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De Oliveira AL, Srivastava A, Espada‐Hinojosa S, Bright M. The complete and closed genome of the facultative generalist Candidatus Endoriftia persephone from deep-sea hydrothermal vents. Mol Ecol Resour 2022; 22:3106-3123. [PMID: 35699368 PMCID: PMC9796809 DOI: 10.1111/1755-0998.13668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 01/07/2023]
Abstract
The mutualistic interactions between Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone (short Endoriftia) have been extensively researched. However, the closed Endoriftia genome is still lacking. Here, by employing single-molecule real-time sequencing we present the closed chromosomal sequence of Endoriftia. In contrast to theoretical predictions of enlarged and mobile genetic element-rich genomes related to facultative endosymbionts, the closed Endoriftia genome is streamlined with fewer than expected coding sequence regions, insertion-, prophage-sequences and transposase-coding sequences. Automated and manually curated functional analyses indicated that Endoriftia is more versatile regarding sulphur metabolism than previously reported. We identified the presence of two identical rRNA operons and two long CRISPR regions in the closed genome. Additionally, pangenome analyses revealed the presence of three types of secretion systems (II, IV and VI) in the different Endoriftia populations indicating lineage-specific adaptations. The in depth mobilome characterization identified the presence of shared genomic islands in the different Endoriftia drafts and in the closed genome, suggesting that the acquisition of foreign DNA predates the geographical dispersal of the different endosymbiont populations. Finally, we found no evidence of epigenetic regulation in Endoriftia, as revealed by gene screenings and absence of methylated modified base motifs in the genome. As a matter of fact, the restriction-modification system seems to be dysfunctional in Endoriftia, pointing to a higher importance of molecular memory-based immunity against phages via spacer incorporation into CRISPR system. The Endoriftia genome is the first closed tubeworm endosymbiont to date and will be valuable for future gene oriented and evolutionary comparative studies.
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Affiliation(s)
| | - Abhishek Srivastava
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | | | - Monika Bright
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
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2
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Pervasive transcription enhances the accessibility of H-NS-silenced promoters and generates bistability in Salmonella virulence gene expression. Proc Natl Acad Sci U S A 2022; 119:e2203011119. [PMID: 35858437 PMCID: PMC9335307 DOI: 10.1073/pnas.2203011119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In Escherichia coli and Salmonella, many genes silenced by the nucleoid structuring protein H-NS are activated upon inhibiting Rho-dependent transcription termination. This response is poorly understood and difficult to reconcile with the view that H-NS acts mainly by blocking transcription initiation. Here we have analyzed the basis for the up-regulation of H-NS-silenced Salmonella pathogenicity island 1 (SPI-1) in cells depleted of Rho-cofactor NusG. Evidence from genetic experiments, semiquantitative 5' rapid amplification of complementary DNA ends sequencing (5' RACE-Seq), and chromatin immunoprecipitation sequencing (ChIP-Seq) shows that transcription originating from spurious antisense promoters, when not stopped by Rho, elongates into a H-NS-bound regulatory region of SPI-1, displacing H-NS and rendering the DNA accessible to the master regulator HilD. In turn, HilD's ability to activate its own transcription triggers a positive feedback loop that results in transcriptional activation of the entire SPI-1. Significantly, single-cell analyses revealed that this mechanism is largely responsible for the coexistence of two subpopulations of cells that either express or do not express SPI-1 genes. We propose that cell-to-cell differences produced by stochastic spurious transcription, combined with feedback loops that perpetuate the activated state, can generate bimodal gene expression patterns in bacterial populations.
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Liang J, Quan Z, Zhu J, Gan M, Shen P. A functional promoter from the archaeon Halobacterium salinarum is also transcriptionally active in E. coli. BMC Microbiol 2022; 22:79. [PMID: 35331139 PMCID: PMC8943987 DOI: 10.1186/s12866-022-02489-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 02/25/2022] [Indexed: 11/18/2022] Open
Abstract
Background Archaea form a third domain of life that is distinct from Bacteria and Eukarya. So far, many scholars have elucidated considerable details about the typical promoter architectures of the three domains of life. However, a functional promoter from the archaeon Halobacterium salinarum has never been studied in Escherichia coli. Results This paper found that the promoter of Halobacterium salinarum showed a promoter function in Escherichia coli. This Escherichia coli promoter structure contains − 10 box, -10 box extension and − 29 elements, however, no -35 box. The − 29 element is exercised by the TATA box in archaea. And we isolated the RM10 fragment that possessed the fusion characteristics of bacteria and archaea, which was overlapped with functionality of TATA box and − 29 elements. Conclusions The − 29 element reflects the evolutionary relationship between the archaeal promoter and the bacterial promoter. The result possibly indicated that there may be a certain internal connection between archaea and bacteria. We hypothesized that it provided a new viewpoint of the evolutionary relationship of archaea and other organisms. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02489-y.
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Affiliation(s)
- Jinye Liang
- Key laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Zhenghui Quan
- College of Life Sciences, Wuhan University, 430000, Wuhan, China
| | - Jianyu Zhu
- Key laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China. .,College of Life Sciences, Wuhan University, 430000, Wuhan, China.
| | - Min Gan
- Key laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China.
| | - Ping Shen
- College of Life Sciences, Wuhan University, 430000, Wuhan, China.
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Ishihama A, Shimada T. Hierarchy of transcription factor network in Escherichia coli K-12: H-NS-mediated silencing and Anti-silencing by global regulators. FEMS Microbiol Rev 2021; 45:6312496. [PMID: 34196371 DOI: 10.1093/femsre/fuab032] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022] Open
Abstract
Transcriptional regulation for genome expression determines growth and adaptation of single-cell bacteria that are directly exposed to environment. The transcriptional apparatus in Escherichia coli K-12 is composed of RNA polymerase core enzyme and two groups of its regulatory proteins, seven species of promoter-recognition subunit sigma and about 300 species of transcription factors. The identification of regulatory targets for all these regulatory proteins is critical toward understanding the genome regulation as a whole. For this purpose, we performed a systematic search in vitro of the whole set of binding sites for each factor by gSELEX system. This review summarizes the accumulated knowledge of regulatory targets for more than 150 TFs from E. coli K-12. Overall TFs could be classified into four families: nucleoid-associated bifunctional TFs; global regulators; local regulators; and single-target regulators, in which the regulatory functions remain uncharacterized for the nucleoid-associated TFs. Here we overview the regulatory targets of two nucleoid-associated TFs, H-NS and its paralog StpA, both together playing the silencing role of a set of non-essential genes. Participation of LeuO and other global regulators have been indicated for the anti-silencing. Finally, we propose the hierarchy of TF network as a key framework of the bacterial genome regulation.
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Affiliation(s)
- Akira Ishihama
- Hosei University, Research Institute for Micro-Nano Technology, Koganei, Tokyo 184-0003, Japan
| | - Tomohiro Shimada
- Meiji University, School of Agriculture, Kawasaki, Kanagawa 214-8571, Japan
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5
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Palazzo A, Marsano RM. Transposable elements: a jump toward the future of expression vectors. Crit Rev Biotechnol 2021; 41:792-808. [PMID: 33622117 DOI: 10.1080/07388551.2021.1888067] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Expression vectors (EVs) are artificial nucleic acid molecules with a modular structure that allows for the transcription of DNA sequences of interest in either cellular or cell-free environments. These vectors have emerged as cross-disciplinary tools with multiple applications in an expanding Life Sciences market. The cis-regulatory sequences (CRSs) that control the transcription in EVs are typically sourced from either viruses or from characterized genes. However, the recent advancement in transposable elements (TEs) technology provides attractive alternatives that may enable a significant improvement in the design of EVs. Commonly known as "jumping genes," due to their ability to move between genetic loci, TEs are constitutive components of both eukaryotic and prokaryotic genomes. TEs harbor native CRSs that allow the regulated transcription of transposition-related genes. However, some TE-related CRSs display striking characteristics, which provides the opportunity to reconsider TEs as lead actors in the design of EVs. In this article, we provide a synopsis of the transcriptional control elements commonly found in EVs together with an extensive discussion of their advantages and limitations. We also highlight the latest findings that may allow for the implementation of TE-derived sequences in the EVs feasible, possibly improving existing vectors. By introducing this new concept of TEs as a source of regulatory sequences, we aim to stimulate a profitable discussion of the potential advantages and benefits of developing a new generation of EVs based on the use of TE-derived control sequences.
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Affiliation(s)
- Antonio Palazzo
- Laboratory of Translational Nanotechnology, "Istituto Tumori Giovanni Paolo II" I.R.C.C.S, Bari, Italy
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Bykov A, Glazunova O, Alikina O, Sukharicheva N, Masulis I, Shavkunov K, Ozoline O. Excessive Promoters as Silencers of Genes Horizontally Acquired by Escherichia coli. Front Mol Biosci 2020; 7:28. [PMID: 32175329 PMCID: PMC7054387 DOI: 10.3389/fmolb.2020.00028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/10/2020] [Indexed: 11/17/2022] Open
Abstract
Horizontally acquired genes are usually transcriptionally inactive, although most of them are associated with genomic loci enriched with promoter-like sequences forming “promoter islands.” We hypothesized that lateral DNA transfer induces local mutagenesis, accumulating AT base pairs and creating promoter-like sequences, whose occupancy with RNA polymerase and a specific silencer H-NS suppresses the transcription of foreign genes. Error-prone mutagenesis was implemented for the “promoter island” of a foreign gene appY and the promoter region of an inherent gene dps. Derivatives with changed transcriptional activity were selected using a reporter plasmid pET28_eGFP. Only one cycle of mutagenesis with negative selection suppressed the activity of the main dps promoter to the background level due to a single substitution in its -10 element, while positive selection gave a sequence with improved -35 element, thus testifying feasibility of the approach. The same suppression for appY was achieved by three cycles, while eightfold transcription activation required nine iterations of mutagenesis. In both cases, the number of potential start points decreased resulting in an ordinary regulatory region with only one dominant promoter in the case of positive selection. Efficiency of H-NS binding remained virtually unchanged in all mutant constructs. Based on these findings we conclude that excessive promoters can adversely affect transcription by providing a platform for interference between several RNA polymerase molecules, which can act as a silencer at promoter-dense regions.
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Affiliation(s)
- Aleksandr Bykov
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research, Moscow, Russia.,Research Institute of Molecular Pathology, Vienna Biocenter Campus, Vienna, Austria
| | - Olga Glazunova
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research, Moscow, Russia
| | - Olga Alikina
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research, Moscow, Russia
| | - Natalia Sukharicheva
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research, Moscow, Russia
| | - Irina Masulis
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research, Moscow, Russia
| | - Konstantin Shavkunov
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research, Moscow, Russia
| | - Olga Ozoline
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research, Moscow, Russia
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Sun Z, Cagliero C, Izard J, Chen Y, Zhou YN, Heinz WF, Schneider TD, Jin DJ. Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli. Nucleic Acids Res 2019; 47:3970-3985. [PMID: 30843055 DOI: 10.1093/nar/gkz159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 11/14/2022] Open
Abstract
RNA polymerase (RNAP), the transcription machinery, shows dynamic binding across the genomic DNA under different growth conditions. The genomic features that selectively redistribute the limited RNAP molecules to dictate genome-wide transcription in response to environmental cues remain largely unknown. We chose the bacterial osmotic stress response model to determine genomic features that direct genome-wide redistribution of RNAP during the stress. Genomic mapping of RNAP and transcriptome profiles corresponding to the different temporal states after salt shock were determined. We found rapid redistribution of RNAP across the genome, primarily at σ70 promoters. Three subsets of genes exhibiting differential salt sensitivities were identified. Sequence analysis using an information-theory based σ70 model indicates that the intergenic regions of salt-responsive genes are enriched with a higher density of σ70 promoter-like sites than those of salt-sensitive genes. In addition, the density of promoter-like sites has a positive linear correlation with RNAP binding at different salt concentrations. The RNAP binding contributed by the non-initiating promoter-like sites is important for gene transcription at high salt concentration. Our study demonstrates that hyperdensity of σ70 promoter-like sites in the intergenic regions of salt-responsive genes drives the RNAP redistribution for reprograming the transcriptome to counter osmotic stress.
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Affiliation(s)
- Zhe Sun
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Cedric Cagliero
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jerome Izard
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yixiong Chen
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yan Ning Zhou
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Thomas D Schneider
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ding Jun Jin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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Ryasik A, Orlov M, Zykova E, Ermak T, Sorokin A. Bacterial promoter prediction: Selection of dynamic and static physical properties of DNA for reliable sequence classification. J Bioinform Comput Biol 2018; 16:1840003. [DOI: 10.1142/s0219720018400036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Predicting promoter activity of DNA fragment is an important task for computational biology. Approaches using physical properties of DNA to predict bacterial promoters have recently gained a lot of attention. To select an adequate set of physical properties for training a classifier, various characteristics of DNA molecule should be taken into consideration. Here, we present a systematic approach that allows us to select less correlated properties for classification by means of both correlation and cophenetic coefficients as well as concordance matrices. To prove this concept, we have developed the first classifier that uses not only sequence and static physical properties of DNA fragment, but also dynamic properties of DNA open states. Therefore, the best performing models with accuracy values up to 90% for all types of sequences were obtained. Furthermore, we have demonstrated that the classifier can serve as a reliable tool enabling promoter DNA fragments to be distinguished from promoter islands despite the similarity of their nucleotide sequences.
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Affiliation(s)
- Artem Ryasik
- Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia
| | - Mikhail Orlov
- Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia
| | - Evgenia Zykova
- Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia
- Department of Applied Research Informatization, State Institute of Information Technologies and Telecommunications (SIIT&T Informika), per. Brusov 21 st.2, Moscow, 125009, Russia
| | - Timofei Ermak
- Laboratory of Molecular Genetics Systems, Institute of Cytology and Genetics, pr. Akademika Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Anatoly Sorokin
- Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia
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9
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Yamamoto K, Yamanaka Y, Shimada T, Sarkar P, Yoshida M, Bhardwaj N, Watanabe H, Taira Y, Chatterji D, Ishihama A. Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the Escherichia coli K-12 Genome. mSystems 2018; 3:e00172-17. [PMID: 29468196 PMCID: PMC5811629 DOI: 10.1128/msystems.00172-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/25/2018] [Indexed: 11/20/2022] Open
Abstract
The RNA polymerase (RNAP) of Escherichia coli K-12 is a complex enzyme consisting of the core enzyme with the subunit structure α2ββ'ω and one of the σ subunits with promoter recognition properties. The smallest subunit, omega (the rpoZ gene product), participates in subunit assembly by supporting the folding of the largest subunit, β', but its functional role remains unsolved except for its involvement in ppGpp binding and stringent response. As an initial approach for elucidation of its functional role, we performed in this study ChIP-chip (chromatin immunoprecipitation with microarray technology) analysis of wild-type and rpoZ-defective mutant strains. The altered distribution of RpoZ-defective RNAP was identified mostly within open reading frames, in particular, of the genes inside prophages. For the genes that exhibited increased or decreased distribution of RpoZ-defective RNAP, the level of transcripts increased or decreased, respectively, as detected by reverse transcription-quantitative PCR (qRT-PCR). In parallel, we analyzed, using genomic SELEX (systemic evolution of ligands by exponential enrichment), the distribution of constitutive promoters that are recognized by RNAP RpoD holoenzyme alone and of general silencer H-NS within prophages. Since all 10 prophages in E. coli K-12 carry only a small number of promoters, the altered occupancy of RpoZ-defective RNAP and of transcripts might represent transcription initiated from as-yet-unidentified host promoters. The genes that exhibited transcription enhanced by RpoZ-defective RNAP are located in the regions of low-level H-NS binding. By using phenotype microarray (PM) assay, alterations of some phenotypes were detected for the rpoZ-deleted mutant, indicating the involvement of RpoZ in regulation of some genes. Possible mechanisms of altered distribution of RNAP inside prophages are discussed. IMPORTANCE The 91-amino-acid-residue small-subunit omega (the rpoZ gene product) of Escherichia coli RNA polymerase plays a structural role in the formation of RNA polymerase (RNAP) as a chaperone in folding the largest subunit (β', of 1,407 residues in length), but except for binding of the stringent signal ppGpp, little is known of its role in the control of RNAP function. After analysis of genomewide distribution of wild-type and RpoZ-defective RNAP by the ChIP-chip method, we found alteration of the RpoZ-defective RNAP inside open reading frames, in particular, of the genes within prophages. For a set of the genes that exhibited altered occupancy of the RpoZ-defective RNAP, transcription was found to be altered as observed by qRT-PCR assay. All the observations here described indicate the involvement of RpoZ in recognition of some of the prophage genes. This study advances understanding of not only the regulatory role of omega subunit in the functions of RNAP but also the regulatory interplay between prophages and the host E. coli for adjustment of cellular physiology to a variety of environments in nature.
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Affiliation(s)
- Kaneyoshi Yamamoto
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Micro-Nano Technology Research Center, Hosei University, Tokyo, Japan
| | - Yuki Yamanaka
- Micro-Nano Technology Research Center, Hosei University, Tokyo, Japan
| | - Tomohiro Shimada
- Micro-Nano Technology Research Center, Hosei University, Tokyo, Japan
- Meiji University, School of Agriculture, Kawasaki, Kanagawa, Japan
| | - Paramita Sarkar
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Indian Institute of Science, Molecular Biophysics Unit, Bangalore, India
| | - Myu Yoshida
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Neerupma Bhardwaj
- Indian Institute of Science, Molecular Biophysics Unit, Bangalore, India
| | - Hiroki Watanabe
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Yuki Taira
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Dipankar Chatterji
- Indian Institute of Science, Molecular Biophysics Unit, Bangalore, India
| | - Akira Ishihama
- Micro-Nano Technology Research Center, Hosei University, Tokyo, Japan
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10
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Antipov SS, Tutukina MN, Preobrazhenskaya EV, Kondrashov FA, Patrushev MV, Toshchakov SV, Dominova I, Shvyreva US, Vrublevskaya VV, Morenkov OS, Sukharicheva NA, Panyukov VV, Ozoline ON. The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner. PLoS One 2017; 12:e0182800. [PMID: 28800583 PMCID: PMC5553809 DOI: 10.1371/journal.pone.0182800] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 07/25/2017] [Indexed: 11/18/2022] Open
Abstract
Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity. However, deletion of dps changed the profile of proteins in starved cells, SELEX screen revealed genomic regions preferentially bound in vitro and certain affinity of Dps for artificial branched molecules was detected by atomic force microscopy. Here we report a non-random distribution of Dps binding sites across the bacterial chromosome in exponentially growing cells and show their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. In the dps-null mutant we, therefore, observed a differentially altered expression of several targeted genes and found suppressed transcription from the dps promoter. In most cases this can be explained by the relieved interference with Dps for nucleoid proteins exploiting sequence-specific modes of DNA binding. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA polymerase or, vice versa, competing with inhibitors to activate transcription.
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Affiliation(s)
- S. S. Antipov
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Biophysics and Biotechnology, Voronezh State University, Voronezh, Russian Federation
- Department of Genomics of Microorganisms, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - M. N. Tutukina
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) Barcelona, Spain
- Department of Evolutionary Genomics, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Structural and Functional Genomics,–Pushchino Research Center of the Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - E. V. Preobrazhenskaya
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - F. A. Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) Barcelona, Spain
- Department of Evolutionary Genomics, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Pg. Lluís Companys, Barcelona, Spain
| | - M. V. Patrushev
- Department of Genomics of Microorganisms, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - S. V. Toshchakov
- Department of Genomics of Microorganisms, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - I. Dominova
- Department of Genomics of Microorganisms, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - U. S. Shvyreva
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - V. V. Vrublevskaya
- Department of Cell Culture and Cell Engeneering, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - O. S. Morenkov
- Department of Cell Culture and Cell Engeneering, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - N. A. Sukharicheva
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - V. V. Panyukov
- Department of Structural and Functional Genomics,–Pushchino Research Center of the Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Bioinformatics, Institute of Mathematical Problems of Biology—the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - O. N. Ozoline
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Structural and Functional Genomics,–Pushchino Research Center of the Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- * E-mail:
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11
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Shimada T, Tanaka K, Ishihama A. The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase. PLoS One 2017; 12:e0179181. [PMID: 28666008 PMCID: PMC5493296 DOI: 10.1371/journal.pone.0179181] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/06/2017] [Indexed: 12/15/2022] Open
Abstract
The promoter selectivity of Escherichia coli RNA polymerase (RNAP) is determined by the sigma subunit. The model prokaryote Escherichia coli K-12 contains seven species of the sigma subunit, each recognizing a specific set of promoters. For identification of the "constitutive promoters" that are recognized by each RNAP holoenzyme alone in the absence of other supporting factors, we have performed the genomic SELEX screening in vitro for their binding sites along the E. coli K-12 W3110 genome using each of the reconstituted RNAP holoenzymes and a collection of genome DNA segments of E. coli K-12. The whole set of constitutive promoters for each RNAP holoenzyme was then estimated based on the location of RNAP-binding sites. The first successful screening of the constitutive promoters was achieved for RpoD (σ70), the principal sigma for transcription of growth-related genes. As an extension, we performed in this study the screening of constitutive promoters for four minor sigma subunits, stationary-phase specific RpoS (σ38), heat-shock specific RpoH (σ32), flagellar-chemotaxis specific RpoF (σ28) and extra-cytoplasmic stress-response RpoE (σ24). The total number of constitutive promoters were: 129~179 for RpoS; 101~142 for RpoH; 34~41 for RpoF; and 77~106 for RpoE. The list of constitutive promoters were compared with that of known promoters identified in vivo under various conditions and using varieties of E. coli strains, altogether allowing the estimation of "inducible promoters" in the presence of additional supporting factors.
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Affiliation(s)
- Tomohiro Shimada
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
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Shahmuradov IA, Mohamad Razali R, Bougouffa S, Radovanovic A, Bajic VB. bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli. Bioinformatics 2017; 33:334-340. [PMID: 27694198 PMCID: PMC5408793 DOI: 10.1093/bioinformatics/btw629] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/27/2016] [Indexed: 12/01/2022] Open
Abstract
Motivation The computational search for promoters in prokaryotes remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. In any bacterial genome, the transcription start site is chosen mostly by the sigma (σ) factor proteins, which control the gene activation. The majority of published bacterial promoter prediction tools target σ70 promoters in Escherichia coli. Moreover, no σ-specific classification of promoters is available for prokaryotes other than for E. coli. Results Here, we introduce bTSSfinder, a novel tool that predicts putative promoters for five classes of σ factors in Cyanobacteria (σA, σC, σH, σG and σF) and for five classes of sigma factors in E. coli (σ70, σ38, σ32, σ28 and σ24). Comparing to currently available tools, bTSSfinder achieves higher accuracy (MCC = 0.86, F1-score = 0.93) compared to the next best tool with MCC = 0.59, F1-score = 0.79) and covers multiple classes of promoters. Availability and Implementation bTSSfinder is available standalone and online at http://www.cbrc.kaust.edu.sa/btssfinder. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ilham Ayub Shahmuradov
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Rozaimi Mohamad Razali
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Salim Bougouffa
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Aleksandar Radovanovic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
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Awad A Al Ibrahim N, Green J. Regulation of the Escherichia coli ydhY-T operon in the presence of alternative electron acceptors. MICROBIOLOGY-SGM 2017; 163:584-594. [PMID: 28218056 DOI: 10.1099/mic.0.000445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Escherichia coli K-12 ydhY-T operon, coding for a predicted oxidoreductase complex, is activated under anaerobic conditions and repressed in the presence of nitrate or nitrite. Anaerobic activation is mediated by the transcription factor FNR, and nitrate/nitrite repression is mediated by NarXL and NarQP. In vitro transcription reactions revealed that the DNA upstream of ydhY-T contains sufficient information for RNA polymerase alone to initiate transcription from five locations. FNR severely inhibited synthesis of two of these transcripts (located upstream of, and within, the FNR binding site) and activated the FNR-dependent promoter previously identified in vivo. Enhanced expression of ydhY-T in an hns mutant was consistent with the location of ydhY-T within a promoter island and the FNR-independent transcription observed in vitro. FNR-dependent transcription in vitro was decreased in the presence of NarL~P. DNaseI footprinting indicated that FNR and NarL~P simultaneously bound at the ydhY-T promoter region and that NarL~P-mediated repression was due to occupation of the 7-2-7 site located downstream of the FNR-dependent promoter. Expression of ydhY-T during the anaerobic growth cycle was repressed when nitrate was present but less so in the presence of nitrite. In vivo transcription measurements indicated that the alternative electron acceptors, DMSO and fumarate, could also lower ydhY-T expression, whereas trimethylamine-N-oxide (TMAO) permitted high expression. Therefore, expression of ydhY-T is subject to complex regulation in response to electron acceptor availability that involves at least three transcription factors, FNR (anaerobic activation), NarL~P (nitrate repression) and H-NS (repression in the absence of an antagonist; e.g. FNR).
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Affiliation(s)
- Naji Awad A Al Ibrahim
- Department of Molecular Biology and Biotechnology, The Krebs Institute, University of Sheffield, Sheffield S10 2TN, UK.,Present address: General Administration of Laboratories and Quality Control, Ministry of Commerce and Industry, Riyadh 11162, Kingdom of Saudi Arabia
| | - Jeffrey Green
- Department of Molecular Biology and Biotechnology, The Krebs Institute, University of Sheffield, Sheffield S10 2TN, UK
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Choi JW, Kim SC, Hong SH, Lee HJ. Secretable Small RNAs via Outer Membrane Vesicles in Periodontal Pathogens. J Dent Res 2017; 96:458-466. [PMID: 28068479 DOI: 10.1177/0022034516685071] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs) have been shown to be major regulators of eukaryotic gene expression. However, bacterial RNAs comparable in size to eukaryotic miRNAs (18-22 nucleotides) have received little attention. Recently, a novel class of small RNAs similar in size to miRNAs (miRNA-size, small RNAs or msRNAs) have also been found in several bacteria. Like miRNAs, msRNAs are approximately 15 to 25 nucleotides in length, and their precursors are predicted to form a hairpin loop secondary structure. Here, we identified msRNAs in the periodontal pathogens Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and Treponema denticola. We examined these msRNAs using a deep sequencing method and characterized dozens of msRNAs through bioinformatic analysis. Highly expressed msRNAs were selected for further validation. The findings suggest that this class of small RNAs is well conserved across the domains of life. Indeed, msRNAs secreted via bacterial outer membrane vesicles (OMVs) were detected. The ability of bacterial OMVs to deliver RNAs into eukaryotic cells was also observed. These msRNAs in OMVs allowed us to identify their potential human immune-related target genes. Furthermore, we found that exogenous msRNAs could suppress expression of certain cytokines in Jurkat T cells. We propose msRNAs may function as novel bacterial signaling molecules that mediate bacteria-to-human interactions. Furthermore, this study may provide fresh insight into bacterial pathogenic mechanisms of periodontal diseases.
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Affiliation(s)
- J-W Choi
- 1 Department of Oral Microbiology and Immunology, School of Dentistry, Kyungpook National University, Daegu, South Korea
| | - S-C Kim
- 1 Department of Oral Microbiology and Immunology, School of Dentistry, Kyungpook National University, Daegu, South Korea
| | - S-H Hong
- 1 Department of Oral Microbiology and Immunology, School of Dentistry, Kyungpook National University, Daegu, South Korea
| | - H-J Lee
- 1 Department of Oral Microbiology and Immunology, School of Dentistry, Kyungpook National University, Daegu, South Korea.,2 Brain Science and Engineering Institute, Kyungpook National University, Daegu, South Korea
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Visualizing the activity of Escherichia coli divergent promoters and probing their dependence on superhelical density using dual-colour fluorescent reporter vector. Sci Rep 2015; 5:11449. [PMID: 26081797 PMCID: PMC4469952 DOI: 10.1038/srep11449] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/27/2015] [Indexed: 12/11/2022] Open
Abstract
Mosaic pattern of transcription in alternating directions is a common feature of prokaryotic and eukaryotic genomes which rationality and origin remain enigmatic. In Escherichia coli approximately 25% of genes comprise pairs of topologically linked divergently transcribed units. Given that transcriptional complex formation at each promoter in the pair induces topological changes and is itself sensitive to DNA structural perturbations, study of the functional anatomy in such areas requires special approaches. Here we suggested the dual-colour promoter probe vector which may become an ideal tool for divergent transcription profiling. The vector was used to characterize the specific genomic region nearby appY with multiple bidirectional promoters predicted in silico. Only three promoters of this region were shown to be engaged in the transcription initiation resulting in the expression of reporter genes. RNA product transcribed in antisense direction is suggested as a novel RNA. Nalidixin-induced topological modulation differentially affected transcription in sense and antisense directions thus exemplifying anticooperative mode in the response to topological alterations.
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16
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H-NS and RNA polymerase: a love-hate relationship? Curr Opin Microbiol 2015; 24:53-9. [PMID: 25638302 DOI: 10.1016/j.mib.2015.01.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/24/2014] [Accepted: 01/10/2015] [Indexed: 01/23/2023]
Abstract
Histone-like nucleoid structuring (H-NS) protein is a component of bacterial chromatin and influences gene expression both locally and on a global scale. Although H-NS is broadly considered a silencer of transcription, the mechanisms by which H-NS inhibits gene expression remain poorly understood. Here we discuss recent advances in the context of a 'love-hate' relationship between H-NS and RNA polymerase, in which these factors recognise similar DNA sequences but interfere with each other's activity. Understanding the complex relationship between H-NS and RNA polymerase may unite the multiple models that have been proposed to describe gene silencing by H-NS.
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Pervasive transcription: illuminating the dark matter of bacterial transcriptomes. Nat Rev Microbiol 2014; 12:647-53. [DOI: 10.1038/nrmicro3316] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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18
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Purtov YA, Glazunova OA, Antipov SS, Pokusaeva VO, Fesenko EE, Preobrazhenskaya EV, Shavkunov KS, Tutukina MN, Lukyanov VI, Ozoline ON. Promoter islands as a platform for interaction with nucleoid proteins and transcription factors. J Bioinform Comput Biol 2014; 12:1441006. [PMID: 24712533 DOI: 10.1142/s0219720014410066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Seventy-eight promoter islands with an extraordinarily high density of potential promoters have been recently found in the genome of Escherichia coli. It has been shown that RNA polymerase binds internal promoters of these islands and produces short oligonucleotides, while the synthesis of normal mRNAs is suppressed. This quenching may be biologically relevant, as most islands are associated with foreign genes, which expression may deplete cellular resources. However, a molecular mechanism of silencing with the participation of these promoter-rich regions remains obscure. It has been demonstrated that all islands interact with histone-like protein H-NS--a specific sentinel of foreign genes. In this study, we demonstrated the inhibitory effect of H-NS using Δhns mutant of Escherichia coli and showed that deletion of dps, encoding another protein of bacterial nucleoid, tended to decrease rather than increase the amount of island-specific transcripts. This observation precluded consideration of promoter islands as sites for targeted heterochromatization only and a computer search for the binding sites of 53 transcription factors (TFs) revealed six proteins, which may specifically regulate their transcriptional output.
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Affiliation(s)
- Yuri A Purtov
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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Shimada T, Yamazaki Y, Tanaka K, Ishihama A. The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli. PLoS One 2014; 9:e90447. [PMID: 24603758 PMCID: PMC3946193 DOI: 10.1371/journal.pone.0090447] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/01/2014] [Indexed: 01/08/2023] Open
Abstract
The promoter selectivity of Escherichia coli RNA polymerase is determined by the sigma subunit with promoter recognition activity. The model prokaryote Escherichia coli contains seven species of the sigma subunit, each recognizing a specific set of promoters. The major sigma subunit, sigma-70 encoded by rpoD, plays a major role in transcription of growth-related genes. Concomitant with the increase in detection of promoters functioning in vivo under various stressful conditions, the variation is expanding in the consensus sequence of RpoD promoters. In order to identify the canonical sequence of "constitutive promoters" that are recognized by the RNA polymerase holoenzyme containing RpoD sigma in the absence of supporting transcription factors, an in vitro mixed transcription assay was carried out using a whole set of variant promoters, each harboring one base replacement, within the model promoter with the conserved -35 and -10 sequences of RpoD promoters. The consensus sequences, TTGACA(-35) and TATAAT(-10), were identified to be ideal for the maximum level of open complex formation and the highest rate of promoter opening, respectively. For identification of the full range of constitutive promoters on the E. coli genome, a total of 2,701 RpoD holoenzyme-binding sites were identified by Genomic SELEX screening, and using the reconfirmed consensus promoter sequence, a total of maximum 669 constitutive promoters were identified, implying that the majority of hitherto identified promoters represents the TF-dependent "inducible promoters". One unique feature of the constitutive promoters is the high level of promoter sequence conservation, about 85% carrying five-out-of-six agreements with -35 or -10 consensus sequence. The list of constitutive promoters provides the community resource toward estimation of the inducible promoters that operate under various stressful conditions in nature.
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Affiliation(s)
- Tomohiro Shimada
- Department of Frontier Biosience, Hosei University, Koganai, Tokyo, Japan
- Micro-Nano Technology Research Center, Hosei University, Koganai, Tokyo, Japan
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan
| | - Yukiko Yamazaki
- Genetics Strains Research Institute, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kan Tanaka
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan
| | - Akira Ishihama
- Department of Frontier Biosience, Hosei University, Koganai, Tokyo, Japan
- Micro-Nano Technology Research Center, Hosei University, Koganai, Tokyo, Japan
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