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Ishihara JI, Mekubo T, Kusaka C, Kondo S, Oiko R, Igarashi K, Aiba H, Ishikawa S, Ogasawara N, Oshima T, Takahashi H. A critical role of the periplasm in copper homeostasis in Gram-negative bacteria. Biosystems 2023; 231:104980. [PMID: 37453610 DOI: 10.1016/j.biosystems.2023.104980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/18/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Copper is essential for life, but is toxic in excess. Copper homeostasis is achieved in the cytoplasm and the periplasm as a unique feature of Gram-negative bacteria. Especially, it has become clear the role of the periplasm and periplasmic proteins regarding whole-cell copper homeostasis. Here, we addressed the role of the periplasm and periplasmic proteins in copper homeostasis using a Systems Biology approach integrating experiments with models. Our analysis shows that most of the copper-bound molecules localize in the periplasm but not cytoplasm, suggesting that Escherichia coli utilizes the periplasm to sense the copper concentration in the medium and sequester copper ions. In particular, a periplasmic multi-copper oxidase CueO and copper-responsive transcriptional factor CusS contribute both to protection against Cu(I) toxicity and to incorporating copper into the periplasmic components/proteins. We propose that Gram-negative bacteria have evolved mechanisms to sense and store copper in the periplasm to expand their living niches.
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Affiliation(s)
- Jun-Ichi Ishihara
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba, 260-8673, Japan
| | - Tomohiro Mekubo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Chikako Kusaka
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Suguru Kondo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Ryotaro Oiko
- Graduate School of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu City, Toyama, 939-0398, Japan
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohiraku, Sapporo, Hokkaido, 062-8517, Japan
| | - Hirofumi Aiba
- Graduate School of Pharmaceutical Sciences, Nagoya University, Pharmaceutical Sciences Building, Furocho, Chikusa-ku, Aichi, 464-8601, Japan
| | - Shu Ishikawa
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku Kobe, 657-8501, Japan
| | - Naotake Ogasawara
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Taku Oshima
- Graduate School of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu City, Toyama, 939-0398, Japan.
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba, 260-8673, Japan; Molecular Chirality Research Center, Chiba University, Chiba, Japan; Plant Molecular Science Center, Chiba University, Chiba, Japan.
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Yano H, Shintani M, Tomita M, Suzuki H, Oshima T. Reconsidering plasmid maintenance factors for computational plasmid design. Comput Struct Biotechnol J 2018; 17:70-81. [PMID: 30619542 PMCID: PMC6312765 DOI: 10.1016/j.csbj.2018.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/08/2018] [Accepted: 12/09/2018] [Indexed: 12/18/2022] Open
Abstract
Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.
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Affiliation(s)
- Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1, Hamamatsu 432-8561, Japan
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 3-5-1, Hamamatsu 432-8561, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka, Yamagata 997-0035, Japan
- Faculty of Environment and Information Studies, Keio University, 5322, Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka, Yamagata 997-0035, Japan
- Faculty of Environment and Information Studies, Keio University, 5322, Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Taku Oshima
- Department of Biotechnology, Toyama Prefectural University, 5180, Kurokawa, Imizu, Toyama 939-0398, Japan
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Abstract
Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid carriage, only a fraction of a local population carries plasmids or is permissive to plasmid uptake. Plasmids provide various accessory traits which might be beneficial under particular conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness toward environmental changes. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens. Here we summarize the state-of-the-art methods to study the occurrence, abundance, and diversity of plasmids in environmental bacteria. Increasingly, cultivation-independent total-community DNA-based methods are being used to characterize and quantify the diversity and abundance of plasmids in relation to various biotic and abiotic factors. An improved understanding of the ecology of plasmids and their hosts is crucial in the development of intervention strategies for antibiotic-resistance-gene spread. We discuss the potentials and limitations of methods used to determine the host range of plasmids, as the ecology of plasmids is tightly linked to their hosts. The recent advances in sequencing technologies provide an enormous potential for plasmid classification, diversity, and evolution studies, but numerous challenges still exist.
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Takahashi H, Oshima T, Hobman JL, Doherty N, Clayton SR, Iqbal M, Hill PJ, Tobe T, Ogasawara N, Kanaya S, Stekel DJ. The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress. J R Soc Interface 2016; 12:rsif.2015.0069. [PMID: 25808337 PMCID: PMC4424684 DOI: 10.1098/rsif.2015.0069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Zinc is essential for life, but toxic in excess. Thus all cells must control their internal zinc concentration. We used a systems approach, alternating rounds of experiments and models, to further elucidate the zinc control systems in Escherichia coli. We measured the response to zinc of the main specific zinc import and export systems in the wild-type, and a series of deletion mutant strains. We interpreted these data with a detailed mathematical model and Bayesian model fitting routines. There are three key findings: first, that alternate, non-inducible importers and exporters are important. Second, that an internal zinc reservoir is essential for maintaining the internal zinc concentration. Third, our data fitting led us to propose that the cells mount a heterogeneous response to zinc: some respond effectively, while others die or stop growing. In a further round of experiments, we demonstrated lower viable cell counts in the mutant strain tested exposed to excess zinc, consistent with this hypothesis. A stochastic model simulation demonstrated considerable fluctuations in the cellular levels of the ZntA exporter protein, reinforcing this proposal. We hypothesize that maintaining population heterogeneity could be a bet-hedging response allowing a population of cells to survive in varied and fluctuating environments.
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Affiliation(s)
- Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Chiba 260-8673, Japan
| | - Taku Oshima
- Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Jon L Hobman
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK
| | - Neil Doherty
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK
| | - Selina R Clayton
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK
| | - Mudassar Iqbal
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK
| | - Philip J Hill
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK
| | - Toru Tobe
- Laboratory of Molecular Medical Microbiology, Department of Biomedical Informatics, Osaka University Graduate School of Medicine, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Shigehiko Kanaya
- Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Dov J Stekel
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK
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Fletcher SJ, Iqbal M, Jabbari S, Stekel D, Rappoport JZ. Analysis of occludin trafficking, demonstrating continuous endocytosis, degradation, recycling and biosynthetic secretory trafficking. PLoS One 2014; 9:e111176. [PMID: 25422932 PMCID: PMC4244031 DOI: 10.1371/journal.pone.0111176] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/02/2014] [Indexed: 12/15/2022] Open
Abstract
Tight junctions (TJs) link adjacent cells and are critical for maintenance of apical-basolateral polarity in epithelial monolayers. The TJ protein occludin functions in disparate processes, including wound healing and Hepatitis C Virus infection. Little is known about steady-state occludin trafficking into and out of the plasma membrane. Therefore, we determined the mechanisms responsible for occludin turnover in confluent Madin-Darby canine kidney (MDCK) epithelial monolayers. Using various biotin-based trafficking assays we observed continuous and rapid endocytosis of plasma membrane localised occludin (the majority internalised within 30 minutes). By 120 minutes a significant reduction in internalised occludin was observed. Inhibition of lysosomal function attenuated the reduction in occludin signal post-endocytosis and promoted co-localisation with the late endocytic system. Using a similar method we demonstrated that ∼20% of internalised occludin was transported back to the cell surface. Consistent with these findings, significant co-localisation between internalised occludin and recycling endosomal compartments was observed. We then quantified the extent to which occludin synthesis and transport to the plasma membrane contributes to plasma membrane occludin homeostasis, identifying inhibition of protein synthesis led to decreased plasma membrane localised occludin. Significant co-localisation between occludin and the biosynthetic secretory pathway was demonstrated. Thus, under steady-state conditions occludin undergoes turnover via a continuous cycle of endocytosis, recycling and degradation, with degradation compensated for by biosynthetic exocytic trafficking. We developed a mathematical model to describe the endocytosis, recycling and degradation of occludin, utilising experimental data to provide quantitative estimates for the rates of these processes.
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Affiliation(s)
- Sarah J. Fletcher
- The Centre for Cardiovascular Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
- * E-mail:
| | - Mudassar Iqbal
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Sara Jabbari
- School of Mathematics and Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Joshua Z. Rappoport
- Northwestern University, Feinberg School of Medicine, 303 E. Chicago Avenue, Chicago, Illinois, United States of America
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Quantification of IncP-1 plasmid prevalence in environmental samples. Appl Environ Microbiol 2012; 79:1410-3. [PMID: 23241977 DOI: 10.1128/aem.03728-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To study the role of broad-host-range IncP-1 plasmids in bacterial adaptability to irregular environmental challenges, a quantitative real-time PCR assay was developed that specifically detects the korB gene, which is conserved in all IncP-1 plasmids, in environmental samples. IncP-1 plasmid dynamics in a biopurification system for pesticide wastes were analyzed.
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Abstract
The korAB operon in RK2 plasmids is a beautiful natural example of a negatively and cooperatively self-regulating operon. It has been particularly well characterized both experimentally and with mathematical models. We have carried out a detailed investigation of the role of the regulatory mechanism using a biologically grounded mechanistic multi-scale stochastic model that includes plasmid gene regulation and replication in the context of host growth and cell division. We use the model to compare four hypotheses for the action of the regulatory mechanism: increased robustness to extrinsic factors, decreased protein fluctuations, faster response-time of the operon and reduced host burden through improved efficiency of protein production. We find that the strongest impact of all elements of the regulatory architecture is on improving the efficiency of protein synthesis by reduction in the number of mRNA molecules needed to be produced, leading to a greater than ten-fold reduction in host energy required to express these plasmid proteins. A smaller but still significant role is seen for speeding response times, but this is not materially improved by the cooperativity. The self-regulating mechanisms have the least impact on protein fluctuations and robustness. While reduction of host burden is evident in a plasmid context, negative self-regulation is a widely seen motif for chromosomal genes. We propose that an important evolutionary driver for negatively self-regulated genes is to improve the efficiency of protein synthesis.
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Affiliation(s)
- Dorota Herman
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
- Department of Plant Systems Biology, VIB – Ghent University, Ghent, Belgium
| | | | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
- * E-mail:
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Abstract
In the present paper, we report that transcription affects the location of a DNA target in Escherichia coli K-12. A strain whose chromosome had been engineered to encode a lac repressor-GFP (green fluorescent protein) fusion was used as a host for a low copy number plasmid that carries an array of five lac operator sites. Individual cells of this strain exhibited a diffuse fluorescence signal, suggesting that the plasmid is distributed throughout the cell cytoplasm. However, a derivative of this plasmid carrying a cloned constitutive promoter is targeted to a location at the edge of the nucleoid towards the pole of the host cell. We conclude that transcription from the cloned promoter is driving the location of the plasmid and that specific locations in bacterial cells may favour gene expression.
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