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Chen S, Xie Z, Yang Y, Sun N, Guo Z, Li M, Wang C. A self-activating electron transfer antibacterial strategy: Co 3O 4/TiO 2 P-N heterojunctions combined with photothermal therapy. Biomater Sci 2024; 12:1573-1589. [PMID: 38319143 DOI: 10.1039/d3bm01550e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Implant-associated infections are significant impediments to successful surgical outcomes, often resulting from persistent bacterial contamination. It has been hypothesized that bacteria can transfer electrons to semiconductors with comparable potential to the biological redox potential (BRP). Building on this concept, we developed an antibiotic-free bactericidal system, Co3O4/TiO2-Ti, capable of achieving real-time and sustainable bactericidal effects. Our study demonstrated that Co3O4/TiO2-Ti, possessing an appropriately set valence band, initiated charge transfer, reactive oxygen species (ROS) production, and membrane damage in adherent Staphylococcus aureus (S. aureus). Notably, in vivo experiments illustrated the remarkable antibacterial activity of Co3O4/TiO2-Ti, while promoting soft-tissue reconstruction and demonstrating excellent cytocompatibility. Transcriptomic analysis further revealed a down-regulation of aerobic respiration-associated genes and an up-regulation of ROS-associated genes in S. aureus in the presence of Co3O4/TiO2-Ti compared to Ti. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and gene set enrichment analysis (GSEA) identified alterations in respiratory metabolism, oxidative phosphorylation, and the synthesis of amino acid in S. aureus cultured on Co3O4/TiO2-Ti. Furthermore, when combined with near-infrared (NIR) irradiation and photothermal therapy (PTT), Co3O4/TiO2-Ti eliminated 95.71% of floating and adherent S. aureus in vitro. The findings suggest that this antibiotic-free strategy holds substantial promise in enhancing implant sterilization capabilities, thereby contributing to the prevention and treatment of bacterial infections through bandgap engineering of implants and NIR irradiation.
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Affiliation(s)
- Siyuan Chen
- Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
- Jiangsu Key Laboratory of Oral Diseases, Nanjing, China
| | - Zhe Xie
- Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
- Jiangsu Key Laboratory of Oral Diseases, Nanjing, China
| | - Yuchen Yang
- Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
- Jiangsu Key Laboratory of Oral Diseases, Nanjing, China
| | - Nuo Sun
- Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
- Jiangsu Key Laboratory of Oral Diseases, Nanjing, China
| | - Zhengnong Guo
- Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
- Jiangsu Key Laboratory of Oral Diseases, Nanjing, China
| | - Miaomiao Li
- Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
- Jiangsu Key Laboratory of Oral Diseases, Nanjing, China
| | - Chen Wang
- Department of Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
- Jiangsu Key Laboratory of Oral Diseases, Nanjing, China
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2
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Si Y, Liu H, Li M, Jiang X, Yu H, Sun D. An efficient metal-organic framework-based drug delivery platform for synergistic antibacterial activity and osteogenesis. J Colloid Interface Sci 2023; 640:521-539. [PMID: 36878070 DOI: 10.1016/j.jcis.2023.02.149] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/18/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Bone implants for clinical application should be endowed with antibacterial activity, biocompatibility, and even osteogenesis-promoting properties. In this work, metal-organic framework (MOF) based drug delivery platform was used to modify titanium implants for improved clinical applicability. Methyl Vanillate@Zeolitic Imidazolate Framework-8 (MV@ZIF-8) was immobilized on the polydopamine (PDA) modified titanium. The sustainable release of the Zn2+ and MV causes substantial oxidative damage to Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). The increased reactive oxygen species (ROS) significantly up-regulates the expression of oxidative stress and DNA damage response genes. Meanwhile, the structural disruption of lipid membranes caused by the ROS, the damage caused by Zinc active sites and the damage accelerated by the MV are both involved in inhibiting bacterial proliferation. The up-regulated expression of the osteogenic-related genes and proteins indicated that the MV@ZIF-8 could effectively promote the osteogenic differentiation of the human bone mesenchymal stem cells (hBMSCs). RNA sequencing and Western blotting analysis revealed that the MV@ZIF-8 coating activates the canonical Wnt/β-catenin signaling pathway through the regulation of tumor necrosis factor (TNF) pathway, thereby promoting the osteogenic differentiation of the hBMSCs. This work demonstrates a promising application of the MOF-based drug delivery platform in bone tissue engineering.
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Affiliation(s)
- Yunhui Si
- School of Materials, Sun Yat-sen University, Shenzhen, 518107, PR China
| | - Huanyao Liu
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Mengsha Li
- School of Materials Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Xuzhou Jiang
- School of Materials Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, PR China; Nanotechnology Research Center, Sun Yat-sen University, Guangzhou 510275, PR China.
| | - Hongying Yu
- School of Materials, Sun Yat-sen University, Shenzhen, 518107, PR China.
| | - Dongbai Sun
- School of Materials Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, PR China.
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3
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Sudhakari PA, Ramisetty BCM. Modeling endonuclease colicin-like bacteriocin operons as 'genetic arms' in plasmid-genome conflicts. Mol Genet Genomics 2022; 297:763-777. [PMID: 35320397 DOI: 10.1007/s00438-022-01884-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/06/2022] [Indexed: 11/28/2022]
Abstract
Plasmids are acellular propagating entities that depend on bacteria, as molecular parasites, for propagation. A 'tussle' between bacteria and plasmid ensues; bacteria for riddance of the plasmid and plasmid for persistence within a live host. Plasmid-maintenance systems such as endonuclease Colicin-Like Bacteriocins (CLBs) ensure plasmid propagation within the population; (i) the plasmid-cured cells are killed by the CLBs; (ii) damaged cells lyse and release the CLBs that eliminate the competitors, and (iii) the released plasmids invade new bacteria. Surprisingly, endonuclease CLB operons occur on bacterial genomes whose significance is unknown. Here, we study genetics, eco-evolutionary drive, and physiological relevance of genomic endonuclease CLB operons. We investigated plasmidic and genomic endonuclease CLB operons using sequence analyses from an eco-evolutionary perspective. We found 1266 genomic and plasmidic endonuclease CLB operons across 30 bacterial genera. Although 51% of the genomes harbor endonuclease CLB operons, the majority of the genomic endonuclease CLB operons lacked a functional lysis gene, suggesting the negative selection of lethal genes. The immunity gene of the endonuclease CLB operon protects the plasmid-cured host, eliminating the metabolic burden. We show mutual exclusivity of endonuclease CLB operons on genomes and plasmids. We propose an anti-addiction hypothesis for genomic endonuclease CLB operons. Using a stochastic hybrid agent-based model, we show that the endonuclease CLB operons on genomes confer an advantage to the host genome in terms of immunity to the toxin and elimination of plasmid burden. The conflict between bacterial genome and plasmids allows the emergence of 'genetic arms' such as CLB operons that regulate the ecological interplay of bacterial genomes and plasmids.
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Affiliation(s)
- Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India.
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4
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Hill PWS, Moldoveanu AL, Sargen M, Ronneau S, Glegola-Madejska I, Beetham C, Fisher RA, Helaine S. The vulnerable versatility of Salmonella antibiotic persisters during infection. Cell Host Microbe 2021; 29:1757-1773.e10. [PMID: 34731646 DOI: 10.1016/j.chom.2021.10.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/23/2021] [Accepted: 10/08/2021] [Indexed: 11/30/2022]
Abstract
Tolerance and persistence are superficially similar phenomena by which bacteria survive bactericidal antibiotics. It is assumed that the same physiology underlies survival of individual tolerant and persistent bacteria. However, by comparing tolerance and persistence during Salmonella Typhimurium infection, we reveal that these two phenomena are underpinned by different bacterial physiologies. Multidrug-tolerant mutant Salmonella enter a near-dormant state protected from immune-mediated genotoxic damages. However, the numerous tolerant cells, optimized for survival, lack the capabilities necessary to initiate infection relapse following antibiotic withdrawal. In contrast, persisters retain an active state. This leaves them vulnerable to accumulation of macrophage-induced dsDNA breaks but concurrently confers the versatility to initiate infection relapse if protected by RecA-mediated DNA repair. Accordingly, recurrent, invasive, non-typhoidal Salmonella clinical isolates display hallmarks of persistence rather than tolerance during antibiotic treatment. Our study highlights the complex trade-off that antibiotic-recalcitrant Salmonella balance to act as a reservoir for infection relapse.
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Affiliation(s)
- Peter W S Hill
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
| | - Ana Laura Moldoveanu
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Molly Sargen
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Séverin Ronneau
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Izabela Glegola-Madejska
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Catrin Beetham
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Robert A Fisher
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Sophie Helaine
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK; Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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5
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Yang Z, Xi Y, Bai J, Jiang Z, Wang S, Zhang H, Dai W, Chen C, Gou Z, Yang G, Gao C. Covalent grafting of hyperbranched poly-L-lysine on Ti-based implants achieves dual functions of antibacteria and promoted osteointegration in vivo. Biomaterials 2020; 269:120534. [PMID: 33243425 DOI: 10.1016/j.biomaterials.2020.120534] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/29/2020] [Accepted: 11/03/2020] [Indexed: 12/25/2022]
Abstract
The dual functional implants of antibacteria and osteointegration are highly demanded in orthopedic and dentistry, especially for patients who suffer from diabetes or osteoporosis simultaneously. However, there is lack of the facile and robust method to produce clinically applicable implants with this dual function although coatings possessing single function have been extensively developed. Herein, hyperbranched poly-L-lysine (HBPL) polymers were covalently immobilized onto the alkali-heat treated titanium (Ti) substrates and implants by using 3-glycidyloxypropyltrimethoxysilane (GPTMS) as the coupling agent, which displayed excellent antibacterial activity against S. aureus and E. coli with an efficiency as high as 89.4% and 92.2% in vitro, respectively. The HBPL coating also significantly promoted the adhesion, spreading, proliferation and osteogenic differentiation of MC3T3-E1 cells in vitro. Furthermore, the results of a S. aureus infection rat model in vivo ulteriorly verified that the HBPL-modified screws had good antibacterial and anti-inflammatory abilities at an early stage of implantation and better osteointegration compared with the control Ti screws.
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Affiliation(s)
- Zhijian Yang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Yue Xi
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Jun Bai
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhiwei Jiang
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Shuqin Wang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haolan Zhang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Wei Dai
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Chaozhen Chen
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Zhongru Gou
- Bio-nanomaterials and Regenerative Medicine Research Division, Zhejiang-California International Nanosystem Institute, Zhejiang University, Hangzhou, 310058, China
| | - Guoli Yang
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China.
| | - Changyou Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, 310058, China.
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6
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Sharma DK, Bihani SC, Siddiqui MQ, Misra HS, Rajpurohit YS. WD40 domain of RqkA regulates its kinase activity and role in extraordinary radioresistance of D. radiodurans. J Biomol Struct Dyn 2020; 40:1246-1259. [PMID: 32990194 DOI: 10.1080/07391102.2020.1824810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
RqkA, a DNA damage responsive serine/threonine kinase, is characterized for its role in DNA repair and cell division in D. radiodurans. It has a unique combination of a kinase domain at N-terminus and a WD40 type domain at C-terminus joined through a linker. WD40 domain is comprised of eight β-propeller repeats held together via 'tryptophan-docking motifs' and forming a typical 'velcro' closure structure. RqkA mutants lacking the WD40 region (hereafter referred to as WD mutant) could not complement RqkA loss in γ radiation resistance in D. radiodurans and lacked γ radiation-mediated activation of kinase activity in vivo. WD mutants failed to phosphorylate its cognate substrate (e.g. DrRecA) in surrogate E. coli cells. Unlike wild-type enzyme, the kinase activity of its WD40 mutants was not stimulated by pyrroloquinoline quinine (PQQ) indicating the role of the WD motifs in PQQ interaction and stimulation of its kinase activity. Together, results highlighted the importance of the WD40 domain in the regulation of RqkA kinase signaling functions in vivo, and thus, the role of WD40 domain in the regulation of any STPK is first time demonstrated in bacteria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhirendra K Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Subhash C Bihani
- Radiation Biology and Health Science Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Mohammad Q Siddiqui
- Alberta RNA Research & Training Institute, Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
| | - Yogendra S Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
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7
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The PafBC-mediated response sensitizes a bistable DNA damage response in Mycobacteria. J Theor Biol 2020; 508:110462. [PMID: 32890555 DOI: 10.1016/j.jtbi.2020.110462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/05/2020] [Accepted: 08/24/2020] [Indexed: 01/03/2023]
Abstract
Due to the genotoxically challenging environments in which they live in, Mycobacteria have a complex DNA damage repair system that is governed by two major DNA damage responses, namely, the LexA/RecA-dependent response and the newly characterized PafBC-mediated response (Müller et al., 2018). The LexA/RecA-dependent response is a well-known bistable response found in different types of bacteria, and the Mycobacteria-specific PafBC-mediated response interacts with and modifies the LexA/RecA-dependent response (Müller et al., 2018). The interaction between the LexA/RecA-dependent response and the PafBC-mediated response has not been characterized mathematically. Our analysis shows that the addition of the PafBC-mediated response sensitizes the overall DNA damage response, effectively lowering the DNA damage rate threshold for activation.
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Ojkic N, Lilja E, Direito S, Dawson A, Allen RJ, Waclaw B. A Roadblock-and-Kill Mechanism of Action Model for the DNA-Targeting Antibiotic Ciprofloxacin. Antimicrob Agents Chemother 2020; 64:e02487-19. [PMID: 32601161 PMCID: PMC7449190 DOI: 10.1128/aac.02487-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/19/2020] [Indexed: 12/19/2022] Open
Abstract
Fluoroquinolones, antibiotics that cause DNA damage by inhibiting DNA topoisomerases, are clinically important, but their mechanism of action is not yet fully understood. In particular, the dynamical response of bacterial cells to fluoroquinolone exposure has hardly been investigated, although the SOS response, triggered by DNA damage, is often thought to play a key role. Here, we investigated the growth inhibition of the bacterium Escherichia coli by the fluoroquinolone ciprofloxacin at low concentrations. We measured the long-term and short-term dynamical response of the growth rate and DNA production rate to ciprofloxacin at both the population and single-cell levels. We show that, despite the molecular complexity of DNA metabolism, a simple roadblock-and-kill model focusing on replication fork blockage and DNA damage by ciprofloxacin-poisoned DNA topoisomerase II (gyrase) quantitatively reproduces long-term growth rates in the presence of ciprofloxacin. The model also predicts dynamical changes in the DNA production rate in wild-type E. coli and in a recombination-deficient mutant following a step-up of ciprofloxacin. Our work highlights that bacterial cells show a delayed growth rate response following fluoroquinolone exposure. Most importantly, our model explains why the response is delayed: it takes many doubling times to fragment the DNA sufficiently to inhibit gene expression. We also show that the dynamical response is controlled by the timescale of DNA replication and gyrase binding/unbinding to the DNA rather than by the SOS response, challenging the accepted view. Our work highlights the importance of including detailed biophysical processes in biochemical-systems models to quantitatively predict the bacterial response to antibiotics.
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Affiliation(s)
- Nikola Ojkic
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Elin Lilja
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Susana Direito
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Angela Dawson
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosalind J Allen
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, Edinburgh, United Kingdom
| | - Bartlomiej Waclaw
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, Edinburgh, United Kingdom
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9
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Dynamics of ColicinE2 production and release determine the competitive success of a toxin-producing bacterial population. Sci Rep 2020; 10:4052. [PMID: 32132643 PMCID: PMC7055308 DOI: 10.1038/s41598-020-61086-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/20/2020] [Indexed: 11/08/2022] Open
Abstract
The release of toxins is one mechanism used by bacterial species to establish dominance over competitors, but how the dynamics of toxin expression determine the competitive success of a toxin-producing population is largely unknown. Here, we investigate how the expression dynamics of ColicinE2 - a toxic bacteriocin - affect competition between toxin-producing and toxin-sensitive strains of Escherichia coli. We demonstrate that, in addition to genetic modifications in the toxin expression system, alterations of the growth medium can be used to modulate the timing of toxin production and the amount of toxin released. Thus cells that release the toxin at later times can accumulate more colicin. In experiments, we found that delaying toxin release does not significantly alter competition outcome. However, our theoretical analysis allowed us to assess the relative contributions of release time and toxin level to the competitive success of the producer strain, that might counteract each other in experiments. The results reveal that the importance of delaying toxin release lies in increasing the toxin amount. This is a more effective strategy for the toxin-producing strain than prompt discharge of the colicin. In summary, our study shows how the toxin release dynamics influence the competitive success of the toxin-producing bacterial population.
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10
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Goetz A, Mader A, von Bronk B, Weiss AS, Opitz M. Gene expression noise in a complex artificial toxin expression system. PLoS One 2020; 15:e0227249. [PMID: 31961890 PMCID: PMC6974158 DOI: 10.1371/journal.pone.0227249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/16/2019] [Indexed: 01/29/2023] Open
Abstract
Gene expression is an intrinsically stochastic process. Fluctuations in transcription and translation lead to cell-to-cell variations in mRNA and protein levels affecting cellular function and cell fate. Here, using fluorescence time-lapse microscopy, we quantify noise dynamics in an artificial operon in Escherichia coli, which is based on the native operon of ColicinE2, a toxin. In the natural system, toxin expression is controlled by a complex regulatory network; upon induction of the bacterial SOS response, ColicinE2 is produced (cea gene) and released (cel gene) by cell lysis. Using this ColicinE2-based operon, we demonstrate that upon induction of the SOS response noise of cells expressing the operon is significantly lower for the (mainly) transcriptionally regulated gene cea compared to the additionally post-transcriptionally regulated gene cel. Likewise, we find that mutations affecting the transcriptional regulation by the repressor LexA do not significantly alter the population noise, whereas specific mutations to post-transcriptionally regulating units, strongly influence noise levels of both genes. Furthermore, our data indicate that global factors, such as the plasmid copy number of the operon encoding plasmid, affect gene expression noise of the entire operon. Taken together, our results provide insights on how noise in a native toxin-producing operon is controlled and underline the importance of post-transcriptional regulation for noise control in this system.
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Affiliation(s)
- Alexandra Goetz
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Andreas Mader
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Benedikt von Bronk
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Anna S. Weiss
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Madeleine Opitz
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
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11
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Uphoff S. A Quantitative Model Explains Single-Cell Dynamics of the Adaptive Response in Escherichia coli. Biophys J 2019; 117:1156-1165. [PMID: 31466698 PMCID: PMC6818145 DOI: 10.1016/j.bpj.2019.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/26/2019] [Accepted: 08/12/2019] [Indexed: 01/05/2023] Open
Abstract
DNA damage caused by alkylating chemicals induces an adaptive response in Escherichia coli that increases the tolerance of cells to further damage. Signaling of the response occurs through irreversible methylation of the Ada protein, which acts as a DNA repair protein and damage sensor. Methylated Ada induces its own gene expression through a positive feedback loop. However, random fluctuations in the abundance of Ada jeopardize the reliability of the induction signal. I developed a quantitative model to test how gene expression noise and feedback amplification affect the fidelity of the adaptive response. A remarkably simple model accurately reproduced experimental observations from single-cell measurements of gene expression dynamics in a microfluidic device. Stochastic simulations showed that delays in the adaptive response are a direct consequence of the very low number of Ada molecules present to signal DNA damage. For cells that have zero copies of Ada, response activation becomes a memoryless process that is dictated by an exponential waiting time distribution between basal Ada expression events. Experiments also confirmed the model prediction that the strength of the adaptive response drops with an increasing growth rate of cells.
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Affiliation(s)
- Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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12
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Yokoi T, Itaya M, Mori H, Kataoka M. Optimization of RK2-based gene introduction system for Bacillus subtilis. J GEN APPL MICROBIOL 2019; 65:265-272. [DOI: 10.2323/jgam.2018.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Takahiro Yokoi
- Interdisciplinary Graduate School of Science and Technology, Shinshu University
| | | | - Hirotada Mori
- Graduate School of Biological Sciences, Nara Institute of Science and Technology
| | - Masakazu Kataoka
- Interdisciplinary Graduate School of Science and Technology, Shinshu University
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13
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von Bronk B, Götz A, Opitz M. Locality of interactions in three-strain bacterial competition in E. coli. Phys Biol 2018; 16:016002. [PMID: 30376449 DOI: 10.1088/1478-3975/aae671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The population dynamics that determine the composition and stability of ecosystems ultimately emerge from interactions between individual organisms. One well-studied system is the three-strain E. coli interaction of a heterogeneously toxin-producing C strain that interacts with a toxin-sensitive S and a toxin-resistant R strain. Here, we employ a multi-scale fluorescence microscopy approach, that has been proven useful in identifying previously unknown or underestimated stochastic effects in C-S competition. This approach allows us to investigate the microscopic interaction of the R strain and to quantify the role of stochastic effects in the spatially structured C-R-S interaction. We show that the early colony patterning at 12 h and at small length scales (near single cell level) is characterized by a number of microscopic variables (the number of C and R cell clusters and the area occupied by S) and is subject to random processes in positioning and toxin production. Then, in a second competition phase, mainly deterministic processes such as bacterial growth and global toxin action determine the following population dynamics. Consequently, together with environmental factors, the microscopic variables were predictive of the competition outcome. However, interactions of neighboring R and C clusters could amplify local variations. If R clusters originated near a C cell cluster, R could profit from the toxin produced by C without bearing the cost of production-a mechanism called cheating. By combining information from the micro- and macro-scale dynamics, we can estimate the distance at which the cheating interaction significantly changes to be in the order of 250 µm. In summary, after an initial phase influenced by stochastic patterning, largely deterministic growth dynamics follow, which are additionally affected by local interactions of neighboring clusters. As such, the results underline the importance of stochasticity and local effects in the context of ecological interactions.
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Affiliation(s)
- Benedikt von Bronk
- Center for NanoScience, Faculty of Physics, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 München, Germany
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Culyba MJ, Kubiak JM, Mo CY, Goulian M, Kohli RM. Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network. PLoS Genet 2018; 14:e1007405. [PMID: 29856734 PMCID: PMC5999292 DOI: 10.1371/journal.pgen.1007405] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 06/13/2018] [Accepted: 05/09/2018] [Indexed: 01/25/2023] Open
Abstract
Biochemical pathways are often genetically encoded as simple transcription regulation networks, where one transcription factor regulates the expression of multiple genes in a pathway. The relative timing of each promoter’s activation and shut-off within the network can impact physiology. In the DNA damage repair pathway (known as the SOS response) of Escherichia coli, approximately 40 genes are regulated by the LexA repressor. After a DNA damaging event, LexA degradation triggers SOS gene transcription, which is temporally separated into subsets of ‘early’, ‘middle’, and ‘late’ genes. Although this feature plays an important role in regulating the SOS response, both the range of this separation and its underlying mechanism are not experimentally defined. Here we show that, at low doses of DNA damage, the timing of promoter activities is not separated. Instead, timing differences only emerge at higher levels of DNA damage and increase as a function of DNA damage dose. To understand mechanism, we derived a series of synthetic SOS gene promoters which vary in LexA-operator binding kinetics, but are otherwise identical, and then studied their activity over a large dose-range of DNA damage. In distinction to established models based on rapid equilibrium assumptions, the data best fit a kinetic model of repressor occupancy at promoters, where the drop in cellular LexA levels associated with higher doses of DNA damage leads to non-equilibrium binding kinetics of LexA at operators. Operators with slow LexA binding kinetics achieve their minimal occupancy state at later times than operators with fast binding kinetics, resulting in a time separation of peak promoter activity between genes. These data provide insight into this remarkable feature of the SOS pathway by demonstrating how a single transcription factor can be employed to control the relative timing of each gene’s transcription as a function of stimulus dose. As the precise timing of gene expression is critical for cells to respond and adapt to new environments, it is important to understand the underlying mechanisms which control this timing. In this report, we studied the timing of transcription for genes in the bacterial DNA damage repair pathway (known as the SOS response), a regulatory system where each gene is controlled by the same transcriptional repressor, LexA. By specifically isolating the role of the LexA binding interaction at SOS gene promoters, we found a relationship between the amount of DNA damage incurred by the cell, LexA binding kinetics at a promoter, and the timing of promoter activation. Our data fit a kinetic model that reveals how a disequilibrium between the LexA-operator binding reaction and cellular LexA concentrations causes timing differences between genes to emerge only at higher doses of DNA damage. Taken together, we show that non-equilibrium DNA binding kinetics is the mechanism by which a single transcription factor can modulate timing differences across an entire network of genes as a function of stimulus dose.
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Affiliation(s)
- Matthew J. Culyba
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States of America
- * E-mail:
| | - Jeffrey M. Kubiak
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States of America
| | - Charlie Y. Mo
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States of America
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Rahul M. Kohli
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States of America
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States of America
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15
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von Bronk B, Schaffer SA, Götz A, Opitz M. Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli. PLoS Biol 2017; 15:e2001457. [PMID: 28459803 PMCID: PMC5411026 DOI: 10.1371/journal.pbio.2001457] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/28/2017] [Indexed: 11/20/2022] Open
Abstract
In phenotypically heterogeneous microbial populations, the decision to adopt one or another phenotype is often stochastically regulated. However, how this stochasticity affects interactions between competing microbes in mixed communities is difficult to assess. One example of such an interaction system is the competition of an Escherichia coli strain C, which performs division of labor between reproducers and self-sacrificing toxin producers, with a toxin-sensitive strain S. The decision between reproduction or toxin production within a single C cell is inherently stochastic. Here, combining experimental and theoretical approaches, we demonstrate that this stochasticity in the initial phase of colony formation is the crucial determinant for the competition outcome. In the initial phase (t < 12h), stochasticity influences the formation of viable C clusters at the colony edge. In the subsequent phase, the effective fitness differences (set primarily by the degree of division of labor in the C strain population) dictate the deterministic population dynamics and consequently competition outcome. In particular, we observe that competitive success of the C strain is only found if (i) a C edge cluster has formed at the end of the initial competition phase and (ii) the beneficial and detrimental effects of toxin production are balanced, which is the case at intermediate toxin producer fractions. Our findings highlight the importance of stochastic processes during the initial phase of colony formation, which might be highly relevant for other microbial community interactions in which the random choice between phenotypes can have long-lasting consequences for community fate.
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Affiliation(s)
- Benedikt von Bronk
- Center for NanoScience, Faculty of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Sophia Anna Schaffer
- Center for NanoScience, Faculty of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Alexandra Götz
- Center for NanoScience, Faculty of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Madeleine Opitz
- Center for NanoScience, Faculty of Physics, Ludwig-Maximilians-Universität München, München, Germany
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16
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Efficient genetic approaches for improvement of plasmid based expression of recombinant protein in Escherichia coli : A review. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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17
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Lechner M, Schwarz M, Opitz M, Frey E. Hierarchical Post-transcriptional Regulation of Colicin E2 Expression in Escherichia coli. PLoS Comput Biol 2016; 12:e1005243. [PMID: 27977665 PMCID: PMC5157957 DOI: 10.1371/journal.pcbi.1005243] [Citation(s) in RCA: 11] [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: 03/14/2016] [Accepted: 11/09/2016] [Indexed: 01/21/2023] Open
Abstract
Post-transcriptional regulation of gene expression plays a crucial role in many bacterial pathways. In particular, the translation of mRNA can be regulated by trans-acting, small, non-coding RNAs (sRNAs) or mRNA-binding proteins, each of which has been successfully treated theoretically using two-component models. An important system that includes a combination of these modes of post-transcriptional regulation is the Colicin E2 system. DNA damage, by triggering the SOS response, leads to the heterogeneous expression of the Colicin E2 operon including the cea gene encoding the toxin colicin E2, and the cel gene that codes for the induction of cell lysis and release of colicin. Although previous studies have uncovered the system's basic regulatory interactions, its dynamical behavior is still unknown. Here, we develop a simple, yet comprehensive, mathematical model of the colicin E2 regulatory network, and study its dynamics. Its post-transcriptional regulation can be reduced to three hierarchically ordered components: the mRNA including the cel gene, the mRNA-binding protein CsrA, and an effective sRNA that regulates CsrA. We demonstrate that the stationary state of this system exhibits a pronounced threshold in the abundance of free mRNA. As post-transcriptional regulation is known to be noisy, we performed a detailed stochastic analysis, and found fluctuations to be largest at production rates close to the threshold. The magnitude of fluctuations can be tuned by the rate of production of the sRNA. To study the dynamics in response to an SOS signal, we incorporated the LexA-RecA SOS response network into our model. We found that CsrA regulation filtered out short-lived activation peaks and caused a delay in lysis gene expression for prolonged SOS signals, which is also seen in experiments. Moreover, we showed that a stochastic SOS signal creates a broad lysis time distribution. Our model thus theoretically describes Colicin E2 expression dynamics in detail and reveals the importance of the specific regulatory components for the timing of toxin release.
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Affiliation(s)
- Matthias Lechner
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mathias Schwarz
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
- Institute for Biological and Medical Imaging, Technische Universität München and Helmholtz Zentrum München, Neuherberg, Germany
| | - Madeleine Opitz
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Erwin Frey
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
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18
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Intracellular d-Serine Accumulation Promotes Genetic Diversity via Modulated Induction of RecA in Enterohemorrhagic Escherichia coli. J Bacteriol 2016; 198:3318-3328. [PMID: 27698085 DOI: 10.1128/jb.00548-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/27/2016] [Indexed: 01/28/2023] Open
Abstract
We recently discovered that exposure of enterohemorrhagic Escherichia coli (EHEC) to d-serine resulted in accumulation of this unusual amino acid, induction of the SOS regulon, and downregulation of the type III secretion system that is essential for efficient colonization of the host. Here, we have investigated the physiological relevance of this elevated SOS response, which is of particular interest given the presence of Stx toxin-carrying lysogenic prophages on the EHEC chromosome that are activated during the SOS response. We found that RecA elevation in response to d-serine, while being significant, was heterogeneous and not capable of activating stx expression or stx phage transduction to a nonlysogenic recipient. This "SOS-like response" was, however, capable of increasing the mutation frequency associated with low-level RecA activity, thus promoting genetic diversity. Furthermore, this response was entirely dependent on RecA and enhanced in the presence of a DNA-damaging agent, indicating a functional SOS response, but did not result in observable cleavage of the LexA repressor alone, indicating a controlled mechanism of induction. This work demonstrates that environmental factors not usually associated with DNA damage are capable of promoting an SOS-like response. We propose that this modulated induction of RecA allows EHEC to adapt to environmental insults such as d-serine while avoiding unwanted phage-induced lysis. IMPORTANCE The SOS response is a global stress network that is triggered by the presence of DNA damage due to breakage or stalled replication forks. Activation of the SOS response can trigger the replication of lytic bacteriophages and promote genetic diversification through error-prone polymerases. We have demonstrated that the host-associated metabolite d-serine contributes to Escherichia coli niche specification and accumulates inside cells that cannot catabolize it. This results in a modulated activation of the SOS antirepressor RecA that is insufficient to trigger lytic bacteriophage but capable of increasing the SOS-associated mutation frequency. These findings describe how relevant signals not normally associated with DNA damage can hijack the SOS response, promoting diversity as E. coli strains adapt while avoiding unwanted phage lysis.
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19
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Uphoff S, Kapanidis AN. Studying the organization of DNA repair by single-cell and single-molecule imaging. DNA Repair (Amst) 2014; 20:32-40. [PMID: 24629485 PMCID: PMC4119245 DOI: 10.1016/j.dnarep.2014.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 12/26/2022]
Abstract
Single-cell experiments to study stochastic events and heterogeneity in DNA repair. Quantifying DNA repair protein concentration, diffusion, and localization in cells. Direct observation of DNA repair using photoactivated single-molecule tracking.
DNA repair safeguards the genome against a diversity of DNA damaging agents. Although the mechanisms of many repair proteins have been examined separately in vitro, far less is known about the coordinated function of the whole repair machinery in vivo. Furthermore, single-cell studies indicate that DNA damage responses generate substantial variation in repair activities across cells. This review focuses on fluorescence imaging methods that offer a quantitative description of DNA repair in single cells by measuring protein concentrations, diffusion characteristics, localizations, interactions, and enzymatic rates. Emerging single-molecule and super-resolution microscopy methods now permit direct visualization of individual proteins and DNA repair events in vivo. We expect much can be learned about the organization of DNA repair by linking cell heterogeneity to mechanistic observations at the molecular level.
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Affiliation(s)
- Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
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20
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The importance of regulatory RNAs in Staphylococcus aureus. INFECTION GENETICS AND EVOLUTION 2014; 21:616-26. [DOI: 10.1016/j.meegid.2013.11.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/12/2013] [Accepted: 11/13/2013] [Indexed: 12/14/2022]
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21
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Kreuzer KN. DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks. Cold Spring Harb Perspect Biol 2013; 5:a012674. [PMID: 24097899 DOI: 10.1101/cshperspect.a012674] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent advances in the area of bacterial DNA damage responses are reviewed here. The SOS pathway is still the major paradigm of bacterial DNA damage response, and recent studies have clarified the mechanisms of SOS induction and key physiological roles of SOS including a very major role in genetic exchange and variation. When considering diverse bacteria, it is clear that SOS is not a uniform pathway with one purpose, but rather a platform that has evolved for differing functions in different bacteria. Relating in part to the SOS response, the field has uncovered multiple apparent cell-cycle checkpoints that assist cell survival after DNA damage and remarkable pathways that induce programmed cell death in bacteria. Bacterial DNA damage responses are also much broader than SOS, and several important examples of LexA-independent regulation will be reviewed. Finally, some recent advances that relate to the replication and repair of damaged DNA will be summarized.
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Affiliation(s)
- Kenneth N Kreuzer
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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22
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Ye R, Xu H, Wan C, Peng S, Wang L, Xu H, Aguilar ZP, Xiong Y, Zeng Z, Wei H. Antibacterial activity and mechanism of action of ε-poly-l-lysine. Biochem Biophys Res Commun 2013; 439:148-53. [DOI: 10.1016/j.bbrc.2013.08.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 08/01/2013] [Indexed: 11/25/2022]
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23
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Rajpurohit YS, Misra HS. Structure-function study of deinococcal serine/threonine protein kinase implicates its kinase activity and DNA repair protein phosphorylation roles in radioresistance of Deinococcus radiodurans. Int J Biochem Cell Biol 2013; 45:2541-52. [PMID: 23994692 DOI: 10.1016/j.biocel.2013.08.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/31/2013] [Accepted: 08/18/2013] [Indexed: 11/26/2022]
Abstract
The DR2518 (RqkA) a eukaryotic type serine/threonine protein kinase in Deinococcus radiodurans was characterized for its role in bacterial response to oxidative stress and DNA damage. The K42A, S162A, T169A and S171A mutation in RqkA differentially affected its kinase activity and functional complementation for γ radiation resistance in Δdr2518 mutant. For example, K42A mutant was completely inactive and showed no complementation while S171A, T169A and T169A/S171A mutants were less active and complemented proportionally to different levels as compared to wild type. Amongst, different DNA binding proteins that purified RqkA could phosphorylate, PprA a DNA repair protein, phosphorylation had improved its affinity to DNA by 4 fold and could enhance its supportive role in intermolecular ligation by T4 DNA ligase. RqkA phosphorylates PprA at threonine 72 (T72), serine 112 (S112) and threonine 144 (T144) in vitro with the majority of it goes to T72 site. Unlike wild type PprA and single mutants of T72, S112 and T144 residues, the T72AS112A double and T72AS112AT144A triple mutant derivatives of PprA did not phosphorylate in vivo and also failed to complement PprA loss in D. radiodurans. Deletion of rqkA in pprA::cat background enhanced radiosensitivity of pprA mutant, which became nearly similar to ΔrqkA resistance to γ radiation. These results suggested that K42 of RqkA is essential for catalytic functions and the kinase activity of RqkA as well as phosphorylation of PprA have roles in γ radiation resistance of D. radiodurans.
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24
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Szekely P, Sheftel H, Mayo A, Alon U. Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems. PLoS Comput Biol 2013; 9:e1003163. [PMID: 23950698 PMCID: PMC3738462 DOI: 10.1371/journal.pcbi.1003163] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 06/05/2013] [Indexed: 11/20/2022] Open
Abstract
Biological regulatory systems face a fundamental tradeoff: they must be effective but at the same time also economical. For example, regulatory systems that are designed to repair damage must be effective in reducing damage, but economical in not making too many repair proteins because making excessive proteins carries a fitness cost to the cell, called protein burden. In order to see how biological systems compromise between the two tasks of effectiveness and economy, we applied an approach from economics and engineering called Pareto optimality. This approach allows calculating the best-compromise systems that optimally combine the two tasks. We used a simple and general model for regulation, known as integral feedback, and showed that best-compromise systems have particular combinations of biochemical parameters that control the response rate and basal level. We find that the optimal systems fall on a curve in parameter space. Due to this feature, even if one is able to measure only a small fraction of the system's parameters, one can infer the rest. We applied this approach to estimate parameters in three biological systems: response to heat shock and response to DNA damage in bacteria, and calcium homeostasis in mammals. Many systems in the cell work to keep homeostasis, or balance. For example, damage repair systems make special repair proteins to resolve damage. These systems typically have many biochemical parameters such as biochemical rate constants, and it is not clear how much of the huge parameter space is filled by actual biological systems. We examined how natural selection acts on these systems when there are two important tasks: effectiveness – rapidly repairing damage, and economy – avoiding excessive production of repair proteins. We find that this multi-task optimization situation leads to natural selection of circuits that lie on a curve in parameter space. Thus, most of parameter space is empty. Estimating only a few parameters of the circuit is enough to predict the rest. This approach allowed us to estimate parameters for bacterial heat shock and DNA repair systems, and for a mammalian hormone system responsible for calcium homeostasis.
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Affiliation(s)
- Pablo Szekely
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Sheftel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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25
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Romilly C, Caldelari I, Parmentier D, Lioliou E, Romby P, Fechter P. Current knowledge on regulatory RNAs and their machineries in Staphylococcus aureus. RNA Biol 2012; 9:402-13. [PMID: 22546940 DOI: 10.4161/rna.20103] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Staphylococcus aureus is one of the major human pathogens, which causes numerous community-associated and hospital-acquired infections. The regulation of the expression of numerous virulence factors is coordinated by complex interplays between two component systems, transcriptional regulatory proteins, and regulatory RNAs. Recent studies have identified numerous novel RNAs comprising cis-acting regulatory RNAs, antisense RNAs, small non coding RNAs and small mRNAs encoding peptides. We present here several examples of RNAs regulating S. aureus pathogenicity and describe various aspects of antisense regulation.
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Affiliation(s)
- Cédric Romilly
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
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26
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Salavati A, Bushehri AAS, Taleei A, Hiraga S, Komatsu S. A comparative proteomic analysis of the early response to compatible symbiotic bacteria in the roots of a supernodulating soybean variety. J Proteomics 2012; 75:819-32. [PMID: 22005398 DOI: 10.1016/j.jprot.2011.09.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/04/2011] [Accepted: 09/26/2011] [Indexed: 02/03/2023]
Abstract
To reveal the processes involved in the early stages of symbiosis between soybean plants and root nodule bacteria, we conducted a proteomic analysis of the response to bacterial inoculation in the roots of supernodulating (En-b0-1) and non-nodulating (En1282) varieties, and their parental normal-nodulating variety (Enrei). A total of 56 proteins were identified from 48 differentially expressed protein spots in normal-nodulating variety after bacterial inoculation. Among 56 proteins, metabolism- and energy production-related proteins were upregulated in supernodulating and downregulated in non-nodulating varieties compared to normal-nodulating variety. The supernodulating and non-nodulating varieties responded oppositely to bacterial inoculation with respect to the expression of 11 proteins. Seven proteins of these proteins was downregulated in supernodulating varieties compared to non-nodulating variety, but expression of proteasome subunit alpha type 6, gamma glutamyl hydrolase, glucan endo-1,3-beta glucosidase, and nodulin 35 was upregulated. The expression of seven proteins mirrored the degree of nodule formation. At the transcript level, expression of stem 31kDa glycoprotein, leucine aminopeptidase, phosphoglucomutase, and peroxidase was downregulated in the supernodulating variety compared to the non-nodulating variety, and their expression in the normal-nodulating variety was intermediate. These results suggest that suppression of the autoregulatory mechanism in the supernodulating variety might be due to negative regulation of defense and signal transduction-related processes.
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Affiliation(s)
- Afshin Salavati
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
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27
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Shimoni Y, Nudelman G, Hayot F, Sealfon SC. Multi-scale stochastic simulation of diffusion-coupled agents and its application to cell culture simulation. PLoS One 2011; 6:e29298. [PMID: 22216238 PMCID: PMC3244460 DOI: 10.1371/journal.pone.0029298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 11/23/2011] [Indexed: 11/18/2022] Open
Abstract
Many biological systems consist of multiple cells that interact by secretion and binding of diffusing molecules, thus coordinating responses across cells. Techniques for simulating systems coupling extracellular and intracellular processes are very limited. Here we present an efficient method to stochastically simulate diffusion processes, which at the same time allows synchronization between internal and external cellular conditions through a modification of Gillespie's chemical reaction algorithm. Individual cells are simulated as independent agents, and each cell accurately reacts to changes in its local environment affected by diffusing molecules. Such a simulation provides time-scale separation between the intra-cellular and extra-cellular processes. We use our methodology to study how human monocyte-derived dendritic cells alert neighboring cells about viral infection using diffusing interferon molecules. A subpopulation of the infected cells reacts early to the infection and secretes interferon into the extra-cellular medium, which helps activate other cells. Findings predicted by our simulation and confirmed by experimental results suggest that the early activation is largely independent of the fraction of infected cells and is thus both sensitive and robust. The concordance with the experimental results supports the value of our method for overcoming the challenges of accurately simulating multiscale biological signaling systems.
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Affiliation(s)
- Yishai Shimoni
- Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, New York, United States of America
- * E-mail: (YS); (GN)
| | - German Nudelman
- Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail: (YS); (GN)
| | - Fernand Hayot
- Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Stuart C. Sealfon
- Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
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28
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Richard M, Fryett M, Miller S, Booth I, Grebogi C, Moura A. Optimality in DNA repair. J Theor Biol 2011; 292:39-43. [PMID: 21945337 PMCID: PMC4071444 DOI: 10.1016/j.jtbi.2011.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 07/07/2011] [Accepted: 08/22/2011] [Indexed: 12/25/2022]
Abstract
DNA within cells is subject to damage from various sources. Organisms have evolved a number of mechanisms to repair DNA damage. The activity of repair enzymes carries its own risk, however, because the repair of two nearby lesions may lead to the breakup of DNA and result in cell death. We propose a mathematical theory of the damage and repair process in the important scenario where lesions are caused in bursts. We use this model to show that there is an optimum level of repair enzymes within cells which optimises the cell's response to damage. This optimal level is explained as the best trade-off between fast repair and a low probability of causing double-stranded breaks. We derive our results analytically and test them using stochastic simulations, and compare our predictions with current biological knowledge.
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Affiliation(s)
- Morgiane Richard
- Institute of Complex Systems and Mathematical Biology, King's College, University of Aberdeen, Aberdeen, UK
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Desai SS, Rajpurohit YS, Misra HS, Deobagkar DN. Characterization of the role of the RadS/RadR two-component system in the radiation resistance of Deinococcus radiodurans. MICROBIOLOGY-SGM 2011; 157:2974-2982. [PMID: 21737498 DOI: 10.1099/mic.0.049361-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Deinococcus radiodurans shows extraordinary tolerance to DNA damage, and exhibits differential gene expression and protein recycling. A putative response regulator, the DRB0091 (RadR) ORF, was identified from a pool of DNA-binding proteins induced in response to gamma radiation in this bacterium. radR is located upstream of drB0090, which encodes a putative sensor histidine kinase (RadS) on the megaplasmid. Deletion of these genes both individually and together resulted in hypersensitivity to DNA-damaging agents and a delayed or altered double-strand break repair. A ΔradRradS double mutant and a ΔradR single mutant showed nearly identical responses to gamma radiation and UVC. Wild-type RadR and RadS complemented the corresponding mutant strains, but also exhibited significant cross-complementation, albeit at lower doses of gamma radiation. The radS transcript was not detected in the ΔradR mutant, suggesting the existence of a radRS operon. Recombinant RadS was autophosphorylated and could catalyse the transfer of γ phosphate from ATP to RadR in vitro. These results indicated the functional interaction of RadS and RadR, and suggested a role for the RadS/RadR two-component system in the radiation resistance of this bacterium.
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Affiliation(s)
- Shruti S Desai
- Centre for Advanced Studies in Zoology, Department of Zoology, University of Pune, Pune 411007, India.,Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | | | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Dileep N Deobagkar
- Centre for Advanced Studies in Zoology, Department of Zoology, University of Pune, Pune 411007, India
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Hilbert L, Albrecht D, Mackey MC. Small delay, big waves: a minimal delayed negative feedback model captures Escherichia coli single cell SOS kinetics. ACTA ACUST UNITED AC 2011; 7:2599-607. [DOI: 10.1039/c1mb05122a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Rivera-Gómez N, Segovia L, Pérez-Rueda E. Diversity and distribution of transcription factors: their partner domains play an important role in regulatory plasticity in bacteria. MICROBIOLOGY-SGM 2011; 157:2308-2318. [PMID: 21636649 DOI: 10.1099/mic.0.050617-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The ability of bacteria to deal with diverse environmental changes depends on their repertoire of genes and their ability to regulate their expression. In this process, DNA-binding transcription factors (TFs) have a fundamental role because they affect gene expression positively and/or negatively depending on operator context and ligand-binding status. Here, we show an exhaustive analysis of winged helix-turn-helix domains (wHTHs), a class of DNA-binding TFs. These proteins were identified in high proportions and widely distributed in bacteria, representing around half of the total TFs identified so far. In addition, we evaluated the repertoire of wHTHs in terms of their partner domains (PaDos), identifying a similar trend, as with TFs, i.e. they are abundant and widely distributed in bacteria. Based on the PaDos, we defined three main groups of families: (i) monolithic, those families with little PaDo diversity, such as LysR; (ii) promiscuous, those families with a high PaDo diversity; and (iii) monodomain, with families of small sizes, such as MarR. These findings suggest that PaDos have a very important role in the diversification of regulatory responses in bacteria, probably contributing to their regulatory complexity. Thus, the TFs discriminate over longer regions on the DNA through their diverse DNA-binding domains. On the other hand, the PaDos would allow a great flexibility for transcriptional regulation due to their ability to sense diverse stimuli through a variety of ligand-binding compounds.
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Affiliation(s)
- Nancy Rivera-Gómez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Lorenzo Segovia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ernesto Pérez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Hu J, Nudelman G, Shimoni Y, Kumar M, Ding Y, López C, Hayot F, Wetmur JG, Sealfon SC. Role of cell-to-cell variability in activating a positive feedback antiviral response in human dendritic cells. PLoS One 2011; 6:e16614. [PMID: 21347441 PMCID: PMC3035661 DOI: 10.1371/journal.pone.0016614] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 01/03/2011] [Indexed: 12/22/2022] Open
Abstract
In the first few hours following Newcastle disease viral infection of human monocyte-derived dendritic cells, the induction of IFNB1 is extremely low and the secreted type I interferon response is below the limits of ELISA assay. However, many interferon-induced genes are activated at this time, for example DDX58 (RIGI), which in response to viral RNA induces IFNB1. We investigated whether the early induction of IFNBI in only a small percentage of infected cells leads to low level IFN secretion that then induces IFN-responsive genes in all cells. We developed an agent-based mathematical model to explore the IFNBI and DDX58 temporal dynamics. Simulations showed that a small number of early responder cells provide a mechanism for efficient and controlled activation of the DDX58-IFNBI positive feedback loop. The model predicted distributions of single cell responses that were confirmed by single cell mRNA measurements. The results suggest that large cell-to-cell variation plays an important role in the early innate immune response, and that the variability is essential for the efficient activation of the IFNB1 based feedback loop.
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Affiliation(s)
- Jianzhong Hu
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - German Nudelman
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Yishai Shimoni
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Madhu Kumar
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Yaomei Ding
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Carolina López
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Fernand Hayot
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - James G. Wetmur
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Stuart C. Sealfon
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
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Noise-induced modulation of the relaxation kinetics around a non-equilibrium steady state of non-linear chemical reaction networks. PLoS One 2011; 6:e16045. [PMID: 21297975 PMCID: PMC3030564 DOI: 10.1371/journal.pone.0016045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Accepted: 12/02/2010] [Indexed: 12/11/2022] Open
Abstract
Stochastic effects from correlated noise non-trivially modulate the kinetics of non-linear chemical reaction networks. This is especially important in systems where reactions are confined to small volumes and reactants are delivered in bursts. We characterise how the two noise sources confinement and burst modulate the relaxation kinetics of a non-linear reaction network around a non-equilibrium steady state. We find that the lifetimes of species change with burst input and confinement. Confinement increases the lifetimes of all species that are involved in any non-linear reaction as a reactant. Burst monotonically increases or decreases lifetimes. Competition between burst-induced and confinement-induced modulation may hence lead to a non-monotonic modulation. We quantify lifetime as the integral of the time autocorrelation function (ACF) of concentration fluctuations around a non-equilibrium steady state of the reaction network. Furthermore, we look at the first and second derivatives of the ACF, each of which is affected in opposite ways by burst and confinement. This allows discriminating between these two noise sources. We analytically derive the ACF from the linear Fokker–Planck approximation of the chemical master equation in order to establish a baseline for the burst-induced modulation at low confinement. Effects of higher confinement are then studied using a partial-propensity stochastic simulation algorithm. The results presented here may help understand the mechanisms that deviate stochastic kinetics from its deterministic counterpart. In addition, they may be instrumental when using fluorescence-lifetime imaging microscopy (FLIM) or fluorescence-correlation spectroscopy (FCS) to measure confinement and burst in systems with known reaction rates, or, alternatively, to correct for the effects of confinement and burst when experimentally measuring reaction rates.
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Weigand MR, Tran VN, Sundin GW. Growth parameter components of adaptive specificity during experimental evolution of the UVR-inducible mutator Pseudomonas cichorii 302959. PLoS One 2011; 6:e15975. [PMID: 21264242 PMCID: PMC3021522 DOI: 10.1371/journal.pone.0015975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 12/07/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Mutagenic DNA repair (MDR) transiently increases mutation rate through the activation of low-fidelity repair polymerases in response to specific, DNA-damaging environmental stress conditions such as ultraviolet radiation (UVR) exposure. These repair polymerases also confer UVR tolerance, intimately linking mutability and survival in bacteria that colone habitats subject to regular UVR exposure. METHODOLOGY/PRINCIPAL FINDINGS Here, we investigate adaptive specificity in experimental lineages of the highly UVR-mutable epiphytic plant pathogen Pseudomonas cichorii 302959. Relative fitness measurements of isolates and population samples from replicate lineages indicated that adaptive improvements emerged early in all lineages of our evolution experiment and specific increases in relative fitness correlated with distinct improvements in doubling and lag times. Adaptive improvements gained under UVR and non-UVR conditions were acquired preferentially, and differentially contributed to relative fitness under varied growth conditions. CONCLUSIONS These results support our earlier observations that MDR activation may contribute to gains in relative fitness without impeding normal patterns of adaptive specificity in P. cichorii 302959.
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Affiliation(s)
- Michael R. Weigand
- Program in Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Vinh N. Tran
- Department of Plant Pathology, Michigan State University, East Lansing, Michigan, United States of America
| | - George W. Sundin
- Program in Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant Pathology, Michigan State University, East Lansing, Michigan, United States of America
- Centers for Microbial Ecology and Pathogenesis, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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Rajpurohit YS, Misra HS. Characterization of a DNA damage-inducible membrane protein kinase from Deinococcus radiodurans and its role in bacterial radioresistance and DNA strand break repair. Mol Microbiol 2010; 77:1470-82. [PMID: 20633226 DOI: 10.1111/j.1365-2958.2010.07301.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deinococcus radiodurans mutant lacking pyrroloquinoline-quinone (PQQ) synthesis shows sensitivity to γ-rays and impairment of DNA double strand break repair. The genome of this bacterium encodes five putative proteins having multiple PQQ binding motifs. The deletion mutants of corresponding genes were generated, and their response to DNA damage was monitored. Only the Δdr2518 mutant exhibited higher sensitivity to DNA damage. Survival of these cells decreased by 3-log cycle both at 6 kGy γ-rays and 1200 Jm(-2) UV (254 nm) radiation, and 2.5-log cycle upon 14 days desiccation at 5% humidity. The Δdr2518 mutant showed complete inhibition of DSB repair until 24 h PIR and disappearance of a few phosphoproteins. The Δdr2518pqqE:cat double mutant showed γ-ray sensitivity similar to Δdr2518 indicating functional interaction of these genes in D. radiodurans. DR2518 contains a eukaryotic type Ser/Thr kinase domain and structural topology suggesting stress responsive transmembrane protein. Its autokinase activity in solution was stimulated by nearly threefold with PQQ and twofold with linear DNA, but not with circular plasmid DNA. More than 15-fold increase in dr2518 transcription and several-fold enhanced in vivo phosphorylation of DR2518 were observed in response to γ irradiation. These results suggest that DR2518 as a DNA damage-responsive protein kinase plays an important role in radiation resistance and DNA strand break repair in D. radiodurans.
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Plato's cave algorithm: inferring functional signaling networks from early gene expression shadows. PLoS Comput Biol 2010; 6:e1000828. [PMID: 20585619 PMCID: PMC2891706 DOI: 10.1371/journal.pcbi.1000828] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 05/21/2010] [Indexed: 11/19/2022] Open
Abstract
Improving the ability to reverse engineer biochemical networks is a major goal of systems biology. Lesions in signaling networks lead to alterations in gene expression, which in principle should allow network reconstruction. However, the information about the activity levels of signaling proteins conveyed in overall gene expression is limited by the complexity of gene expression dynamics and of regulatory network topology. Two observations provide the basis for overcoming this limitation: a. genes induced without de-novo protein synthesis (early genes) show a linear accumulation of product in the first hour after the change in the cell's state; b. The signaling components in the network largely function in the linear range of their stimulus-response curves. Therefore, unlike most genes or most time points, expression profiles of early genes at an early time point provide direct biochemical assays that represent the activity levels of upstream signaling components. Such expression data provide the basis for an efficient algorithm (Plato's Cave algorithm; PLACA) to reverse engineer functional signaling networks. Unlike conventional reverse engineering algorithms that use steady state values, PLACA uses stimulated early gene expression measurements associated with systematic perturbations of signaling components, without measuring the signaling components themselves. Besides the reverse engineered network, PLACA also identifies the genes detecting the functional interaction, thereby facilitating validation of the predicted functional network. Using simulated datasets, the algorithm is shown to be robust to experimental noise. Using experimental data obtained from gonadotropes, PLACA reverse engineered the interaction network of six perturbed signaling components. The network recapitulated many known interactions and identified novel functional interactions that were validated by further experiment. PLACA uses the results of experiments that are feasible for any signaling network to predict the functional topology of the network and to identify novel relationships.
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