability when compared with other bacterial cold-shock proteins.
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Affiliation(s)
- Kyle P Gerarden
- Department of Chemistry, University of Wisconsin-Whitewater, 800 West Main Street, Whitewater, WI 53190, USA
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141
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ncRNAs and thermoregulation: a view in prokaryotes and eukaryotes. FEBS Lett 2012; 586:4061-9. [PMID: 23098758 DOI: 10.1016/j.febslet.2012.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/09/2012] [Accepted: 10/10/2012] [Indexed: 11/24/2022]
Abstract
During cellular stress response, a widespread inhibition of transcription and blockade of splicing and other post-transcriptional processing is detected, while certain specific genes are induced. In particular, free-living cells constantly monitor temperature. When the thermal condition changes, they activate a set of genes coding for proteins that participate in the response. Non-coding RNAs, ncRNAs, and conformational changes in specific regions of mRNAs seem also to be crucial regulators that enable the cell to adjust its physiology to environmental changes. They exert their effects following the same principles in all organisms and may affect all steps of gene expression. These ncRNAs and structural elements as related to thermal stress response in bacteria are reviewed. The resemblances to eukaryotic ncRNAs are highlighted.
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142
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Shapiro RS, Cowen LE. Thermal control of microbial development and virulence: molecular mechanisms of microbial temperature sensing. mBio 2012; 3:e00238-12. [PMID: 23033469 PMCID: PMC3518907 DOI: 10.1128/mbio.00238-12] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Temperature is a critical and ubiquitous environmental signal that governs the development and virulence of diverse microbial species, including viruses, archaea, bacteria, fungi, and parasites. Microbial survival is contingent upon initiating appropriate responses to the cellular stress induced by severe environmental temperature change. In the case of microbial pathogens, development and virulence are often coupled to sensing host physiological temperatures. As such, microbes have developed diverse molecular strategies to sense fluctuations in temperature, and nearly all cellular molecules, including proteins, lipids, RNA, and DNA, can act as thermosensors that detect changes in environmental temperature and initiate relevant cellular responses. The myriad of molecular mechanisms by which microbes sense and respond to temperature reveals an elegant repertoire of strategies to orchestrate cellular signaling, developmental programs, and virulence with spatial and temporal environmental cues.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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143
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Cold shock genes cspA and cspB from Caulobacter crescentus are posttranscriptionally regulated and important for cold adaptation. J Bacteriol 2012; 194:6507-17. [PMID: 23002229 DOI: 10.1128/jb.01422-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cold shock proteins (CSPs) are nucleic acid binding chaperones, first described as being induced to solve the problem of mRNA stabilization after temperature downshift. Caulobacter crescentus has four CSPs: CspA and CspB, which are cold induced, and CspC and CspD, which are induced only in stationary phase. In this work we have determined that the synthesis of both CspA and CspB reaches the maximum levels early in the acclimation phase. The deletion of cspA causes a decrease in growth at low temperature, whereas the strain with a deletion of cspB has a very subtle and transient cold-related growth phenotype. The cspA cspB double mutant has a slightly more severe phenotype than that of the cspA mutant, suggesting that although CspA may be more important to cold adaptation than CspB, both proteins have a role in this process. Gene expression analyses were carried out using cspA and cspB regulatory fusions to the lacZ reporter gene and showed that both genes are regulated at the transcriptional and posttranscriptional levels. Deletion mapping of the long 5'-untranslated region (5'-UTR) of each gene identified a common region important for cold induction, probably via translation enhancement. In contrast to what was reported for other bacteria, these cold shock genes have no regulatory regions downstream from ATG that are important for cold induction. This work shows that the importance of CspA and CspB to C. crescentus cold adaptation, mechanisms of regulation, and pattern of expression during the acclimation phase apparently differs in many aspects from what has been described so far for other bacteria.
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144
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Brites CDS, Lima PP, Silva NJO, Millán A, Amaral VS, Palacio F, Carlos LD. Thermometry at the nanoscale. NANOSCALE 2012; 4:4799-829. [PMID: 22763389 DOI: 10.1039/c2nr30663h] [Citation(s) in RCA: 604] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Non-invasive precise thermometers working at the nanoscale with high spatial resolution, where the conventional methods are ineffective, have emerged over the last couple of years as a very active field of research. This has been strongly stimulated by the numerous challenging requests arising from nanotechnology and biomedicine. This critical review offers a general overview of recent examples of luminescent and non-luminescent thermometers working at nanometric scale. Luminescent thermometers encompass organic dyes, QDs and Ln(3+)ions as thermal probes, as well as more complex thermometric systems formed by polymer and organic-inorganic hybrid matrices encapsulating these emitting centres. Non-luminescent thermometers comprise of scanning thermal microscopy, nanolithography thermometry, carbon nanotube thermometry and biomaterials thermometry. Emphasis has been put on ratiometric examples reporting spatial resolution lower than 1 micron, as, for instance, intracellular thermometers based on organic dyes, thermoresponsive polymers, mesoporous silica NPs, QDs, and Ln(3+)-based up-converting NPs and β-diketonate complexes. Finally, we discuss the challenges and opportunities in the development for highly sensitive ratiometric thermometers operating at the physiological temperature range with submicron spatial resolution.
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Affiliation(s)
- Carlos D S Brites
- Department of Physics, CICECO, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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145
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Dynamic modulation of DNA replication and gene transcription in deep-sea filamentous phage SW1 in response to changes of host growth and temperature. PLoS One 2012; 7:e41578. [PMID: 22870232 PMCID: PMC3411601 DOI: 10.1371/journal.pone.0041578] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 06/22/2012] [Indexed: 11/28/2022] Open
Abstract
Little is known about the response of deep-sea virus and their relationship with their host towards environmental change. Although viruses are thought to play key roles in the deep-sea ecological evolution and biogeochemical cycling, these roles are yet to be defined. This study aims to delineate the relationship between a deep-sea filamentous phage SW1 and its host Shewanella piezotolerans (S. piezotolerans) WP3, and their response towards temperature change. The copy number of SW1’s replicative form (RF-) DNA and single-stranded (ss-) DNA along the different growth phases of WP3 were quantified at 20°C and 4°C, respectively. The copy number of SW1 RF-DNA was found to be temperature and growth phase-dependent, while the ssDNA of SW1 was only produced at 4°C. This is the first report showing low-temperature dependence of phage DNA replication. The transcription of SW1 key genes fpsA and fpsR were also found to be induced at low temperature during all the monitored growth periods of WP3. Additionally, the transcription of SW1 was found to be induced by cold-shock while its DNA replication was not changed. Our data demonstrates a dynamic change of virus DNA replication and transcription in accordance with host growth, and the low temperature adapted mechanisms for SW1 activities in the deep sea. This low temperature adapted deep-sea virus-bacterium system could serve as an ideal model to further study the mechanism and relationship of deep-sea virus-bacteria ecosystems.
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146
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Hwang J, Lee K, Phadtare S, Inouye M. Identification of two DNA helicases UvrD and DinG as suppressors for lethality caused by mutant cspA mRNAs. J Mol Microbiol Biotechnol 2012; 22:135-46. [PMID: 22832783 DOI: 10.1159/000339832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
CspA is a major cold shock-inducible protein (70 aa), and its major role in the cold shock response was shown to be as an RNA chaperone destabilizing secondary structure of mRNAs at low temperature. Previously, we showed that the overexpression of mutant cspA containing premature non-sense codons at various positions led to stalled ribosomes on mutant cspA transcripts, ultimately leading to cell death. This lethality is primarily due to the highly translatable cspA 5'-UTR that recruits most of the ribosomes from other mRNAs, which are then stalled at the abnormal stop codon. This was called the 'LACE' effect. We show here that non-sense mutation even at the 67th position as well as substitutions of aromatic amino acid residues present on the RNA-binding surface of CspA protein to alanine caused the LACE effect by trapping a substantial amount of ribosomes on cspA mRNAs. In an attempt to identify a suppressor(s), which may help the cells to recover from the inhibitory LACE effect, genetic screening of an Escherichia coli genomic library was performed. We isolated suppressors that contained the genomic fragments encoding uvrD and dinG, respectively, whose gene products are ATP-dependent DNA helicases. The nucleic acid-binding and ATPase activities of these two helicases were found to be essential for their suppression activity. This genomic screening offers an approach to shed light on the mechanistic of 5'-UTR of cspA mRNA and novel roles of E. coli helicases that function in DNA repair.
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Affiliation(s)
- Jihwan Hwang
- Department of Biochemistry, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
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147
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148
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Yang C, Wang L, Siva VS, Shi X, Jiang Q, Wang J, Zhang H, Song L. A novel cold-regulated cold shock domain containing protein from scallop Chlamys farreri with nucleic acid-binding activity. PLoS One 2012; 7:e32012. [PMID: 22359656 PMCID: PMC3281114 DOI: 10.1371/journal.pone.0032012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 01/20/2012] [Indexed: 11/26/2022] Open
Abstract
Background The cold shock domain (CSD) containing proteins (CSDPs) are one group of the evolutionarily conserved nucleic acid-binding proteins widely distributed in bacteria, plants, animals, and involved in various cellular processes, including adaptation to low temperature, cellular growth, nutrient stress and stationary phase. Methodology The cDNA of a novel CSDP was cloned from Zhikong scallop Chlamys farreri (designated as CfCSP) by expressed sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE) approach. The full length cDNA of CfCSP was of 1735 bp containing a 927 bp open reading frame which encoded an N-terminal CSD with conserved nucleic acids binding motif and a C-terminal domain with four Arg-Gly-Gly (RGG) repeats. The CSD of CfCSP shared high homology with the CSDs from other CSDPs in vertebrate, invertebrate and bacteria. The mRNA transcripts of CfCSP were mainly detected in the tissue of adductor and also marginally detectable in gill, hepatopancreas, hemocytes, kidney, mantle and gonad of healthy scallop. The relative expression level of CfCSP was up-regulated significantly in adductor and hemocytes at 1 h and 24 h respectively after low temperature treatment (P<0.05). The recombinant CfCSP protein (rCfCSP) could bind ssDNA and in vitro transcribed mRNA, but it could not bind dsDNA. BX04, a cold sensitive Escherichia coli CSP quadruple-deletion mutant, was used to examine the cold adaptation ability of CfCSP. After incubation at 17°C for 120 h, the strain of BX04 containing the vector pINIII showed growth defect and failed to form colonies, while strain containing pINIII-CSPA or pINIII-CfCSP grew vigorously, indicating that CfCSP shared a similar function with E. coli CSPs for the cold adaptation. Conclusions These results suggest that CfCSP is a novel eukaryotic cold-regulated nucleic acid-binding protein and may function as an RNA chaperone in vivo during the cold adaptation process.
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Affiliation(s)
- Chuanyan Yang
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Lingling Wang
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- * E-mail: (LW); (LS)
| | - Vinu S. Siva
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Xiaowei Shi
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Qiufen Jiang
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Jingjing Wang
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Huan Zhang
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
| | - Linsheng Song
- The Key laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese 7 Academy of Sciences, Qingdao, China
- * E-mail: (LW); (LS)
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149
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Mellin JR, Cossart P. The non-coding RNA world of the bacterial pathogen Listeria monocytogenes. RNA Biol 2012; 9:372-8. [PMID: 22336762 DOI: 10.4161/rna.19235] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In the past ten years, Listeria monocytogenes has emerged as a model organism in infection biology and also become an attractive system for the study of regulatory RNAs in pathogenic bacteria. Due to the recent completion of several transcriptomic studies, it is now clear that L. monocytogenes possesses a large repertoire of both cis- and trans-encoded RNAs. These include numerous small RNAs (sRNAs) expressed during infection, widespread transcription of both short and long antisense RNAs (asRNAs) and an array of cis-acting regulatory RNA elements. In this review we highlight the recent advances in non-coding RNA research in L. monocytogenes with a particular focus on emerging themes of RNA-based regulation.
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Affiliation(s)
- Jeffery R Mellin
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, France
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150
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Klinkert B, Cimdins A, Gaubig LC, Roßmanith J, Aschke-Sonnenborn U, Narberhaus F. Thermogenetic tools to monitor temperature-dependent gene expression in bacteria. J Biotechnol 2012; 160:55-63. [PMID: 22285954 DOI: 10.1016/j.jbiotec.2012.01.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 12/29/2011] [Accepted: 01/12/2012] [Indexed: 10/14/2022]
Abstract
Free-living bacteria constantly monitor their ambient temperature. Drastic deviations elicit immediate protective responses known as cold shock or heat shock response. Many mammalian pathogens use temperature surveillance systems to recognize the successful invasion of a host by its body temperature, usually 37°C. Translation of temperature-responsive genes can be modulated by RNA thermometers (RNATs). RNATs form complex structures primarily in the 5'-untranslated region of their transcripts. Most RNATs block the ribosome binding site at low temperatures. Translation is induced at increasing temperature by melting of the RNA structure. The analysis of such temperature-dependent RNA elements calls for adequate test systems that function in the appropriate temperature range. Here, we summarize previously established reporter gene systems based on the classical β-galactosidase LacZ, the heat-stable β-galactosidase BgaB and the green fluorescent protein GFP. We validate these systems by testing known RNATs and describe the construction and application of an optimized bgaB system. Finally, two novel RNA thermometer candidates from Escherichia coli and Salmonella will be presented.
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Affiliation(s)
- Birgit Klinkert
- Microbial Biology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
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