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Understanding the Genome-Wide Transcription Response To Various cAMP Levels in Bacteria Using Phenomenological Models. mSystems 2022; 7:e0090022. [PMID: 36409084 PMCID: PMC9765429 DOI: 10.1128/msystems.00900-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Attempts to understand gene regulation by global transcription factors have largely been limited to expression studies under binary conditions of presence and absence of the transcription factor. Studies addressing genome-wide transcriptional responses to changing transcription factor concentration at high resolution are lacking. Here, we create a data set containing the entire Escherichia coli transcriptome in Luria-Bertani (LB) broth as it responds to 10 different cAMP concentrations spanning the biological range. We use the Hill's model to accurately summarize individual gene responses into three intuitively understandable parameters, Emax, n, and k, reflecting the sensitivity, nonlinearity, and midpoint of the dynamic range. Our data show that most cAMP-regulated genes have an n of >2, with their k values centered around the wild-type concentration of cAMP. Additionally, cAMP receptor protein (CRP) affinity to a promoter is correlated with Emax but not k, hinting that a high-affinity CRP promoter need not ensure transcriptional activation at lower cAMP concentrations and instead affects the magnitude of the response. Finally, genes belonging to different functional classes are tuned to have different k, n, and Emax values. We demonstrate that phenomenological models are a better alternative for studying gene expression trends than classical clustering methods, with the phenomenological constants providing greater insights into how genes are tuned in a regulatory network. IMPORTANCE Different genes may follow different trends in response to various transcription factor concentrations. In this study, we ask two questions: (i) what are the trends that different genes follow in response to changing transcription factor concentrations and (ii) what methods can be used to extract information from the gene trends so obtained. We demonstrate a method to analyze transcription factor concentration-dependent genome-wide expression data using phenomenological models. Conventional clustering methods and principal-component analysis (PCA) can be used to summarize trends in data but have limited interpretability. The use of phenomenological models greatly enhances the interpretability and thus utility of conventional clustering. Transformation of dose-response data into phenomenological constants opens up avenues to ask and answer many different kinds of question. We show that the phenomenological constants obtained from the model fits can be used to generate insights about network topology and allows integration of other experimental data such as chromatin immunoprecipitation sequencing (ChIP-seq) to understand the system in greater detail.
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2
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Real-time detection of response regulator phosphorylation dynamics in live bacteria. Proc Natl Acad Sci U S A 2022; 119:e2201204119. [PMID: 35994658 PMCID: PMC9436347 DOI: 10.1073/pnas.2201204119] [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] [Indexed: 11/18/2022] Open
Abstract
Bacteria utilize two-component system (TCS) signal transduction pathways to sense and adapt to changing environments. In a typical TCS, a stimulus induces a sensor histidine kinase (SHK) to phosphorylate a response regulator (RR), which then dimerizes and activates a transcriptional response. Here, we demonstrate that oligomerization-dependent depolarization of excitation light by fused mNeonGreen fluorescent protein probes enables real-time monitoring of RR dimerization dynamics in live bacteria. Using inducible promoters to independently express SHKs and RRs, we detect RR dimerization within seconds of stimulus addition in several model pathways. We go on to combine experiments with mathematical modeling to reveal that TCS phosphosignaling accelerates with SHK expression but decelerates with RR expression and SHK phosphatase activity. We further observe pulsatile activation of the SHK NarX in response to addition and depletion of the extracellular electron acceptor nitrate when the corresponding TCS is expressed from both inducible systems and the native chromosomal operon. Finally, we combine our method with polarized light microscopy to enable single-cell measurements of RR dimerization under changing stimulus conditions. Direct in vivo characterization of RR oligomerization dynamics should enable insights into the regulation of bacterial physiology.
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3
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Kobayashi I, Mochizuki K, Teramoto J, Imamura S, Takaya K, Ishihama A, Shimada T. Transcription Factor SrsR (YgfI) Is a Novel Regulator for the Stress-Response Genes in Stationary Phase in Escherichia coli K-12. Int J Mol Sci 2022; 23:ijms23116055. [PMID: 35682733 PMCID: PMC9181523 DOI: 10.3390/ijms23116055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 02/04/2023] Open
Abstract
Understanding the functional information of all genes and the biological mechanism based on the comprehensive genome regulation mechanism is an important task in life science. YgfI is an uncharacterized LysR family transcription factor in Escherichia coli. To identify the function of YgfI, the genomic SELEX (gSELEX) screening was performed for YgfI regulation targets on the E. coli genome. In addition, regulatory and phenotypic analyses were performed. A total of 10 loci on the E. coli genome were identified as the regulatory targets of YgfI with the YgfI binding activity. These predicted YgfI target genes were involved in biofilm formation, hydrogen peroxide resistance, and antibiotic resistance, many of which were expressed in the stationary phase. The TCAGATTTTGC sequence was identified as an YgfI box in in vitro gel shift assay and DNase-I footprinting assays. RT-qPCR analysis in vivo revealed that the expression of YgfI increased in the stationary phase. Physiological analyses suggested the participation of YgfI in biofilm formation and an increase in the tolerability against hydrogen peroxide. In summary, we propose to rename ygfI as srsR (a stress-response regulator in stationary phase).
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Affiliation(s)
- Ikki Kobayashi
- School of Agriculture, Meiji University, Kawasaki 214-8571, Kanagawa, Japan;
| | - Kenji Mochizuki
- Micro-Nano Technology Research Center, Hosei University, Koganei 184-0003, Tokyo, Japan; (K.M.); (J.T.)
| | - Jun Teramoto
- Micro-Nano Technology Research Center, Hosei University, Koganei 184-0003, Tokyo, Japan; (K.M.); (J.T.)
| | - Sousuke Imamura
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi 180-8585, Tokyo, Japan; (S.I.); (K.T.)
| | - Kazuhiro Takaya
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi 180-8585, Tokyo, Japan; (S.I.); (K.T.)
| | - Akira Ishihama
- Micro-Nano Technology Research Center, Hosei University, Koganei 184-0003, Tokyo, Japan; (K.M.); (J.T.)
- Correspondence: (A.I.); (T.S.)
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, Kawasaki 214-8571, Kanagawa, Japan;
- Correspondence: (A.I.); (T.S.)
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4
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Shimada T, Murayama R, Mashima T, Kawano N, Ishihama A. Regulatory role of CsuR (YiaU) in determination of cell surface properties of Escherichia coli K-12. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35438626 DOI: 10.1099/mic.0.001166] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genomic SELEX screening was performed to identify the binding sites of YiaU, an uncharacterized LysR family transcription factor, on the Escherichia coli K-12 genome. Five high-affinity binding targets of YiaU were identified, all of which were involved in the structures of the bacterial cell surface such as outer and inner membrane proteins, and lipopolysaccharides. Detailed in vitro and in vivo analyses suggest that YiaU activates these target genes. To gain insight into the effects of YiaU in vivo on physiological properties, we used phenotype microarrays, biofilm screening assays and the sensitivity against serum complement analysed using a yiaU deletion mutant or YiaU expression strain. Together, these results suggest that the YiaU regulon confers resistance to some antibiotics, and increases biofilm formation and complement sensitivity. We propose renaming YiaU as CsuR (regulator of cell surface).
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Affiliation(s)
- Tomohiro Shimada
- Meiji University, School of Agriculture, Kawasaki, Kanagawa 214-8571, Japan.,Hosei University, Department of Frontier Bioscience, Koganei, Tokyo 184-8584, Japan
| | - Rie Murayama
- Hosei University, Research Institute of Micro-Nano Technology, Koganei, Tokyo 184-0003, Japan
| | - Tomoki Mashima
- Meiji University, School of Agriculture, Kawasaki, Kanagawa 214-8571, Japan
| | - Natsuko Kawano
- Meiji University, School of Agriculture, Kawasaki, Kanagawa 214-8571, Japan
| | - Akira Ishihama
- Hosei University, Department of Frontier Bioscience, Koganei, Tokyo 184-8584, Japan.,Hosei University, Research Institute of Micro-Nano Technology, Koganei, Tokyo 184-0003, Japan
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5
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Abstract
The DNA-binding protein from starved cells, Dps, is a universally conserved prokaryotic ferritin that, in many species, also binds DNA. Dps homologs have been identified in the vast majority of bacterial species and several archaea. Dps also may play a role in the global regulation of gene expression, likely through chromatin reorganization. Dps has been shown to use both its ferritin and DNA-binding functions to respond to a variety of environmental pressures, including oxidative stress. One mechanism that allows Dps to achieve this is through a global nucleoid restructuring event during stationary phase, resulting in a compact, hexacrystalline nucleoprotein complex called the biocrystal that occludes damaging agents from DNA. Due to its small size, hollow spherical structure, and high stability, Dps is being developed for applications in biotechnology.
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6
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McGuire BE, Mela JE, Thompson VC, Cucksey LR, Stevens CE, McWhinnie RL, Winkler DFH, Pelech S, Nano FE. Escherichia coli recombinant expression of SARS-CoV-2 protein fragments. Microb Cell Fact 2022; 21:21. [PMID: 35123472 PMCID: PMC8817660 DOI: 10.1186/s12934-022-01753-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/28/2022] [Indexed: 12/16/2022] Open
Abstract
We have developed a method for the inexpensive, high-level expression of antigenic protein fragments of SARS-CoV-2 proteins in Escherichia coli. Our approach uses the thermophilic family 9 carbohydrate-binding module (CBM9) as an N-terminal carrier protein and affinity tag. The CBM9 module was joined to SARS-CoV-2 protein fragments via a flexible proline–threonine linker, which proved to be resistant to E. coli proteases. Two CBM9-spike protein fragment fusion proteins and one CBM9-nucleocapsid fragment fusion protein largely resisted protease degradation, while most of the CBM9 fusion proteins were degraded at some site in the SARS-CoV-2 protein fragment. All of the fusion proteins were highly expressed in E. coli and the CBM9-ID-H1 fusion protein was shown to yield 122 mg/L of purified product. Three purified CBM9-SARS-CoV-2 fusion proteins were tested and found to bind antibodies directed to the appropriate SARS-CoV-2 antigenic regions. The largest intact CBM9 fusion protein, CBM9-ID-H1, incorporates spike protein amino acids 540–588, which is a conserved region overlapping and C-terminal to the receptor binding domain that is widely recognized by human convalescent sera and contains a putative protective epitope.
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7
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Kamagata K, Itoh Y, Tan C, Mano E, Wu Y, Mandali S, Takada S, Johnson RC. Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo. Nucleic Acids Res 2021; 49:8642-8664. [PMID: 34352099 PMCID: PMC8421229 DOI: 10.1093/nar/gkab658] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/10/2021] [Accepted: 07/22/2021] [Indexed: 01/06/2023] Open
Abstract
Architectural DNA-binding proteins (ADBPs) are abundant constituents of eukaryotic or bacterial chromosomes that bind DNA promiscuously and function in diverse DNA reactions. They generate large conformational changes in DNA upon binding yet can slide along DNA when searching for functional binding sites. Here we investigate the mechanism by which ADBPs diffuse on DNA by single-molecule analyses of mutant proteins rationally chosen to distinguish between rotation-coupled diffusion and DNA surface sliding after transient unbinding from the groove(s). The properties of yeast Nhp6A mutant proteins, combined with molecular dynamics simulations, suggest Nhp6A switches between two binding modes: a static state, in which the HMGB domain is bound within the minor groove with the DNA highly bent, and a mobile state, where the protein is traveling along the DNA surface by means of its flexible N-terminal basic arm. The behaviors of Fis mutants, a bacterial nucleoid-associated helix-turn-helix dimer, are best explained by mobile proteins unbinding from the major groove and diffusing along the DNA surface. Nhp6A, Fis, and bacterial HU are all near exclusively associated with the chromosome, as packaged within the bacterial nucleoid, and can be modeled by three diffusion modes where HU exhibits the fastest and Fis the slowest diffusion.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Cheng Tan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yining Wu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Sridhar Mandali
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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8
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Wang M, Zhou T, Liang Y, Li G, Sun Y. Response characteristics of nirS-type denitrifier Paracoccus denitrificans under florfenicol stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 219:112355. [PMID: 34049225 DOI: 10.1016/j.ecoenv.2021.112355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/13/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Florfenicol (FF) is widely used in aquaculture and can interfere with denitrification when released into natural ecosystems. The aim of this study was to analyze the response characteristics of nirS-type denitrifier Paracoccus denitrificans under FF stress and further mine antibiotic-responsive factors in aquatic environment. Phenotypic analysis revealed that FF delayed the nitrate removal with a maximum inhibition value of 82.4% at exponential growth phase, leading to nitrite accumulation reached to 21.9-fold and biofilm biomass decreased by ~38.6%, which were due to the lower bacterial population count (P < 0.01). RNA-seq transcriptome analyses indicated that FF treatment decreased the expression of nirS, norB, nosD and nosZ genes that encoded enzymes required for NO2- to N2 conversion from 1.02- to 2.21-fold (P < 0.001). Furthermore, gene associated with the flagellar system FlgL was also down-regulated by 1.03-fold (P < 0.001). Moreover, 10 confirmed sRNAs were significantly induced, which regulated a wide range of metabolic pathways and protein expression. Interestingly, different bacteria contained the same sRNAs means that sRNAs can spread between them. Overall, this study suggests that the denitrification of nirS-type denitrifiers can be hampered widely by FF and the key sRNAs have great potential to be antibiotic-responsive factors.
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Affiliation(s)
- Mei Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Tong Zhou
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Yi Liang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yongxue Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
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9
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Pietrzyk-Brzezinska AJ, Cociurovscaia A. Structures of the TetR-like transcription regulator RcdA alone and in complexes with ligands. Proteins 2021; 90:33-44. [PMID: 34288132 DOI: 10.1002/prot.26183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/20/2021] [Accepted: 07/11/2021] [Indexed: 01/25/2023]
Abstract
RcdA is a helix-turn-helix (HTH) transcriptional regulator belonging to the TetR family. The protein regulates the transcription of curlin subunit gene D, the master regulator of biofilm formation. Moreover, it was predicted that it might be involved in the regulation of up to 27 different genes. However, an effector of RcdA and the environmental conditions which trigger RcdA action remain unknown. Herein, we report the first crystal structures of RcdA in complexes with ligands, trimethylamine N-oxide (TMAO) and tris(hydroxymethyl)aminomethane (Tris), which might serve as RcdA effectors. Based on these structures, the ligand-binding pocket of RcdA was characterized in detail. The conservation of the amino acid residues forming the ligand-binding cavity was analyzed and the comprehensive search for RcdA structural homologs was performed. This analysis indicated that RcdA is structurally similar to multidrug-binding TetR family members, however, its ligand-binding cavity differs significantly from the pockets of its structural homologs. The interaction of RcdA with TMAO and Tris indicates that the protein might be involved in alkaline stress response.
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Affiliation(s)
- Agnieszka J Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Anna Cociurovscaia
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
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10
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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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11
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Kamagata K, Ouchi K, Tan C, Mano E, Mandali S, Wu Y, Takada S, Takahashi S, Johnson RC. The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA. Nucleic Acids Res 2020; 48:10820-10831. [PMID: 32997109 PMCID: PMC7641734 DOI: 10.1093/nar/gkaa799] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/13/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
DNA binding proteins rapidly locate their specific DNA targets through a combination of 3D and 1D diffusion mechanisms, with the 1D search involving bidirectional sliding along DNA. However, even in nucleosome-free regions, chromosomes are highly decorated with associated proteins that may block sliding. Here we investigate the ability of the abundant chromatin-associated HMGB protein Nhp6A from Saccharomyces cerevisiae to travel along DNA in the presence of other architectural DNA binding proteins using single-molecule fluorescence microscopy. We observed that 1D diffusion by Nhp6A molecules is retarded by increasing densities of the bacterial proteins Fis and HU and by Nhp6A, indicating these structurally diverse proteins impede Nhp6A mobility on DNA. However, the average travel distances were larger than the average distances between neighboring proteins, implying Nhp6A is able to bypass each of these obstacles. Together with molecular dynamics simulations, our analyses suggest two binding modes: mobile molecules that can bypass barriers as they seek out DNA targets, and near stationary molecules that are associated with neighboring proteins or preferred DNA structures. The ability of mobile Nhp6A molecules to bypass different obstacles on DNA suggests they do not block 1D searches by other DNA binding proteins.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Faculty of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Kana Ouchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Sridhar Mandali
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737 USA
| | - Yining Wu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Faculty of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Faculty of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737 USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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12
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Brandi A, Giangrossi M, Fabbretti A, Falconi M. The hns Gene of Escherichia coli Is Transcriptionally Down-Regulated by (p)ppGpp. Microorganisms 2020; 8:microorganisms8101558. [PMID: 33050410 PMCID: PMC7601328 DOI: 10.3390/microorganisms8101558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 11/16/2022] Open
Abstract
Second messenger nucleotides, such as guanosine penta- or tetra-phosphate, commonly referred to as (p)ppGpp, are powerful signaling molecules, used by all bacteria to fine-tune cellular metabolism in response to nutrient availability. Indeed, under nutritional starvation, accumulation of (p)ppGpp reduces cell growth, inhibits stable RNAs synthesis, and selectively up- or down- regulates the expression of a large number of genes. Here, we show that the E. coli hns promoter responds to intracellular level of (p)ppGpp. hns encodes the DNA binding protein H-NS, one of the major components of bacterial nucleoid. Currently, H-NS is viewed as a global regulator of transcription in an environment-dependent mode. Combining results from relA (ppGpp synthetase) and spoT (ppGpp synthetase/hydrolase) null mutants with those from an inducible plasmid encoded RelA system, we have found that hns expression is inversely correlated with the intracellular concentration of (p)ppGpp, particularly in exponential phase of growth. Furthermore, we have reproduced in an in vitro system the observed in vivo (p)ppGpp-mediated transcriptional repression of hns promoter. Electrophoretic mobility shift assays clearly demonstrated that this unusual nucleotide negatively affects the stability of RNA polymerase-hns promoter complex. Hence, these findings demonstrate that the hns promoter is subjected to an RNA polymerase-mediated down-regulation by increased intracellular levels of (p)ppGpp.
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13
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Schmutzer M, Wagner A. Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments. PLoS Comput Biol 2020; 16:e1007727. [PMID: 33104710 PMCID: PMC7644098 DOI: 10.1371/journal.pcbi.1007727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 11/05/2020] [Accepted: 09/15/2020] [Indexed: 02/03/2023] Open
Abstract
Nongenetic phenotypic variation can either speed up or slow down adaptive evolution. We show that it can speed up evolution in environments where available carbon and energy sources change over time. To this end, we use an experimentally validated model of Escherichia coli growth on two alternative carbon sources, glucose and acetate. On the superior carbon source (glucose), all cells achieve high growth rates, while on the inferior carbon source (acetate) only a small fraction of the population manages to initiate growth. Consequently, populations experience a bottleneck when the environment changes from the superior to the inferior carbon source. Growth on the inferior carbon source depends on a circuit under the control of a transcription factor that is repressed in the presence of the superior carbon source. We show that noise in the expression of this transcription factor can increase the probability that cells start growing on the inferior carbon source. In doing so, it can decrease the severity of the bottleneck and increase mean population fitness whenever this fitness is low. A modest amount of noise can also enhance the fitness effects of a beneficial allele that increases the fraction of a population initiating growth on acetate. Additionally, noise can protect this allele from extinction, accelerate its spread, and increase its likelihood of going to fixation. Central to the adaptation-enhancing principle we identify is the ability of noise to mitigate population bottlenecks, particularly in environments that fluctuate periodically. Because such bottlenecks are frequent in fluctuating environments, and because periodically fluctuating environments themselves are common, this principle may apply to a broad range of environments and organisms.
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Affiliation(s)
- Michael Schmutzer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Santa Fe Institute, Santa Fe, New Mexico, USA
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14
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Ishida R, Adachi T, Yokota A, Yoshihara H, Aoki K, Nakamura Y, Hamada M. RaptRanker: in silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information. Nucleic Acids Res 2020; 48:e82. [PMID: 32537639 PMCID: PMC7641312 DOI: 10.1093/nar/gkaa484] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 01/02/2023] Open
Abstract
Aptamers are short single-stranded RNA/DNA molecules that bind to specific target molecules. Aptamers with high binding-affinity and target specificity are identified using an in vitro procedure called high throughput systematic evolution of ligands by exponential enrichment (HT-SELEX). However, the development of aptamer affinity reagents takes a considerable amount of time and is costly because HT-SELEX produces a large dataset of candidate sequences, some of which have insufficient binding-affinity. Here, we present RNA aptamer Ranker (RaptRanker), a novel in silico method for identifying high binding-affinity aptamers from HT-SELEX data by scoring and ranking. RaptRanker analyzes HT-SELEX data by evaluating the nucleotide sequence and secondary structure simultaneously, and by ranking according to scores reflecting local structure and sequence frequencies. To evaluate the performance of RaptRanker, we performed two new HT-SELEX experiments, and evaluated binding affinities of a part of sequences that include aptamers with low binding-affinity. In both datasets, the performance of RaptRanker was superior to Frequency, Enrichment and MPBind. We also confirmed that the consideration of secondary structures is effective in HT-SELEX data analysis, and that RaptRanker successfully predicted the essential subsequence motifs in each identified sequence.
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Affiliation(s)
- Ryoga Ishida
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | | | - Aya Yokota
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | | | | | | | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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15
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Ogasawara H, Ishizuka T, Hotta S, Aoki M, Shimada T, Ishihama A. Novel regulators of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli K-12. Microbiology (Reading) 2020; 166:880-890. [DOI: 10.1099/mic.0.000947] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Under stressful conditions,
Escherichia coli
forms biofilm for survival by sensing a variety of environmental conditions. CsgD, the master regulator of biofilm formation, controls cell aggregation by directly regulating the synthesis of Curli fimbriae. In agreement of its regulatory role, as many as 14 transcription factors (TFs) have so far been identified to participate in regulation of the csgD promoter, each monitoring a specific environmental condition or factor. In order to identify the whole set of TFs involved in this typical multi-factor promoter, we performed in this study ‘promoter-specific transcription-factor’ (PS-TF) screening in vitro using a set of 198 purified TFs (145 TFs with known functions and 53 hitherto uncharacterized TFs). A total of 48 TFs with strong binding to the csgD promoter probe were identified, including 35 known TFs and 13 uncharacterized TFs, referred to as Y-TFs. As an attempt to search for novel regulators, in this study we first analysed a total of seven Y-TFs, including YbiH, YdcI, YhjC, YiaJ, YiaU, YjgJ and YjiR. After analysis of curli fimbriae formation, LacZ-reporter assay, Northern-blot analysis and biofilm formation assay, we identified at least two novel regulators, repressor YiaJ (renamed PlaR) and activator YhjC (renamed RcdB), of the csgD promoter.
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Affiliation(s)
- Hiroshi Ogasawara
- Academic Assembly School of Humanities and Social Sciences Institute of Humanities, Shinshu University, Asahi 3-1-1, Matsumoto, 390–8621, Japan
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Toshiyuki Ishizuka
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Shuhei Hotta
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Michiko Aoki
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, 1-1-1 Higashi Mita, Tama-ku, Kawasaki, Kanagawa 214–8571, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
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16
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Seibt H, Aung KM, Ishikawa T, Sjöström A, Gullberg M, Atkinson GC, Wai SN, Shingler V. Elevated levels of VCA0117 (VasH) in response to external signals activate the type VI secretion system of Vibrio cholerae O1 El Tor A1552. Environ Microbiol 2020; 22:4409-4423. [PMID: 32592280 DOI: 10.1111/1462-2920.15141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 11/29/2022]
Abstract
The type VI nanomachine is critical for Vibrio cholerae to establish infections and to thrive in niches co-occupied by competing bacteria. The genes for the type VI structural proteins are encoded in one large and two small auxiliary gene clusters. VCA0117 (VasH) - a σ54 -transcriptional activator - is strictly required for functionality of the type VI secretion system since it controls production of the structural protein Hcp. While some strains constitutively produce a functional system, others do not and require specific growth conditions of low temperature and high osmolarity for expression of the type VI machinery. Here, we trace integration of these regulatory signals to the promoter activity of the large gene cluster in which many components of the machinery and VCA0117 itself are encoded. Using in vivo and in vitro assays and variants of VCA0117, we show that activation of the σ54 -promoters of the auxiliary gene clusters by elevated VCA0117 levels are all that is required to overcome the need for specialized growth conditions. We propose a model in which signal integration via the large operon promoter directs otherwise restrictive levels of VCA0117 that ultimately dictates a sufficient supply of Hcp for completion of a functional type VI secretion system.
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Affiliation(s)
- Henrik Seibt
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
| | - Kyaw Min Aung
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, SE-901 87, Sweden
| | - Takahiko Ishikawa
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, SE-901 87, Sweden
| | - Annika Sjöström
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
| | - Martin Gullberg
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
| | - Gemma Catherine Atkinson
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, SE-901 87, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, SE-901 87, Sweden
| | - Victoria Shingler
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
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17
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Ji Y, Feng G, Hou Y, Yu Y, Wang R, Yuan H. Long noncoding RNA MEG3 decreases the growth of head and neck squamous cell carcinoma by regulating the expression of miR-421 and E-cadherin. Cancer Med 2020; 9:3954-3963. [PMID: 32277605 PMCID: PMC7286453 DOI: 10.1002/cam4.3002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/25/2020] [Accepted: 03/03/2020] [Indexed: 01/04/2023] Open
Abstract
Background Maternally expressed 3 (MEG3), a long chain noncoding RNA (lncRNA), has verified its function as a suppressor in several kinds of cancers. However, the downstream mechanism of MEG3 in regulating the molecular mechanism of epithelial‐mesenchymal transformation (EMT) in head and neck squamous cell carcinoma (HNSCC) progression demands further investigation. Methods Quantitative real‐time polymerase chain reaction (qRT‐PCR) was used to determine the expression level of MEG3 in HNSCC and adjacent normal tissues of 51 cases. Luciferase report assay was used to detect the correlation between miR‐421 and MEG3, and miR‐421 and E‐cadherin in HNSCC cell lines. Cell invasion and proliferation capacity were assessed through transwell and CCK8 assays. Scratch wound assay was used to assess cell migration capacity. Results Firstly, this study demonstrated that the expression of MEG3 was significantly downregulated in HNSCC compared to adjacent normal tissues. Overexpressed MEG3 inhibited cell proliferation, migration, and invasion in vitro. Secondly, MEG3 upregulated the expression of E‐cadherin, which was instead downregulated by miR‐421. MiR‐421 was negatively regulated by MEG3 in HNSCC. Therefore, MEG3 regulated EMT by sponging miR‐421 targeting E‐cadherin in HNSCC. Conclusions This study indicated that the MEG3‐miR‐421‐E‐cadherin axis could be a new therapeutic target for HNSCC.
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Affiliation(s)
- Yefeng Ji
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Guanying Feng
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yunwen Hou
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yang Yu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Ruixia Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Hua Yuan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
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18
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Miyake Y, Yamamoto K. Epistatic Effect of Regulators to the Adaptive Growth of Escherichia coli. Sci Rep 2020; 10:3661. [PMID: 32108145 PMCID: PMC7046781 DOI: 10.1038/s41598-020-60353-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 02/11/2020] [Indexed: 11/09/2022] Open
Abstract
Bacteria survive in the environment with three steps: a sensing environmental conditions, a responding to sensed signals, and an adaptation for proper survival in the environment. An adapting bacterial cell occurs cell division to increase the number of sister cells, termed adaptive growth. Two-component systems (TCSs), representing the main bacterial signal transduction systems, consist of a pair of one sensor kinase (SK) and one response regulator (RR), and RR genes are abundant in most bacterial genomes as part of the core genome. The OmpR gene family, a group of RR genes, is conserved in 95% of known bacterial genomes. The Escherichia coli genome has an estimated 34 RR genes in total, including 14 genes of OmpR family genes. To reveal the contribution of TCSs for fast growth as an adaptive growth strategy of E. coli, we isolated a set of gene knockout strains by using newly developed genome editing technology, the HoSeI (Homologous Sequence Integration) method, based on CRISPR-Cas9. The statistics of single cell observation show a knockout of an arbitrary pair of phoP, phoB, and ompR genes, stably expressed by positive feedback regulation, dramatically inhibit the optimum adaptive growth of E. coli. These insights suggest that the adaptive growth of bacteria is fulfilled by the optimum high intracellular level of regulators acquired during growth under environmental conditions.
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Affiliation(s)
- Yukari Miyake
- Hosei University, Department of Frontier Bioscience, Koganei, Tokyo, 184-8584, Japan
| | - Kaneyoshi Yamamoto
- Hosei University, Department of Frontier Bioscience, Koganei, Tokyo, 184-8584, Japan.
- Hosei University, Research Institute of Micro-Nano Technology, Koganei, Tokyo, 184-8584, Japan.
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19
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Shimada T, Yokoyama Y, Anzai T, Yamamoto K, Ishihama A. Regulatory Role of PlaR (YiaJ) for Plant Utilization in Escherichia coli K-12. Sci Rep 2019; 9:20415. [PMID: 31892694 PMCID: PMC6958661 DOI: 10.1038/s41598-019-56886-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022] Open
Abstract
Outside a warm-blooded animal host, the enterobacterium Escherichia coli K-12 is also able to grow and survive in stressful nature. The major organic substance in nature is plant, but the genetic system of E. coli how to utilize plant-derived materials as nutrients is poorly understood. Here we describe the set of regulatory targets for uncharacterized IclR-family transcription factor YiaJ on the E. coli genome, using gSELEX screening system. Among a total of 18 high-affinity binding targets of YiaJ, the major regulatory target was identified to be the yiaLMNOPQRS operon for utilization of ascorbate from fruits and galacturonate from plant pectin. The targets of YiaJ also include the genes involved in the utilization for other plant-derived materials as nutrients such as fructose, sorbitol, glycerol and fructoselysine. Detailed in vitro and in vivo analyses suggest that L-ascorbate and α-D-galacturonate are the effector ligands for regulation of YiaJ function. These findings altogether indicate that YiaJ plays a major regulatory role in expression of a set of the genes for the utilization of plant-derived materials as nutrients for survival. PlaR was also suggested to play protecting roles of E. coli under stressful environments in nature, including the formation of biofilm. We then propose renaming YiaJ to PlaR (regulator of plant utilization). The natural hosts of enterobacterium Escherichia coli are warm-blooded animals, but even outside hosts, E. coli can survive even under stressful environments. On earth, the most common organic materials to be used as nutrients by E. coli are plant-derived components, but up to the present time, the genetic system of E. coli for plant utilization is poorly understand. In the course of gSELEX screening of the regulatory targets for hitherto uncharacterized TFs, we identified in this study the involvement of the IclR-family YiaJ in the regulation of about 20 genes or operons, of which the majority are related to the catabolism of plant-derived materials such as ascorbate, galacturonate, sorbitol, fructose and fructoselysine. Therefore, we propose to rename YiaJ to PlaR (regulator of plant utilization).
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Affiliation(s)
- Tomohiro Shimada
- Meiji University, School of Agriculture, Kawasaki, Kanagawa, 214-8571, Japan. .,Hosei University, Research Institute of Micro-Nano Technology, Koganei, Tokyo, 184-0003, Japan.
| | - Yui Yokoyama
- Hosei University, Department of Frontier Bioscience, Koganei, Tokyo, 184-8584, Japan
| | - Takumi Anzai
- Meiji University, School of Agriculture, Kawasaki, Kanagawa, 214-8571, Japan
| | - Kaneyoshi Yamamoto
- Hosei University, Department of Frontier Bioscience, Koganei, Tokyo, 184-8584, Japan
| | - Akira Ishihama
- Hosei University, Research Institute of Micro-Nano Technology, Koganei, Tokyo, 184-0003, Japan. .,Hosei University, Department of Frontier Bioscience, Koganei, Tokyo, 184-8584, Japan.
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20
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Yoshida H, Wada A, Shimada T, Maki Y, Ishihama A. Coordinated Regulation of Rsd and RMF for Simultaneous Hibernation of Transcription Apparatus and Translation Machinery in Stationary-Phase Escherichia coli. Front Genet 2019; 10:1153. [PMID: 31867037 PMCID: PMC6904343 DOI: 10.3389/fgene.2019.01153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/22/2019] [Indexed: 02/01/2023] Open
Abstract
Transcription and translation in growing phase of Escherichia coli, the best-studied model prokaryote, are coupled and regulated in coordinate fashion. Accordingly, the growth rate-dependent control of the synthesis of RNA polymerase (RNAP) core enzyme (the core component of transcription apparatus) and ribosomes (the core component of translation machinery) is tightly coordinated to keep the relative level of transcription apparatus and translation machinery constant for effective and efficient utilization of resources and energy. Upon entry into the stationary phase, transcription apparatus is modulated by replacing RNAP core-associated sigma (promoter recognition subunit) from growth-related RpoD to stationary-phase-specific RpoS. The anti-sigma factor Rsd participates for the efficient replacement of sigma, and the unused RpoD is stored silent as Rsd–RpoD complex. On the other hand, functional 70S ribosome is transformed into inactive 100S dimer by two regulators, ribosome modulation factor (RMF) and hibernation promoting factor (HPF). In this review article, we overview how we found these factors and what we know about the molecular mechanisms for silencing transcription apparatus and translation machinery by these factors. In addition, we provide our recent findings of promoter-specific transcription factor (PS-TF) screening of the transcription factors involved in regulation of the rsd and rmf genes. Results altogether indicate the coordinated regulation of Rsd and RMF for simultaneous hibernation of transcription apparatus and translation machinery.
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Affiliation(s)
- Hideji Yoshida
- Department of Physics, Osaka Medical College, Takatsuki, Japan
| | - Akira Wada
- Yoshida Biological Laboratory, Kyoto, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, Kawasaki, Japan.,Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
| | - Yasushi Maki
- Department of Physics, Osaka Medical College, Takatsuki, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
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21
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Stoof R, Wood A, Goñi-Moreno Á. A Model for the Spatiotemporal Design of Gene Regulatory Circuits †. ACS Synth Biol 2019; 8:2007-2016. [PMID: 31429541 DOI: 10.1021/acssynbio.9b00022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mathematical modeling assists the design of synthetic regulatory networks by providing a detailed mechanistic understanding of biological systems. Models that can predict the performance of a design are fundamental for synthetic biology since they minimize iterations along the design-build-test lifecycle. Such predictability depends crucially on what assumptions (i.e., biological simplifications) the model considers. Here, we challenge a common assumption when it comes to the modeling of bacterial-based gene regulation: considering negligible the effects of intracellular physical space. It is commonly assumed that molecules, such as transcription factors (TF), are homogeneously distributed inside a cell, so there is no need to model their diffusion. We describe a mathematical model that accounts for molecular diffusion and show how simulations of network performance are decisively affected by the distance between its components. Specifically, the model focuses on the search by a TF for its target promoter. The combination of local searches, via one-dimensional sliding along the chromosome, and global searches, via three-dimensional diffusion through the cytoplasm, determine TF-promoter interplay. Previous experimental results with engineered bacteria in which the distance between TF source and target was minimized or enlarged were successfully reproduced by the spatially resolved model we introduce here. This suggests that the spatial specification of the circuit alone can be exploited as a design parameter in synthetic biology to select programmable output levels.
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Affiliation(s)
- Ruud Stoof
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, U.K
| | - Alexander Wood
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, U.K
| | - Ángel Goñi-Moreno
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, U.K
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22
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Shimada T, Ogasawara H, Ishihama A. Single-target regulators form a minor group of transcription factors in Escherichia coli K-12. Nucleic Acids Res 2019. [PMID: 29529243 PMCID: PMC5934670 DOI: 10.1093/nar/gky138] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The identification of regulatory targets of all TFs is critical for understanding the entire network of the genome regulation. The lac regulon of Escherichia coli K-12 W3110 is composed of the lacZYA operon and its repressor lacI gene, and has long been recognized as the seminal model of transcription regulation in bacteria with only one highly preferred target. After the Genomic SELEX screening in vitro of more than 200 transcription factors (TFs) from E. coli K-12, however, we found that most TFs regulate multiple target genes. With respect to the number of regulatory targets, a total of these 200 E. coli TFs form a hierarchy ranging from a single target to as many as 1000 targets. Here we focus a total of 13 single-target TFs, 9 known TFs (BetI, KdpE, LacI, MarR, NanR, RpiR, TorR, UlaR and UxuR) and 4 uncharacterized TFs (YagI, YbaO, YbiH and YeaM), altogether forming only a minor group of TFs in E. coli. These single-target TFs were classified into three groups based on their functional regulation.
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Affiliation(s)
- Tomohiro Shimada
- Meiji University, School of Agriculture, Kawasaki, Kanagawa 214-8571, Japan
| | - Hiroshi Ogasawara
- Shinshu University, Research Center for Supports to Advanced Science, Division of Gene Research, Ueda, Nagano 386-8567, Japan.,Shinshu University, Research Center for Fungal and Microbial Dynamism, Kamiina, Nagano 399-4598, Japan
| | - Akira Ishihama
- Hosei University, Micro-Nano Technology Research Center, Koganei, Tokyo 184-8584, Japan
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23
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Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli. Amino Acids 2019; 51:1103-1127. [DOI: 10.1007/s00726-019-02757-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
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24
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Ultee E, Ramijan K, Dame RT, Briegel A, Claessen D. Stress-induced adaptive morphogenesis in bacteria. Adv Microb Physiol 2019; 74:97-141. [PMID: 31126537 DOI: 10.1016/bs.ampbs.2019.02.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacteria thrive in virtually all environments. Like all other living organisms, bacteria may encounter various types of stresses, to which cells need to adapt. In this chapter, we describe how cells cope with stressful conditions and how this may lead to dramatic morphological changes. These changes may not only allow harmless cells to withstand environmental insults but can also benefit pathogenic bacteria by enabling them to escape from the immune system and the activity of antibiotics. A better understanding of stress-induced morphogenesis will help us to develop new approaches to combat such harmful pathogens.
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Affiliation(s)
- Eveline Ultee
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Karina Ramijan
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Remus T Dame
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands; Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CE Leiden, the Netherlands
| | - Ariane Briegel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
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25
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Shimada T, Yamamoto K, Nakano M, Watanabe H, Schleheck D, Ishihama A. Regulatory role of CsqR (YihW) in transcription of the genes for catabolism of the anionic sugar sulfoquinovose (SQ) in Escherichia coli K-12. MICROBIOLOGY-SGM 2018; 165:78-89. [PMID: 30372406 DOI: 10.1099/mic.0.000740] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The binding sites of YihW, an uncharacterized DeoR-family transcription factor (TF) of Escherichia coli K-12, were identified using Genomic SELEX screening at two closely located sites, one inside the spacer between the bidirectional transcription units comprising the yihUTS operon and the yihV gene, and another one upstream of the yihW gene itself. Recently the YihUTS and YihV proteins were identified as catalysing the catabolism of sulfoquinovose (SQ), a hydrolysis product of sulfoquinovosyl diacylglycerol (SQDG) derived from plants and other photosynthetic organisms. Gel shift assay in vitro and reporter assay in vivo indicated that YihW functions as a repressor for all three transcription units. De-repression of the yih operons was found to be under the control of SQ as inducer, but not of lactose, glucose or galactose. Furthermore, a mode of its cooperative DNA binding was suggested for YihW by atomic force microscopy. Hence, as a regulator of the catabolism of SQ, we renamed YihW as CsqR.
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Affiliation(s)
- Tomohiro Shimada
- 1Meiji University, School of Agriculture, Kawasaki, Kanagawa, Japan
| | - Kaneyoshi Yamamoto
- 2Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan.,3Hosei University, Micro-Nano Technology Research Center, Koganei, Tokyo, Japan
| | - Masahiro Nakano
- 4Kyoto University, Institute for Frontier Life and Medical Sciences, Sakyo-ku, Kyoto, Japan
| | - Hiroki Watanabe
- 2Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - David Schleheck
- 5Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Akira Ishihama
- 3Hosei University, Micro-Nano Technology Research Center, Koganei, Tokyo, Japan
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26
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Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase. mSystems 2018; 3:mSystems00057-18. [PMID: 30225374 PMCID: PMC6134199 DOI: 10.1128/msystems.00057-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
During the growth transition of E. coli from exponential phase to stationary, the genome expression pattern is altered markedly. For this alteration, the transcription apparatus is altered by binding of anti-sigma factor Rsd to the RpoD sigma factor for sigma factor replacement, while the translation machinery is modulated by binding of RMF to 70S ribosome to form inactive ribosome dimer. Using the PS-TF screening system, a number of TFs were found to bind to both the rsd and rmf promoters, of which the regulatory roles of 5 representative TFs (one repressor ArcA and the four activators McbR, RcdA, SdiA, and SlyA) were analyzed in detail. The results altogether indicated the involvement of a common set of TFs, each sensing a specific environmental condition, in coordinated hibernation of the transcriptional and translational apparatus for adaptation and survival under stress conditions. In the process of Escherichia coli K-12 growth from exponential phase to stationary, marked alteration takes place in the pattern of overall genome expression through modulation of both parts of the transcriptional and translational apparatus. In transcription, the sigma subunit with promoter recognition properties is replaced from the growth-related factor RpoD by the stationary-phase-specific factor RpoS. The unused RpoD is stored by binding with the anti-sigma factor Rsd. In translation, the functional 70S ribosome is converted to inactive 100S dimers through binding with the ribosome modulation factor (RMF). Up to the present time, the regulatory mechanisms of expression of these two critical proteins, Rsd and RMF, have remained totally unsolved. In this study, attempts were made to identify the whole set of transcription factors involved in transcription regulation of the rsd and rmf genes using the newly developed promoter-specific transcription factor (PS-TF) screening system. In the first screening, 74 candidate TFs with binding activity to both of the rsd and rmf promoters were selected from a total of 194 purified TFs. After 6 cycles of screening, we selected 5 stress response TFs, ArcA, McbR, RcdA, SdiA, and SlyA, for detailed analysis in vitro and in vivo of their regulatory roles. Results indicated that both rsd and rmf promoters are repressed by ArcA and activated by McbR, RcdA, SdiA, and SlyA. We propose the involvement of a number of TFs in simultaneous and coordinated regulation of the transcriptional and translational apparatus. By using genomic SELEX (gSELEX) screening, each of the five TFs was found to regulate not only the rsd and rmf genes but also a variety of genes for growth and survival. IMPORTANCE During the growth transition of E. coli from exponential phase to stationary, the genome expression pattern is altered markedly. For this alteration, the transcription apparatus is altered by binding of anti-sigma factor Rsd to the RpoD sigma factor for sigma factor replacement, while the translation machinery is modulated by binding of RMF to 70S ribosome to form inactive ribosome dimer. Using the PS-TF screening system, a number of TFs were found to bind to both the rsd and rmf promoters, of which the regulatory roles of 5 representative TFs (one repressor ArcA and the four activators McbR, RcdA, SdiA, and SlyA) were analyzed in detail. The results altogether indicated the involvement of a common set of TFs, each sensing a specific environmental condition, in coordinated hibernation of the transcriptional and translational apparatus for adaptation and survival under stress conditions.
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27
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Yamanaka Y, Winardhi RS, Yamauchi E, Nishiyama SI, Sowa Y, Yan J, Kawagishi I, Ishihama A, Yamamoto K. Dimerization site 2 of the bacterial DNA-binding protein H-NS is required for gene silencing and stiffened nucleoprotein filament formation. J Biol Chem 2018; 293:9496-9505. [PMID: 29695505 DOI: 10.1074/jbc.ra117.001425] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/20/2018] [Indexed: 11/06/2022] Open
Abstract
The bacterial nucleoid-associated protein H-NS is a DNA-binding protein, playing a major role in gene regulation. To regulate transcription, H-NS silences genes, including horizontally acquired foreign genes. Escherichia coli H-NS is 137 residues long and consists of two discrete and independent structural domains: an N-terminal oligomerization domain and a C-terminal DNA-binding domain, joined by a flexible linker. The N-terminal oligomerization domain is composed of two dimerization sites, dimerization sites 1 and 2, which are both required for H-NS oligomerization, but the exact role of dimerization site 2 in gene silencing is unclear. To this end, we constructed a whole set of single amino acid substitution variants spanning residues 2 to 137. Using a well-characterized H-NS target, the slp promoter of the glutamic acid-dependent acid resistance (GAD) cluster promoters, we screened for any variants defective in gene silencing. Focusing on the function of dimerization site 2, we analyzed four variants, I70C/I70A and L75C/L75A, which all could actively bind DNA but are defective in gene silencing. Atomic force microscopy analysis of DNA-H-NS complexes revealed that all of these four variants formed condensed complexes on DNA, whereas WT H-NS formed rigid and extended nucleoprotein filaments, a conformation required for gene silencing. Single-molecule stretching experiments confirmed that the four variants had lost the ability to form stiffened filaments. We conclude that dimerization site 2 of H-NS plays a key role in the formation of rigid H-NS nucleoprotein filament structures required for gene silencing.
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Affiliation(s)
- Yuki Yamanaka
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan.,the Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore, and
| | - Ricksen S Winardhi
- the Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore, and.,the Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542, Singapore
| | - Erika Yamauchi
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - So-Ichiro Nishiyama
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Yoshiyuki Sowa
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Jie Yan
- the Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore, and.,the Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542, Singapore
| | - Ikuro Kawagishi
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Akira Ishihama
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Kaneyoshi Yamamoto
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan, .,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
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28
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Udaondo Z, Ramos JL, Segura A, Krell T, Daddaoua A. Regulation of carbohydrate degradation pathways in Pseudomonas involves a versatile set of transcriptional regulators. Microb Biotechnol 2018; 11:442-454. [PMID: 29607620 PMCID: PMC5902321 DOI: 10.1111/1751-7915.13263] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/22/2018] [Accepted: 03/01/2018] [Indexed: 01/08/2023] Open
Abstract
Bacteria of the genus Pseudomonas are widespread in nature. In the last decades, members of this genus, especially Pseudomonas aeruginosa and Pseudomonas putida, have acquired great interest because of their interactions with higher organisms. Pseudomonas aeruginosa is an opportunistic pathogen that colonizes the lung of cystic fibrosis patients, while P. putida is a soil bacterium able to establish a positive interaction with the plant rhizosphere. Members of Pseudomonas genus have a robust metabolism for amino acids and organic acids as well as aromatic compounds; however, these microbes metabolize a very limited number of sugars. Interestingly, they have three-pronged metabolic system to generate 6-phosphogluconate from glucose suggesting an adaptation to efficiently consume this sugar. This review focuses on the description of the regulatory network of glucose utilization in Pseudomonas, highlighting the differences between P. putida and P. aeruginosa. Most interestingly, It is highlighted a functional link between glucose assimilation and exotoxin A production in P. aeruginosa. The physiological relevance of this connection remains unclear, and it needs to be established whether a similar relationship is also found in other bacteria.
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Affiliation(s)
- Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301W. Markham St., Slot 782, Little Rock, AR, 72205, USA
| | - Juan-Luis Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, C/ Profesor Albareda 1, E-18008, Granada, Spain
| | - Ana Segura
- Department of Environmental Protection, Estación Experimental del Zaidín, C/ Profesor Albareda 1, E-18008, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, C/ Profesor Albareda 1, E-18008, Granada, Spain
| | - Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, Pharmacy School, Granada University, Granada, Spain
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29
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Madoshi B, Mtambo M, Muhairwa A, Lupindu A, Olsen J. Isolation of vancomycin‐resistant
Enterococcus
from apparently healthy human animal attendants, cattle and cattle wastes in Tanzania. J Appl Microbiol 2018; 124:1303-1310. [DOI: 10.1111/jam.13722] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/02/2018] [Accepted: 01/16/2018] [Indexed: 02/02/2023]
Affiliation(s)
- B.P. Madoshi
- Department of Veterinary Medicine and Public Health Sokoine University of agriculture MorogoroTanzania
- Livestock Training Agency – Mpwapwa Campus Mpwapwa DodomaTanzania
| | - M.M.A. Mtambo
- Tanzania Industrial Research Developments Organisation TIRDO Complex DSM Tanzania
| | - A.P. Muhairwa
- Department of Veterinary Medicine and Public Health Sokoine University of agriculture MorogoroTanzania
| | - A.M. Lupindu
- Department of Veterinary Medicine and Public Health Sokoine University of agriculture MorogoroTanzania
| | - J.E. Olsen
- Department of Veterinary and Animal Sciences Faculty of Health and Medical Sciences University of Copenhagen Frederiksberg C Denmark
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30
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Shimada T, Momiyama E, Yamanaka Y, Watanabe H, Yamamoto K, Ishihama A. Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12. FEMS Microbiol Lett 2018; 364:4566516. [PMID: 29087459 DOI: 10.1093/femsle/fnx220] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/24/2017] [Indexed: 01/02/2023] Open
Abstract
The genome of Escherichia coli K-12 contains ten cryptic phages, altogether constituting about 3.6% of the genome in sequence. Among more than 200 predicted genes in these cryptic phages, 14 putative transcription factor (TF) genes exist, but their regulatory functions remain unidentified. As an initial attempt to make a breakthrough for understanding the regulatory roles of cryptic phage-encoded TFs, we tried to identify the regulatory function of CP4-6 cryptic prophage-encoded YagI with unknown function. After SELEX screening, YagI was found to bind mainly at a single site within the spacer of bidirectional transcription units, yagA (encoding another uncharacterized TF) and yagEF (encoding 2-keto-3-deoxy gluconate aldolase, and dehydratase, respectively) within this prophage region. YagEF enzymes are involved in the catabolism of xylose downstream from xylonate. We then designated YagI as XynR (regulator of xylonate catabolism), one of the rare single-target TFs. In agreement with this predicted regulatory function, the activity of XynR was suggested to be controlled by xylonate. Even though low-affinity binding sites of XynR were identified in the E. coli K-12 genome, they all were inside open reading frames, implying that the regulation network of XynR is still fixed within the CR4-6 prophage without significant influence over the host E. coli K-12.
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Affiliation(s)
- Tomohiro Shimada
- Research Center for Micro-Nano Technology, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan.,School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Eri Momiyama
- Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan
| | - Yuki Yamanaka
- Research Center for Micro-Nano Technology, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan.,Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan
| | - Hiroki Watanabe
- Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan
| | - Kaneyoshi Yamamoto
- Research Center for Micro-Nano Technology, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan.,Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan.,Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan
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31
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Ochab-Marcinek A, Jędrak J, Tabaka M. Hill kinetics as a noise filter: the role of transcription factor autoregulation in gene cascades. Phys Chem Chem Phys 2018; 19:22580-22591. [PMID: 28809965 DOI: 10.1039/c7cp00743d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An intuition based on deterministic models of chemical kinetics is that population heterogeneity of transcription factor levels in cells is transmitted unchanged downstream to the target genes. We use a stochastic model of a two-gene cascade with a self-regulating upstream gene to show that, counter to the intuition, there is no simple mapping (bimodal to bimodal, unimodal to unimodal) between the shapes of the distributions of transcription factor numbers and target protein numbers in cells. Due to the presence of the two regulations, the system contains two nonlinear transfer functions, defined by the Hill kinetics of transcription factor binding. The transfer function of the regulator can "interfere" with the transfer function of the target, converting the bimodal input into a unimodal output or vice versa. We show that this effect can be predicted by a geometric construction. As an example application of the method, we present a case study of a system of several downstream genes of different sensitivities, controlled by a common transcription factor which also regulates its own transcription. We show that a single regulator can induce qualitatively different patterns (binary or graded) of responses to a signal in different downstream genes, depending on whether the sensitivity regions of the transfer functions of the upstream and downstream genes overlap or not. Alternatively, the same model can be interpreted as describing a single downstream gene that has different sensitivities in different cell lines due to mutations. Our model shows, therefore, a possible kinetic mechanism by which different genes can interpret the same biological signal in a different manner.
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Affiliation(s)
- Anna Ochab-Marcinek
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Jakub Jędrak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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32
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Kamagata K, Mano E, Ouchi K, Kanbayashi S, Johnson RC. High Free-Energy Barrier of 1D Diffusion Along DNA by Architectural DNA-Binding Proteins. J Mol Biol 2018; 430:655-667. [PMID: 29307468 DOI: 10.1016/j.jmb.2018.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/13/2017] [Accepted: 01/02/2018] [Indexed: 01/25/2023]
Abstract
Architectural DNA-binding proteins function to regulate diverse DNA reactions and have the defining property of significantly changing DNA conformation. Although the 1D movement along DNA by other types of DNA-binding proteins has been visualized, the mobility of architectural DNA-binding proteins on DNA remains unknown. Here, we applied single-molecule fluorescence imaging on arrays of extended DNA molecules to probe the binding dynamics of three structurally distinct architectural DNA-binding proteins: Nhp6A, HU, and Fis. Each of these proteins was observed to move along DNA, and the salt concentration independence of the 1D diffusion implies sliding with continuous contact to DNA. Nhp6A and HU exhibit a single sliding mode, whereas Fis exhibits two sliding modes. Based on comparison of the diffusion coefficients and sizes of many DNA binding proteins, the architectural proteins are categorized into a new group distinguished by an unusually high free-energy barrier for 1D diffusion. The higher free-energy barrier for 1D diffusion by architectural proteins can be attributed to the large DNA conformational changes that accompany binding and impede rotation-coupled movement along the DNA grooves.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Aoba-ku, Sendai980-8577, Japan.
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Kana Ouchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Aoba-ku, Sendai980-8577, Japan
| | - Saori Kanbayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA90095-1737, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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33
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Cadby IT, Faulkner M, Cheneby J, Long J, van Helden J, Dolla A, Cole JA. Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide. Sci Rep 2017; 7:16228. [PMID: 29176637 PMCID: PMC5701242 DOI: 10.1038/s41598-017-16403-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/08/2017] [Indexed: 01/06/2023] Open
Abstract
The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing bacteria, it can also protect itself against nitrosative stress caused by NO generated when nitrite accumulates. By combining in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and how nitrate and nitrite reduction are coordinated with the response to nitrosative stress were revealed. Although nitrate and nitrite reduction are tightly regulated in response to substrate availability, the global responses to nitrate or NO were largely regulated independently. Multiple NADH dehydrogenases, transcription factors of unknown function and genes for iron uptake were differentially expressed in response to electron acceptor availability or nitrosative stress. Amongst many fascinating problems for future research, the data revealed a YtfE orthologue, Ddes_1165, that is implicated in the repair of nitrosative damage. The combined data suggest that three transcription factors coordinate this regulation in which NrfS-NrfR coordinates nitrate and nitrite reduction to minimize toxicity due to nitrite accumulation, HcpR1 serves a global role in regulating the response to nitrate, and HcpR2 regulates the response to nitrosative stress.
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Affiliation(s)
- Ian T Cadby
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Matthew Faulkner
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- The Institute of Integrative Biology, Bioscience building, University of Liverpool, Liverpool, Merseyside, L69 7ZB, UK
| | - Jeanne Cheneby
- Aix Marseille Univ, INSERM, TAGC, UMR_S 1090, 163, Avenue de Luminy, 13288, Marseille, France
| | - Justine Long
- Aix Marseille Univ, INSERM, TAGC, UMR_S 1090, 163, Avenue de Luminy, 13288, Marseille, France
| | - Jacques van Helden
- Aix Marseille Univ, INSERM, TAGC, UMR_S 1090, 163, Avenue de Luminy, 13288, Marseille, France
| | - Alain Dolla
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Jeffrey A Cole
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
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Antipov S, Turishchev S, Purtov Y, Shvyreva U, Sinelnikov A, Semov Y, Preobrazhenskaya E, Berezhnoy A, Shusharina N, Novolokina N, Vakhtel V, Artyukhov V, Ozoline O. The Oligomeric Form of the Escherichia coli Dps Protein Depends on the Availability of Iron Ions. Molecules 2017; 22:molecules22111904. [PMID: 29113077 PMCID: PMC6150300 DOI: 10.3390/molecules22111904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 10/29/2017] [Accepted: 11/02/2017] [Indexed: 11/21/2022] Open
Abstract
The Dps protein of Escherichia coli, which combines ferroxidase activity and the ability to bind DNA, is effectively used by bacteria to protect their genomes from damage. Both activities depend on the integrity of this multi-subunit protein, which has an inner cavity for iron oxides; however, the diversity of its oligomeric forms has only been studied fragmentarily. Here, we show that iron ions stabilize the dodecameric form of Dps. This was found by electrophoretic fractionation and size exclusion chromatography, which revealed several oligomers in highly purified protein samples and demonstrated their conversion to dodecamers in the presence of 1 mM Mohr’s salt. The transmission electron microscopy data contradicted the assumption that the stabilizing effect is given by the optimal core size formed in the inner cavity of Dps. The charge state of iron ions was evaluated using Mössbauer spectroscopy, which showed the presence of Fe3O4, rather than the expected Fe2O3, in the sample. Assuming that Fe2+ can form additional inter-subunit contacts, we modeled the interaction of FeO and Fe2O3 with Dps, but the binding sites with putative functionality were predicted only for Fe2O3. The question of how the dodecameric form can be stabilized by ferric oxides is discussed.
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Affiliation(s)
- Sergey Antipov
- School of Life Sciences, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia.
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia.
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Sergey Turishchev
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Yuriy Purtov
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia.
| | - Uliana Shvyreva
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia.
| | - Alexander Sinelnikov
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Yuriy Semov
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | | | - Andrey Berezhnoy
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Natalia Shusharina
- School of Life Sciences, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia.
| | - Natalia Novolokina
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Viktor Vakhtel
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Valeriy Artyukhov
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Olga Ozoline
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia.
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, 142290 Pushchino, Russia.
- Department of Structural and Functional genomics, Pushchino Scientific Center, 142290 Pushchino, Russia.
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35
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How prokaryotes 'encode' their environment: Systemic tools for organizing the information flow. Biosystems 2017; 164:26-38. [PMID: 28987781 DOI: 10.1016/j.biosystems.2017.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 01/04/2023]
Abstract
An important issue related to code biology concerns the cell's informational relationships with the environment. As an open self-producing system, a great variety of inputs and outputs are necessary for the living cell, not only consisting of matter and energy but also involving information flows. The analysis here of the simplest cells will involve two basic aspects. On the one side, the molecular apparatuses of the prokaryotic signaling system, with all its variety of environmental signals and component pathways (which have been called 1-2-3 Component Systems), including the role of a few second messengers which have been pointed out in bacteria too. And in the other side, the gene transcription system as depending not only on signaling inputs but also on a diversity of factors. Amidst the continuum of energy, matter, and information flows, there seems to be evidence for signaling codes, mostly established around the arrangement of life-cycle stages, in large metabolic changes, or in the relationships with conspecifics (quorum sensing) and within microbial ecosystems. Additionally, and considering the complexity growth of signaling systems from prokaryotes to eukaryotes, four avenues or "roots" for the advancement of such complexity would come out. A comparative will be established in between the signaling strategies and organization of both kinds of cellular systems. Finally, a new characterization of "informational architectures" will be proposed in order to explain the coding spectrum of both prokaryotic and eukaryotic signaling systems. Among other evolutionary aspects, cellular strategies for the construction of novel functional codes via the intermixing of informational architectures could be related to the persistence of retro-elements with obvious viral ancestry.
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36
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Ishihama A. Building a complete image of genome regulation in the model organism Escherichia coli. J GEN APPL MICROBIOL 2017; 63:311-324. [PMID: 28904250 DOI: 10.2323/jgam.2017.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The model organism, Escherichia coli, contains a total of more than 4,500 genes, but the total number of RNA polymerase (RNAP) core enzyme or the transcriptase is only about 2,000 molecules per genome. The regulatory targets of RNAP are, however, modulated by changing its promoter selectivity through two-steps of protein-protein interplay with 7 species of the sigma factor in the first step, and then 300 species of the transcription factor (TF) in the second step. Scientists working in the field of prokaryotic transcription in Japan have made considerable contributions to the elucidation of genetic frameworks and regulatory modes of the genome transcription in E. coli K-12. This review summarizes the findings by this group, first focusing on three sigma factors, the stationary-phase sigma RpoS, the heat-shock sigma RpoH, and the flagellar-chemotaxis sigma RpoF, as examples. It also presents an overview of the current state of the systematic research being carried out to identify the regulatory functions of all TFs from a single and the same bacterium E. coli K-12, using the genomic SELEX and PS-TF screening systems. All these studies have been undertaken with the aim of understanding the genome regulation in E. coli K-12 as a whole.
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Affiliation(s)
- Akira Ishihama
- Research Institute of Micro-Nano Technology, Hosei University
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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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Goñi-Moreno Á, Benedetti I, Kim J, de Lorenzo V. Deconvolution of Gene Expression Noise into Spatial Dynamics of Transcription Factor-Promoter Interplay. ACS Synth Biol 2017; 6:1359-1369. [PMID: 28355056 DOI: 10.1021/acssynbio.6b00397] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Gene expression noise is not only the mere consequence of stochasticity, but also a signal that reflects the upstream physical dynamics of the cognate molecular machinery. Soil bacteria facing recalcitrant pollutants exploit noise of catabolic promoters to deploy beneficial phenotypes such as metabolic bet-hedging and/or division of biochemical labor. Although the role of upstream promoter-regulator interplay in the origin of this noise is little understood, its specifications are probably ciphered in flow cytometry data patterns. We studied Pm promoter activity of the environmental bacterium Pseudomonas putida and its cognate regulator XylS by following expression of Pm-gfp fusions in single cells. Using mathematical modeling and computational simulations, we determined the kinetic properties of the system and used them as a baseline code to interpret promoter activity in terms of upstream regulator dynamics. Transcriptional noise was predicted to depend on the intracellular physical distance between regulator source (where XylS is produced) and the target promoter. Experiments with engineered bacteria in which this distance is minimized or enlarged confirmed the predicted effects of source/target proximity on noise patterns. This approach allowed deconvolution of cytometry data into mechanistic information on gene expression flow. It also provided a basis for selecting programmable noise levels in synthetic regulatory circuits.
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Affiliation(s)
- Ángel Goñi-Moreno
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Campus de Cantoblanco, Madrid 28049, Spain
| | - Ilaria Benedetti
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Campus de Cantoblanco, Madrid 28049, Spain
| | - Juhyun Kim
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Campus de Cantoblanco, Madrid 28049, Spain
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Campus de Cantoblanco, Madrid 28049, Spain
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39
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Pulse Generation in the Quorum Machinery of Pseudomonas aeruginosa. Bull Math Biol 2017; 79:1360-1389. [PMID: 28527130 PMCID: PMC5486814 DOI: 10.1007/s11538-017-0288-z] [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: 09/28/2016] [Accepted: 05/03/2017] [Indexed: 12/03/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that is responsible for a wide range of infections in humans. Colonies employ quorum sensing (QS) to coordinate gene expression, including for virulence factors, swarming motility and complex social traits. The QS signalling system of P. aeruginosa is known to involve multiple control components, notably the las, rhl and pqs systems. In this paper, we examine the las system and, in particular, the repressive interaction of rsaL, an embedded small regulative protein, employing recent biochemical information to aid model construction. Using analytic methods, we show how this feature can give rise to excitable pulse generation in this subsystem with important downstream consequences for rhamnolipid production. We adopt a symmetric competitive inhibition to capture the binding in the lasI–rsaL intergenic region and show our results are not dependent on the exact choice of this functional form. Furthermore, we examine the coupling of lasR to the rhl system, the impact of the predicted capacity for pulse generation and the biophysical consequences of this behaviour. We hypothesize that the interaction between the las and rhl systems may provide a quorum memory to enable cells to trigger rhamnolipid production only when they are at the edge of an established aggregation.
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40
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Facilitated dissociation of transcription factors from single DNA binding sites. Proc Natl Acad Sci U S A 2017; 114:E3251-E3257. [PMID: 28364020 DOI: 10.1073/pnas.1701884114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits that TF off rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key Escherichia coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate [Formula: see text], establishing that FD of Fis occurs at the single-binding site level, and we find that the off rate saturates at large Fis concentrations in solution. Although spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that FD depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF with structure that differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those that we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap.
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41
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Kochanowski K, Gerosa L, Brunner SF, Christodoulou D, Nikolaev YV, Sauer U. Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli. Mol Syst Biol 2017; 13:903. [PMID: 28049137 PMCID: PMC5293157 DOI: 10.15252/msb.20167402] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Transcription networks consist of hundreds of transcription factors with thousands of often overlapping target genes. While we can reliably measure gene expression changes, we still understand relatively little why expression changes the way it does. How does a coordinated response emerge in such complex networks and how many input signals are necessary to achieve it? Here, we unravel the regulatory program of gene expression in Escherichia coli central carbon metabolism with more than 30 known transcription factors. Using a library of fluorescent transcriptional reporters, we comprehensively quantify the activity of central metabolic promoters in 26 environmental conditions. The expression patterns were dominated by growth rate‐dependent global regulation for most central metabolic promoters in concert with highly condition‐specific activation for only few promoters. Using an approximate mathematical description of promoter activity, we dissect the contribution of global and specific transcriptional regulation. About 70% of the total variance in promoter activity across conditions was explained by global transcriptional regulation. Correlating the remaining specific transcriptional regulation of each promoter with the cell's metabolome response across the same conditions identified potential regulatory metabolites. Remarkably, cyclic AMP, fructose‐1,6‐bisphosphate, and fructose‐1‐phosphate alone explained most of the specific transcriptional regulation through their interaction with the two major transcription factors Crp and Cra. Thus, a surprisingly simple regulatory program that relies on global transcriptional regulation and input from few intracellular metabolites appears to be sufficient to coordinate E. coli central metabolism and explain about 90% of the experimentally observed transcription changes in 100 genes.
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Affiliation(s)
- Karl Kochanowski
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Luca Gerosa
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Simon F Brunner
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Dimitris Christodoulou
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Yaroslav V Nikolaev
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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42
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Shimada T, Tanaka K, Ishihama A. Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli. Microbiology (Reading) 2016; 162:1698-1707. [DOI: 10.1099/mic.0.000337] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Tomohiro Shimada
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta, 4259-R1-29, Yokohama 226-8503, Japan
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta, 4259-R1-29, Yokohama 226-8503, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
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43
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Influence of gene copy number on self-regulated gene expression. J Theor Biol 2016; 408:222-236. [PMID: 27528448 DOI: 10.1016/j.jtbi.2016.08.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 07/15/2016] [Accepted: 08/11/2016] [Indexed: 02/06/2023]
Abstract
Using an analytically solvable stochastic model, we study the properties of a simple genetic circuit consisting of multiple copies of a self-regulating gene. We analyse how the variation in gene copy number and the mutations changing the auto-regulation strength affect the steady-state distribution of protein concentration. We predict that one-reporter assay, an experimental method where the extrinsic noise level is inferred from the comparison of expression variance of a single and duplicated reporter gene, may give an incorrect estimation of the extrinsic noise contribution when applied to self-regulating genes. We also show that an imperfect duplication of an auto-activated gene, changing the regulation strength of one of the copies, may lead to a hybrid, binary+graded response of these genes to external signal. The analysis of relative changes in mean gene expression before and after duplication suggests that evolutionary accumulation of gene duplications may, at a given mean burst size, non-trivially depend on the inherent noisiness of a given gene, quantified by the inverse of the maximal mean frequency of bursts. Moreover, we find that the dependence of gene expression noise on gene copy number and auto-regulation strength may qualitatively differ, e.g. in monotonicity, depending on whether the noise is measured by Fano factor or coefficient of variation. Thus, experimentally-based hypotheses linking gene expression noise and evolutionary optimisation in the context of gene copy number variation may be ambiguous as they are dependent on the particular function chosen to quantify noise.
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44
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Yamanaka Y, Shimada T, Yamamoto K, Ishihama A. Transcription factor CecR (YbiH) regulates a set of genes affecting the sensitivity of Escherichia coli against cefoperazone and chloramphenicol. Microbiology (Reading) 2016; 162:1253-1264. [DOI: 10.1099/mic.0.000292] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Yuki Yamanaka
- Research Center for Micro-Nano Technology, Nano Technology, Koganei, Tokyo 184-8584, Japan
| | - Tomohiro Shimada
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan
| | - Kaneyoshi Yamamoto
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Nano Technology, Koganei, Tokyo 184-8584, Japan
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45
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Facilitated Dissociation of a Nucleoid Protein from the Bacterial Chromosome. J Bacteriol 2016; 198:1735-42. [PMID: 27044624 DOI: 10.1128/jb.00225-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/29/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Off-rates of proteins from the DNA double helix are widely considered to be dependent only on the interactions inside the initially bound protein-DNA complex and not on the concentration of nearby molecules. However, a number of recent single-DNA experiments have shown off-rates that depend on solution protein concentration, or "facilitated dissociation." Here, we demonstrate that this effect occurs for the major Escherichia coli nucleoid protein Fis on isolated bacterial chromosomes. We isolated E. coli nucleoids and showed that dissociation of green fluorescent protein (GFP)-Fis is controlled by solution Fis concentration and exhibits an "exchange" rate constant (kexch) of ≈10(4) M(-1) s(-1), comparable to the rate observed in single-DNA experiments. We also show that this effect is strongly salt dependent. Our results establish that facilitated dissociation can be observed in vitro on chromosomes assembled in vivo IMPORTANCE Bacteria are important model systems for the study of gene regulation and chromosome dynamics, both of which fundamentally depend on the kinetics of binding and unbinding of proteins to DNA. In experiments on isolated E. coli chromosomes, this study showed that the prolific transcription factor and chromosome packaging protein Fis displays a strong dependence of its off-rate from the bacterial chromosome on Fis concentration, similar to that observed in in vitro experiments. Therefore, the free cellular DNA-binding protein concentration can strongly affect lifetimes of proteins bound to the chromosome and must be taken into account in quantitative considerations of gene regulation. These results have particularly profound implications for transcription factors where DNA binding lifetimes can be a critical determinant of regulatory function.
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46
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Yüce M, Ullah N, Budak H. Trends in aptamer selection methods and applications. Analyst 2016; 140:5379-99. [PMID: 26114391 DOI: 10.1039/c5an00954e] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aptamers are target specific ssDNA, RNA or peptide sequences generated by an in vitro selection and amplification method called SELEX (Systematic Evolution of Ligands by EXponential Enrichment), which involves repetitive cycles of binding, recovery and amplification steps. Aptamers have the ability to bind with a variety of targets such as drugs, proteins, heavy metals, and pathogens with high specificity and selectivity. Aptamers are similar to monoclonal antibodies regarding their binding affinities, but they offer a number of advantages over the existing antibody-based detection methods, which make the aptamers promising diagnostic and therapeutic tools for future biomedical and analytical applications. The aim of this review article is to provide an overview of the recent advancements in aptamer screening methods along with a concise description of the major application areas of aptamers including biomarker discovery, diagnostics, imaging and nanotechnology.
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Affiliation(s)
- Meral Yüce
- Sabanci University, Nanotechnology Research and Application Centre, 34956, Istanbul, Turkey.
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Ishihama A, Shimada T, Yamazaki Y. Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic Acids Res 2016; 44:2058-74. [PMID: 26843427 PMCID: PMC4797297 DOI: 10.1093/nar/gkw051] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/20/2016] [Indexed: 01/25/2023] Open
Abstract
Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, ‘Transcription Profile of Escherichia coli’ (www.shigen.nig.ac.jp/ecoli/tec/).
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Affiliation(s)
- Akira Ishihama
- Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, 184-8584, Japan
| | - Tomohiro Shimada
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama 226-8503, Japan
| | - Yukiko Yamazaki
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Le Treut G, Képès F, Orland H. Phase Behavior of DNA in the Presence of DNA-Binding Proteins. Biophys J 2016; 110:51-62. [PMID: 26745409 PMCID: PMC4805876 DOI: 10.1016/j.bpj.2015.10.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/28/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022] Open
Abstract
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of nonspecific binding proteins, we implemented a Flory-Huggins free energy model. We explored the dependence on DNA and protein concentrations of the DNA collapse. For physiologically relevant values of the DNA-protein affinity, this collapse gives rise to a biphasic regime with a dense and a dilute phase; the corresponding phase diagram was computed. Using an approach based on Hamiltonian paths, we show that the dense phase has either a molten globule or a crystalline structure, depending on the DNA bending rigidity, which is influenced by the ionic strength. These results are valid at the thermodynamical equilibrium and therefore should be consistent with many biological processes, whose characteristic timescales range typically from 1 ms to 10 s. Our model may thus be applied to biological phenomena that involve DNA-binding proteins, such as DNA condensation with crystalline order, which occurs in some bacteria to protect their chromosome from detrimental factors; or transcription initiation, which occurs in clusters called transcription factories that are reminiscent of the dense phase characterized in this study.
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Affiliation(s)
- Guillaume Le Treut
- Institut de Physique Théorique, Université Paris Saclay, CEA, CNRS, Gif-sur-Yvette, France; Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS, Genopole Campus 1, Evry, France.
| | - François Képès
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS, Genopole Campus 1, Evry, France
| | - Henri Orland
- Institut de Physique Théorique, Université Paris Saclay, CEA, CNRS, Gif-sur-Yvette, France
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Maeda M, Shimada T, Ishihama A. Strength and Regulation of Seven rRNA Promoters in Escherichia coli. PLoS One 2015; 10:e0144697. [PMID: 26717514 PMCID: PMC4696680 DOI: 10.1371/journal.pone.0144697] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 11/23/2015] [Indexed: 11/18/2022] Open
Abstract
The model prokaryote Escherichia coli contains seven copies of the rRNA operon in the genome. The presence of multiple rRNA operons is an advantage for increasing the level of ribosome, the key apparatus of translation, in response to environmental conditions. The complete sequence of E. coli genome, however, indicated the micro heterogeneity between seven rRNA operons, raising the possibility in functional heterogeneity and/or differential mode of expression. The aim of this research is to determine the strength and regulation of the promoter of each rRNA operon in E. coli. For this purpose, we used the double-fluorescent protein reporter pBRP system that was developed for accurate and precise determination of the promoter strength of protein-coding genes. For application of this promoter assay vector for measurement of the rRNA operon promoters devoid of the signal for translation, a synthetic SD sequence was added at the initiation codon of the reporter GFP gene, and then approximately 500 bp-sequence upstream each 16S rRNA was inserted in front of this SD sequence. Using this modified pGRS system, the promoter activity of each rrn operon was determined by measuring the rrn promoter-directed GFP and the reference promoter-directed RFP fluorescence, both encoded by a single and the same vector. Results indicated that: the promoter activity was the highest for the rrnE promoter under all growth conditions analyzed, including different growth phases of wild-type E. coli grown in various media; but the promoter strength of other six rrn promoters was various depending on the culture conditions. These findings altogether indicate that seven rRNA operons are different with respect to the regulation mode of expression, conferring an advantage to E. coli through a more fine-tuned control of ribosome formation in a wide range of environmental situations. Possible difference in the functional role of each rRNA operon is also discussed.
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Affiliation(s)
- Michihisa Maeda
- Meiji University, Faculty of Agriculture Chemistry, Kawasaki, Kanagawa 214–8571, Japan
| | - Tomohiro Shimada
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama 226–8503, Japan
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184–8584, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184–8584, Japan
- * E-mail:
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50
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Marijuán PC, Navarro J, del Moral R. How the living is in the world: An inquiry into the informational choreographies of life. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:469-80. [DOI: 10.1016/j.pbiomolbio.2015.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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