1
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Candra B, Cook D, Hare J. Repression of Acinetobacter baumannii DNA damage response requires DdrR-assisted binding of UmuDAb dimers to atypical SOS box. J Bacteriol 2024; 206:e0043223. [PMID: 38727225 DOI: 10.1128/jb.00432-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/14/2024] [Indexed: 06/21/2024] Open
Abstract
The DNA damage response of the multi-drug-resistant nosocomial pathogen Acinetobacter baumannii possesses multiple features that distinguish it from the commonly used LexA repression system. These include the absence of LexA in this genus, the evolution of a UmuD polymerase manager into the UmuDAb repressor of error-prone polymerases, the use of a corepressor unique to Acinetobacter (DdrR), and an unusually large UmuDAb binding site. We defined cis- and trans-acting factors required for UmuDAb DNA binding and gene repression, and tested whether DdrR directly enhances its DNA binding. We used DNA binding assays to characterize UmuDAb's binding to its proposed operator present upstream of the six co-repressed umuDC or umuC genes. UmuDAb bound tightly and cooperatively to this site with ~10-fold less affinity than LexA. DdrR enhanced the binding of both native and dimerization-deficient UmuDAb forms, but only in greater than equimolar ratios relative to UmuDAb. UmuDAb mutants unable to dimerize or effect gene repression showed impaired DNA binding, and a strain expressing the G124D dimerization mutant could not repress transcription of the UmuDAb-DdrR regulon. Competition electrophoretic mobility shift assays conducted with mutated operator probes showed that, unlike typical SOS boxes, the UmuDAb operator possessed a five-base pair central core whose sequence was more crucial for binding than the flanking palindrome. The presence of only one of the two flanking arms of the palindrome was necessary for UmuDAb binding. Overall, the data supported a model of an operator with two UmuDAb binding sites. The distinct characteristics of UmuDAb and its regulated promoters differ from the typical LexA repression model, demonstrating a novel method of repression.IMPORTANCEAcinetobacter baumannii is a gram-negative bacterium responsible for hospital-acquired infections. Its unique DNA damage response can activate multiple error-prone polymerase genes, allowing it to gain mutations that can increase its virulence and antibiotic resistance. The emergence of infectious strains carrying multiple antibiotic resistance genes, including carbapenem resistance, lends urgency to discovering and developing ways to combat infections resistant to treatment with known antibiotics. Deciphering how the regulators UmuDAb and DdrR repress the error-prone polymerases could lead to developing complementary treatments to halt this mechanism of generating resistance.
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Affiliation(s)
- Belinda Candra
- Baylor College of Medicine, Houston, Texas, USA
- Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, USA
| | - Deborah Cook
- Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, USA
| | - Janelle Hare
- Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, USA
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2
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Cory MB, Li A, Hurley CM, Carman PJ, Pumroy RA, Hostetler ZM, Perez RM, Venkatesh Y, Li X, Gupta K, Petersson EJ, Kohli RM. The LexA-RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation. Nat Struct Mol Biol 2024:10.1038/s41594-024-01317-3. [PMID: 38755298 DOI: 10.1038/s41594-024-01317-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024]
Abstract
The bacterial SOS response plays a key role in adaptation to DNA damage, including genomic stress caused by antibiotics. SOS induction begins when activated RecA*, an oligomeric nucleoprotein filament that forms on single-stranded DNA, binds to and stimulates autoproteolysis of the repressor LexA. Here, we present the structure of the complete Escherichia coli SOS signal complex, constituting full-length LexA bound to RecA*. We uncover an extensive interface unexpectedly including the LexA DNA-binding domain, providing a new molecular rationale for ordered SOS gene induction. We further find that the interface involves three RecA subunits, with a single residue in the central engaged subunit acting as a molecular key, inserting into an allosteric binding pocket to induce LexA cleavage. Given the pro-mutagenic nature of SOS activation, our structural and mechanistic insights provide a foundation for developing new therapeutics to slow the evolution of antibiotic resistance.
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Affiliation(s)
- Michael B Cory
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Christina M Hurley
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter J Carman
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruth A Pumroy
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Ryann M Perez
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Xinning Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Rahul M Kohli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Kamat A, Tran NT, Sharda M, Sontakke N, Le TBK, Badrinarayanan A. Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria. PLoS Biol 2024; 22:e3002540. [PMID: 38466718 PMCID: PMC10957082 DOI: 10.1371/journal.pbio.3002540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/21/2024] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
DNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The mechanisms by which bacteria detect and respond to such damage remain incompletely understood. Here, we discover a highly conserved but previously uncharacterized transcription factor (Cada2), which orchestrates a methylation-dependent adaptive response in Caulobacter. This response operates independently of the SOS response, governs the expression of genes crucial for direct repair, and is essential for surviving methylation-induced damage. Our molecular investigation of Cada2 reveals a cysteine methylation-dependent posttranslational modification (PTM) and mode of action distinct from its Escherichia coli counterpart, a trait conserved across all bacteria harboring a Cada2-like homolog instead. Extending across the bacterial kingdom, our findings support the notion of divergence and coevolution of adaptive response transcription factors and their corresponding sequence-specific DNA motifs. Despite this diversity, the ubiquitous prevalence of adaptive response regulators underscores the significance of a transcriptional switch, mediated by methylation PTM, in driving a specific and essential bacterial DNA damage response.
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Affiliation(s)
- Aditya Kamat
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Ngat T. Tran
- John Innes Centre, Department of Molecular Microbiology, Colney Lane, Norwich, United Kingdom
| | - Mohak Sharda
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Neha Sontakke
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Tung B. K. Le
- John Innes Centre, Department of Molecular Microbiology, Colney Lane, Norwich, United Kingdom
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4
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Raro OHF, Poirel L, Nordmann P. Effect of Zinc Oxide and Copper Sulfate on Antibiotic Resistance Plasmid Transfer in Escherichia coli. Microorganisms 2023; 11:2880. [PMID: 38138025 PMCID: PMC10745819 DOI: 10.3390/microorganisms11122880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/21/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Heavy metals such as zinc (Zn) and copper (Cu) may be associated with antibiotic resistance dissemination. Our aim was to investigate whether sub-lethal dosage of Zn and Cu may enhance plasmid transfer and subsequently resistance genes dissemination. Plasmid conjugation frequencies (PCF) were performed with Escherichia coli strains bearing IncL-blaOXA-48, IncA/C-blaCMY-2, IncI1-blaCTX-M-1, IncF-blaCTX-M-1, and IncX3-blaNDM-5 as donors. Mating-out assays were performed with sub-dosages of zinc oxide (ZnO) and Cu sulfate (CuSO4). Quantification of the SOS response-associated gene expression levels and of the production of reactive oxygen species were determined. Increased PCF was observed for IncL, IncA/C, and IncX3 when treated with ZnO. PCF was only increased for IncL when treated with CuSO4. The ROS production presented an overall positive correlation with PCF after treatment with ZnO for IncL, IncA/C, and IncX3. For CuSO4 treatment, the same was observed only for IncL. No increase was observed for expression of SOS response-associated genes under CuSO4 treatment, and under ZnO treatment, we observed an increase in SOS response-associated genes only for IncX3. Our data showed that sub-dosages of ZnO and CuSO4 could significantly enhance PCF in E. coli, with a more marked effect observed with IncL, IncA/C, and IncX3 scaffolds. Our study suggested that use of certain heavy metals is not the panacea for avoiding use of antibiotics in order to prevent the dissemination of antibiotic resistance.
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Affiliation(s)
- Otávio Hallal Ferreira Raro
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, 1700 Fribourg, Switzerland; (O.H.F.R.); (P.N.)
| | - Laurent Poirel
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, 1700 Fribourg, Switzerland; (O.H.F.R.); (P.N.)
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, 1700 Fribourg, Switzerland
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, 1700 Fribourg, Switzerland; (O.H.F.R.); (P.N.)
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, 1700 Fribourg, Switzerland
- Institute for Microbiology, Lausanne University Hospital and University of Lausanne, 1015 Lausanne, Switzerland
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Thabet MA, Penadés JR, Haag AF. The ClpX protease is essential for inactivating the CI master repressor and completing prophage induction in Staphylococcus aureus. Nat Commun 2023; 14:6599. [PMID: 37852980 PMCID: PMC10584840 DOI: 10.1038/s41467-023-42413-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Bacteriophages (phages) are the most abundant biological entities on Earth, exerting a significant influence on the dissemination of bacterial virulence, pathogenicity, and antimicrobial resistance. Temperate phages integrate into the bacterial chromosome in a dormant state through intricate regulatory mechanisms. These mechanisms repress lytic genes while facilitating the expression of integrase and the CI master repressor. Upon bacterial SOS response activation, the CI repressor undergoes auto-cleavage, producing two fragments with the N-terminal domain (NTD) retaining significant DNA-binding ability. The process of relieving CI NTD repression, essential for prophage induction, remains unknown. Here we show a specific interaction between the ClpX protease and CI NTD repressor fragment of phages Ф11 and 80α in Staphylococcus aureus. This interaction is necessary and sufficient for prophage activation after SOS-mediated CI auto-cleavage, defining the final stage in the prophage induction cascade. Our findings unveil unexpected roles of bacterial protease ClpX in phage biology.
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Affiliation(s)
- Mohammed A Thabet
- School of Infection & Immunity, University of Glasgow, G12 8TA, Glasgow, UK
- Department of Biology, Faculty of Science, Al-Baha University, Al-Baha city, Al Aqiq, 65779, Kingdom of Saudi Arabia
| | - José R Penadés
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Andreas F Haag
- School of Infection & Immunity, University of Glasgow, G12 8TA, Glasgow, UK.
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK.
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6
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Qi W, Jonker MJ, Teichmann L, Wortel M, Ter Kuile BH. The influence of oxygen and oxidative stress on de novo acquisition of antibiotic resistance in E. coli and Lactobacillus lactis. BMC Microbiol 2023; 23:279. [PMID: 37784016 PMCID: PMC10544416 DOI: 10.1186/s12866-023-03031-4] [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: 05/14/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Bacteria can acquire resistance through DNA mutations in response to exposure to sub-lethal concentrations of antibiotics. According to the radical-based theory, reactive oxygen species (ROS), a byproduct of the respiratory pathway, and oxidative stress caused by reactive metabolic byproducts, play a role in cell death as secondary killing mechanism. In this study we address the question whether ROS also affects development of resistance, in the conditions that the cells is not killed by the antibiotic. RESULTS To investigate whether oxygen and ROS affect de novo acquisition of antibiotic resistance, evolution of resistance due to exposure to non-lethal levels of antimicrobials was compared in E. coli wildtype and ΔoxyR strains under aerobic and anaerobic conditions. Since Lactococcus lactis (L. lactis) does not have an active electron transport chain (ETC) even in the presence of oxygen, and thus forms much less ROS, resistance development in L. lactis was used to distinguish between oxygen and ROS. The resistance acquisition in E. coli wildtype under aerobic and anaerobic conditions did not differ much. However, the aerobically grown ΔoxyR strain gained resistance faster than the wildtype or anaerobic ΔoxyR. Inducing an ETC by adding heme increased the rate at which L. lactis acquired resistance. Whole genome sequencing identified specific mutations involved in the acquisition of resistance. These mutations were specific for each antibiotic. The lexA mutation in ΔoxyR strain under aerobic conditions indicated that the SOS response was involved in resistance acquisition. CONCLUSIONS The concept of hormesis can explain the beneficial effects of low levels of ROS and reactive metabolic byproducts, while high levels are lethal. DNA repair and mutagenesis may therefore expedite development of resistance. Taken together, the results suggest that oxygen as such barely affects resistance development. Nevertheless, non-lethal levels of ROS stimulate de novo acquisition of antibiotic resistance.
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Affiliation(s)
- Wenxi Qi
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijs J Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Lisa Teichmann
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Meike Wortel
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Benno H Ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
- Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, The Netherlands.
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7
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Peng J, Li J, Liang J, Li W, Yang Y, Yang Y, Zhang S, Huang X, Han F. A C-type lectin-like receptor CD302 in yellow drum (Nibea albiflora) functioning in antibacterial activity and innate immune signaling. Int J Biol Macromol 2023; 247:125734. [PMID: 37423436 DOI: 10.1016/j.ijbiomac.2023.125734] [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: 03/23/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Molecular dissection of disease resistance against Vibrio harveyi infection in yellow drum at the genome-wide level uncovered a C-type lectin-like receptor cluster of differentiation CD302 (named as YdCD302) in our previous study. Here, the gene expression pattern of YdCD302 and its function in mediating the defense response to V. harveyi attack were investigated. Gene expression analysis demonstrated that YdCD302 was ubiquitously distributed in various tissues with the highest transcript abundance in liver. The YdCD302 protein exhibited agglutination and antibacterial activity against V. harveyi cells. Binding assay indicated that YdCD302 can physically interact with V. harveyi cells in a Ca2+-independent manner, and the interaction can activate reactive oxygen species (ROS) production in the bacterial cells to induce RecA/LexA-mediated cell death. After infection with V. harveyi, the expression of YdCD302 can be up-regulated significantly in the main immune organs of yellow drum and potentially further trigger the cytokines involved innate immunity. These findings provide insight into the genetic basis of the disease resistance trait in yellow drum and shed light on the functioning of the CD302 C-type lectin-like receptor in host-pathogen interactions. The molecular and functional characterization of YdCD302 is a significant step towards a better understanding of disease resistance mechanisms and the development of new strategies for disease control.
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Affiliation(s)
- Jia Peng
- Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fisheries College, Jimei University, Xiamen 361000, China
| | - Jiacheng Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fisheries College, Jimei University, Xiamen 361000, China
| | - Jingjie Liang
- Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fisheries College, Jimei University, Xiamen 361000, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fisheries College, Jimei University, Xiamen 361000, China
| | - Yao Yang
- Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fisheries College, Jimei University, Xiamen 361000, China
| | - Yukai Yang
- Shenzhen Base of South China Sea Fishery Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518121, China; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Sen Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fisheries College, Jimei University, Xiamen 361000, China
| | - Xiaolin Huang
- Shenzhen Base of South China Sea Fishery Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518121, China; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fisheries College, Jimei University, Xiamen 361000, China.
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8
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Zhou Y, Liao H, Pei L, Pu Y. Combatting persister cells: The daunting task in post-antibiotics era. CELL INSIGHT 2023; 2:100104. [PMID: 37304393 PMCID: PMC10250163 DOI: 10.1016/j.cellin.2023.100104] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/25/2023] [Accepted: 04/21/2023] [Indexed: 06/13/2023]
Abstract
Over the years, much attention has been drawn to antibiotic resistance bacteria, but drug inefficacy caused by a subgroup of special phenotypic variants - persisters - has been largely neglected in both scientific and clinical field. Interestingly, this subgroup of phenotypic variants displayed their power of withstanding sufficient antibiotics exposure in a mechanism different from antibiotic resistance. In this review, we summarized the clinical importance of bacterial persisters, the evolutionary link between resistance, tolerance, and persistence, redundant mechanisms of persister formation as well as methods of studying persister cells. In the light of our recent findings of membrane-less organelle aggresome and its important roles in regulating bacterial dormancy depth, we propose an alternative approach for anti-persister therapy. That is, to force a persister into a deeper dormancy state to become a VBNC (viable but non-culturable) cell that is incapable of regrowth. We hope to provide the latest insights on persister studies and call upon more research interest into this field.
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Affiliation(s)
- Yidan Zhou
- Department of Clinical Laboratory, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
| | - Hebin Liao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
| | - Linsen Pei
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
| | - Yingying Pu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
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9
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Yang Y, Wu B, Li W, Han F. Molecular Characterization of Galectin-3 in Large Yellow Croaker Larimichthys crocea Functioning in Antibacterial Activity. Int J Mol Sci 2023; 24:11539. [PMID: 37511297 PMCID: PMC10380712 DOI: 10.3390/ijms241411539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Galectins are proteins that play a crucial role in the innate immune response against pathogenic microorganisms. Previous studies have suggested that Galectin-3 could be a candidate gene for antibacterial immunity in the large yellow croaker Larimichthys crocea. In this study, we cloned the Galectin-3 gene in the large yellow croaker, and named it LcGal-3. The deduced amino acid sequence of LcGal-3 contains a carbohydrate recognition domain with two conserved β-galactoside binding motifs. Quantitative reverse transcription PCR (qRT-PCR) analysis revealed that LcGal-3 was expressed in all the organs/tissues that were tested, with the highest expression level in the gill. In Larimichthys crocea kidney cell lines, LcGal-3 protein was distributed in both the cytoplasm and nucleus. Moreover, we found that the expression of LcGal-3 was significantly upregulated upon infection with Pseudomonas plecoglossicida, as demonstrated by qRT-PCR analyses. We also purified the LcGal-3 protein that was expressed in prokaryotes, and found that it has the ability to agglutinate large yellow croaker red blood cells in a Ca2+-independent manner. The agglutination activity of LcGal-3 was inhibited by lipopolysaccharides (LPS) in a concentration-dependent manner, as shown in the sugar inhibition test. Additionally, LcGal-3 exhibited agglutination and antibacterial activities against three Gram-negative bacteria, including P. plecoglossicida, Vibrio parahaemolyticus, and Vibrio harveyi. Furthermore, we studied the agglutination mechanism of the LcGal-3 protein using blood coagulation tests with LcGal-3 deletion and point mutation proteins. Our results indicate that LcGal-3 protein plays a critical role in the innate immunity of the large yellow croaker, providing a basis for further studies on the immune mechanism and disease-resistant breeding in L. crocea and other marine fish.
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Affiliation(s)
- Yao Yang
- Key Laboratory of Healthy Mariculture for the East China Sea, Minsistry of Agriculture and Rural Affairs Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Jimei University, Xiamen 361021, China
| | - Baolan Wu
- Key Laboratory of Healthy Mariculture for the East China Sea, Minsistry of Agriculture and Rural Affairs Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Jimei University, Xiamen 361021, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Minsistry of Agriculture and Rural Affairs Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Jimei University, Xiamen 361021, China
| | - Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Minsistry of Agriculture and Rural Affairs Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Jimei University, Xiamen 361021, China
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10
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Kamat A, Badrinarayanan A. SOS-independent bacterial DNA damage responses: diverse mechanisms, unifying function. Curr Opin Microbiol 2023; 73:102323. [PMID: 37148591 DOI: 10.1016/j.mib.2023.102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/23/2023] [Accepted: 04/06/2023] [Indexed: 05/08/2023]
Abstract
Cells across domains of life have dedicated pathways to sense and respond to DNA damage. These responses are broadly termed as DNA damage responses (DDRs). In bacteria, the best studied DDR is the Save our Soul (SOS) response. More recently, several SOS-independent DDRs have also been discovered. Studies further report diversity in the types of repair proteins present across bacterial species as well as differences in their mechanisms of action. Although the primary function of DDRs is preservation of genome integrity, the diverse organization, conservation, and function of bacterial DDRs raises important questions about how genome error correction mechanisms could influence or be influenced by the genomes that encode them. In this review, we discuss recent insights on three SOS-independent bacterial DDRs. We consider open questions in our understanding of how diversity in response and repair mechanisms is generated, and how action of these pathways is regulated in cells to ensure maintenance of genome integrity.
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Affiliation(s)
- Aditya Kamat
- National Centre for Biological Sciences (TIFR), Bengaluru 560065, India
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11
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Cory MB, Jones CM, Shaffer KD, Venkatesh Y, Giannakoulias S, Perez RM, Lougee MG, Hummingbird E, Pagar VV, Hurley CM, Li A, Mach RH, Kohli RM, Petersson EJ. FRETing about the details: Case studies in the use of a genetically encoded fluorescent amino acid for distance-dependent energy transfer. Protein Sci 2023; 32:e4633. [PMID: 36974585 PMCID: PMC10108435 DOI: 10.1002/pro.4633] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Förster resonance energy transfer (FRET) is a valuable method for monitoring protein conformation and biomolecular interactions. Intrinsically fluorescent amino acids that can be genetically encoded, such as acridonylalanine (Acd), are particularly useful for FRET studies. However, quantitative interpretation of FRET data to derive distance information requires careful use of controls and consideration of photophysical effects. Here we present two case studies illustrating how Acd can be used in FRET experiments to study small molecule induced conformational changes and multicomponent biomolecular complexes.
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Affiliation(s)
- Michael B. Cory
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Chloe M. Jones
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Kyle D. Shaffer
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Yarra Venkatesh
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Sam Giannakoulias
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Ryann M. Perez
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marshall G. Lougee
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Eshe Hummingbird
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Vinayak V. Pagar
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Christina M. Hurley
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Allen Li
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Robert H. Mach
- Department of RadiologyPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Rahul M. Kohli
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of MedicinePerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - E. James Petersson
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
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12
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Rubio-Canalejas A, Pedraz L, Torrents E. ReViTA: A novel in vitro transcription system to study gene regulation. N Biotechnol 2023; 76:41-48. [PMID: 37080534 DOI: 10.1016/j.nbt.2023.04.005] [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: 12/11/2022] [Revised: 03/17/2023] [Accepted: 04/17/2023] [Indexed: 04/22/2023]
Abstract
ReViTA (Reverse in VitroTranscription Assay) is a novel in vitro transcription-based method to study gene expression under the regulation of specific transcription factors. The ReViTA system uses a plasmid with a control sequence, the promoter region of the studied gene, the transcription factor of interest, and an RNA polymerase saturated with σ70. The main objective of this study was to evaluate the method; thus, as a proof of concept, two different transcription factors were used, a transcriptional inducer, AlgR, and a repressor, LexA, from Pseudomonas aeruginosa. After the promoters were incubated with the transcription factors, the plasmid was transcribed into RNA and reverse transcribed to cDNA. Gene expression was measured using qRTPCR. Using the ReViTA plasmid, transcription induction of 55% was observed when AlgR protein was added and a 27% transcription reduction with the repressor LexA, compared with the samples without transcription factors. The results demonstrated the correct functioning of ReViTA as a novel method to study transcription factors and gene expression. Thus, ReViTA could be a rapid and accessible in vitro method to evaluate genes and regulators of various species.
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Affiliation(s)
- Alba Rubio-Canalejas
- Bacterial infections and antimicrobial therapies group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST). Baldiri Reixac 15-21. 08028 Barcelona, Spain
| | - Lucas Pedraz
- Centre for Microbial Diseases and Immunity Research. University of British Columbia. Vancouver BC V6T1Z4, Canada
| | - Eduard Torrents
- Bacterial infections and antimicrobial therapies group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST). Baldiri Reixac 15-21. 08028 Barcelona, Spain; Microbiology Section, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 643 Diagonal Ave., 08028, Barcelona, Spain.
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13
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Cory MB, Li A, Hurley CM, Hostetler ZM, Venkatesh Y, Jones CM, Petersson EJ, Kohli RM. Engineered RecA Constructs Reveal the Minimal SOS Activation Complex. Biochemistry 2022; 61:2884-2896. [PMID: 36473084 PMCID: PMC9982712 DOI: 10.1021/acs.biochem.2c00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The SOS response is a bacterial DNA damage response pathway that has been heavily implicated in bacteria's ability to evolve resistance to antibiotics. Activation of the SOS response is dependent on the interaction between two bacterial proteins, RecA and LexA. RecA acts as a DNA damage sensor by forming lengthy oligomeric filaments (RecA*) along single-stranded DNA (ssDNA) in an ATP-dependent manner. RecA* can then bind to LexA, the repressor of SOS response genes, triggering LexA degradation and leading to induction of the SOS response. Formation of the RecA*-LexA complex therefore serves as the key "SOS activation signal." Given the challenges associated with studying a complex involving multiple macromolecular interactions, the essential constituents of RecA* that allow LexA cleavage are not well defined. Here, we leverage head-to-tail linked and end-capped RecA constructs as tools to define the minimal RecA* filament that can engage LexA. In contrast to previously postulated models, we found that as few as three linked RecA units are capable of ssDNA binding, LexA binding, and LexA cleavage. We further demonstrate that RecA oligomerization alone is insufficient for LexA cleavage, with an obligate requirement for ATP and ssDNA binding to form a competent SOS activation signal with the linked constructs. Our minimal system for RecA* highlights the limitations of prior models for the SOS activation signal and offers a novel tool that can inform efforts to slow acquired antibiotic resistance by targeting the SOS response.
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Affiliation(s)
- Michael B. Cory
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Allen Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christina M. Hurley
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zachary M. Hostetler
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chloe M. Jones
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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14
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McKenzie AM, Henry C, Myers KS, Place MM, Keck JL. Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli. G3 (BETHESDA, MD.) 2022; 12:jkac295. [PMID: 36326440 PMCID: PMC9713433 DOI: 10.1093/g3journal/jkac295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 11/30/2023]
Abstract
Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in Escherichia coli. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in E. coli and other bacteria. Three replication restart pathways have been identified in E. coli: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon-insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the priB replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel priB interactions were discovered. Targeted genetic and imaging-based experiments with priB and its genetic partners revealed significant double-strand DNA break accumulation in strains with mutations in dam, rep, rdgC, lexA, or polA. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of rdgC or lexA mutations in ΔpriB cells. Taken together, our results highlight roles for several genes in double-strand DNA break homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in E. coli.
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Affiliation(s)
- Aidan M McKenzie
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Camille Henry
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kevin S Myers
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Michael M Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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15
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Nanobodies targeting LexA autocleavage disclose a novel suppression strategy of SOS-response pathway. Structure 2022; 30:1479-1493.e9. [DOI: 10.1016/j.str.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/29/2022] [Accepted: 09/18/2022] [Indexed: 11/05/2022]
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16
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Wang R, Lin X, Zha G, Wang J, Huang W, Wang J, Hou Y, Mou H, Zhang T, Zhu H, Wang J. Mechanism of enrofloxacin-induced multidrug resistance in the pathogenic Vibrio harveyi from diseased abalones. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154738. [PMID: 35331762 DOI: 10.1016/j.scitotenv.2022.154738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Vibrio harveyi infection had caused severe economic losses in aquaculture. A pathogenic V. harveyi strain had been successfully induced to be a multiple-resistant strain by enrofloxacin (EFX), then the mechanism of multidrug resistance was analyzed. It suggested that the minimum inhibitory concentration of EFX increased by 32-folds. Results of the Kirby-Bauer test showed that the inhibitory zone diameter was 25.3 mm for the sensitive strain (labeled as HL-S) and 8.5 mm for the resistant strain (labeled as HL-R). After 20 serial passages, even when the stress of EFX was removed, the resistance persisted. After induction of EFX, HL-R resisted to other fluoroquinolones, it even resisted to furazolidone and streptomycin, although it was sensitive to these antibiotics initially. Its sensitivity to rifampicin and doxycycline also decreased obviously. Results showed that 3522 differentially expressed genes were identified. Expression of the multidrugs efflux resistance-nodulation-cell division was significantly upregulated (164.61-folds) in HL-R. Other key genes connected with drug efflux were also upregulated significantly (p<0.05). Notably, recA encoded for recombination protein was upregulated significantly, lexA was downregulated significantly in HL-R. Research results showed that the efflux system and the save our souls system have played crucial roles during the development of multidrug resistance of V. harveyi.
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Affiliation(s)
- Ruixuan Wang
- Hanshan Normal University, Chaozhou 521041, China
| | - Xiaozhi Lin
- Hanshan Normal University, Chaozhou 521041, China
| | - Guangcai Zha
- Hanshan Normal University, Chaozhou 521041, China
| | - Juan Wang
- Hanshan Normal University, Chaozhou 521041, China
| | - Wei Huang
- Hanshan Normal University, Chaozhou 521041, China
| | | | - Yuee Hou
- Zhuhai Kerric Testing Co., Ltd., Zhuhai 519000, China
| | - Hongli Mou
- South China Sea Fisheries Research Institute, Guangzhou 510300, China
| | - Ting Zhang
- Hanshan Normal University, Chaozhou 521041, China
| | - Hui Zhu
- Hanshan Normal University, Chaozhou 521041, China
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China.
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17
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Cory MB, Hostetler ZM, Kohli RM. Kinetic dissection of macromolecular complex formation with minimally perturbing fluorescent probes. Methods Enzymol 2022; 664:151-171. [PMID: 35331372 DOI: 10.1016/bs.mie.2022.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The formation of macromolecular complexes containing multiple protein binding partners is at the core of many biochemical pathways. Studying the kinetics of complex formation can offer significant biological insights and complement static structural snapshots or approaches that reveal thermodynamic affinities. However, determining the kinetics of macromolecular complex formation can be difficult without significant manipulations to the system. Fluorescence anisotropy using a fluorophore-labeled constituent of the biologic complex offers potential advantages in obtaining time-resolved signals tracking complex assembly. However, an inherent challenge of traditional post-translational protein labeling is the orthogonality of labeling chemistry with regards to protein target and the potential disruption of complex formation. In this chapter, we will discuss the application of unnatural amino acid labeling as a means for generating a minimally perturbing reporter. We then describe the use of fluorescence anisotropy to define the kinetics of complex formation, using the key protein-protein-nucleic acid complex governing the bacterial DNA damage response-RecA nucleoprotein filaments binding to LexA-as a model system. We will also show how this assay can be expanded to ask questions about the kinetics of complex formation for unlabeled variants, thus assessing assembly kinetics in more native contexts and broadening its utility. We discuss the optimization process for our model system and offer guidelines for applying the same principles to other macromolecular systems.
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Affiliation(s)
- Michael B Cory
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Zachary M Hostetler
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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18
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Jones EC, Uphoff S. Single-molecule imaging of LexA degradation in Escherichia coli elucidates regulatory mechanisms and heterogeneity of the SOS response. Nat Microbiol 2021; 6:981-990. [PMID: 34183814 PMCID: PMC7611437 DOI: 10.1038/s41564-021-00930-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 05/27/2021] [Indexed: 12/20/2022]
Abstract
The bacterial SOS response stands as a paradigm of gene networks controlled by a master transcriptional regulator. Self-cleavage of the SOS repressor, LexA, induces a wide range of cell functions that are critical for survival and adaptation when bacteria experience stress conditions1, including DNA repair2, mutagenesis3,4, horizontal gene transfer5–7, filamentous growth, and the induction of bacterial toxins8–12, toxin-antitoxin systems13, virulence factors6,14, and prophages15–17. SOS induction is also implicated in biofilm formation and antibiotic persistence11,18–20. Considering the fitness burden of these functions, it is surprising that the expression of LexA-regulated genes is highly variable across cells10,21–23 and that cell subpopulations induce the SOS response spontaneously even in the absence of stress exposure9,11,12,16,24,25. Whether this reflects a population survival strategy or a regulatory inaccuracy is unclear, as are the mechanisms underlying SOS heterogeneity. Here, we developed a single-molecule imaging approach based on a HaloTag fusion to directly monitor LexA inside live Escherichia coli cells, demonstrating the existence of 3 main states of LexA: DNA-bound stationary molecules, free LexA and degraded LexA species. These analyses elucidate the mechanisms by which DNA-binding and degradation of LexA regulate the SOS response in vivo. We show that self-cleavage of LexA occurs frequently throughout the population during unperturbed growth, rather than being restricted to a subpopulation of cells, which causes substantial cell-to-cell variation in LexA abundances. LexA variability underlies SOS gene expression heterogeneity and triggers spontaneous SOS pulses, which enhance bacterial survival in anticipation of stress.
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Affiliation(s)
- Emma C Jones
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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19
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von Rosen T, Keller LM, Weber-Ban E. Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways. Front Mol Biosci 2021; 8:685757. [PMID: 34179091 PMCID: PMC8223512 DOI: 10.3389/fmolb.2021.685757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteria employ a multitude of strategies to cope with the challenges they face in their natural surroundings, be it as pathogens, commensals or free-living species in rapidly changing environments like soil. Mycobacteria and other Actinobacteria acquired proteasomal genes and evolved a post-translational, ubiquitin-like modification pathway called pupylation to support their survival under rapidly changing conditions and under stress. The proteasomal 20S core particle (20S CP) interacts with ring-shaped activators like the hexameric ATPase Mpa that recruits pupylated substrates. The proteasomal subunits, Mpa and pupylation enzymes are encoded in the so-called Pup-proteasome system (PPS) gene locus. Genes in this locus become vital for bacteria to survive during periods of stress. In the successful human pathogen Mycobacterium tuberculosis, the 20S CP is essential for survival in host macrophages. Other members of the PPS and proteasomal interactors are crucial for cellular homeostasis, for example during the DNA damage response, iron and copper regulation, and heat shock. The multiple pathways that the proteasome is involved in during different stress responses suggest that the PPS plays a vital role in bacterial protein quality control and adaptation to diverse challenging environments.
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Affiliation(s)
- Tatjana von Rosen
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Lena Ml Keller
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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20
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Pipercevic J, Jakob RP, Righetto RD, Goldie KN, Stahlberg H, Maier T, Hiller S. Identification of a Dps contamination in Mitomycin-C-induced expression of Colicin Ia. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183607. [PMID: 33775657 DOI: 10.1016/j.bbamem.2021.183607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 11/29/2022]
Abstract
Colicins are bacterial toxins targeting Gram-negative bacteria, including E. coli and related Enterobacteriaceae strains. Some colicins form ion-gated pores in the inner membrane of attacked bacteria that are lethal to their target. Colicin Ia was the first pore-forming E. coli toxin, for which a high-resolution structure of the monomeric full-length protein was determined. It is so far also the only colicin, for which a low-resolution structure of its membrane-inserted pore was reported by negative-stain electron microscopy. Resolving this structure at the atomic level would allow an understanding of the mechanism of toxin pore formation. Here, we report an observation that we made during an attempt to determine the Colicin Ia pore structure at atomic resolution. Colicin Ia was natively expressed by mitomycin-C induction under a native SOS promotor and purified following published protocols. The visual appearance in the electron microscope of negatively stained preparations and the lattice parameters of 2D crystals obtained from the material were highly similar to those reported earlier resulting from the same purification protocol. However, a higher-resolution structural analysis revealed that the protein is Dps (DNA-binding protein from starved cells), a dodecameric E. coli protein. This finding suggests that the previously reported low-resolution structure of a "Colicin Ia oligomeric pore" actually shows Dps.
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Affiliation(s)
| | - Roman P Jakob
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Ricardo D Righetto
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Kenneth N Goldie
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Timm Maier
- Biozentrum, University of Basel, 4056 Basel, Switzerland
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21
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Cook D, Carrington J, Johnson K, Hare J. Homodimerization and heterodimerization requirements of Acinetobacter baumannii SOS response coregulators UmuDAb and DdrR revealed by two-hybrid analyses. Can J Microbiol 2020; 67:358-371. [PMID: 33180570 DOI: 10.1139/cjm-2020-0219] [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: 12/11/2022]
Abstract
The multidrug-resistant pathogen Acinetobacter baumannii displays unusual control of its SOS mutagenesis genes, as it does not encode a LexA repressor, but instead employs the UmuDAb repressor and a small protein, DdrR, that is uniquely found in Acinetobacter species. We used bacterial adenylate cyclase two-hybrid analyses to determine if UmuDAb and DdrR coregulation might involve physical interactions. Neither quantitative nor qualitative assays showed UmuDAb interaction with DdrR. DdrR hybrid proteins, however, demonstrated modest head-to-tail interactions in a qualitative assay. The similarity of UmuDAb to the homodimer-forming polymerase manager UmuD and LexA repressor proteins suggested that it may form dimers, which we observed. UmuDAb homodimerization required a free C terminus, and either small truncations or addition of a histidine tag at the C terminus abolished this homodimerization. The amino acid N100, crucial for UmuD dimer formation, was dispensable if both C termini were free to interact. However, mutation of the amino acid G124, necessary for LexA dimerization, yielded significantly less UmuDAb dimerization, even if both C termini were free. This suggests that UmuDAb forms dimers like LexA does, but may not coregulate gene expression involving a physical association with DdrR. The homodimerization of these coregulators provides insight into a LexA-independent, coregulatory process of controlling a conserved bacterial action such as the mutagenic DNA damage response.
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Affiliation(s)
- Deborah Cook
- Department of Biology and Chemistry, Morehead State University, Morehead, KY 40351, USA
| | - Jordan Carrington
- Department of Biology and Chemistry, Morehead State University, Morehead, KY 40351, USA
| | - Kevin Johnson
- Department of Biology and Chemistry, Morehead State University, Morehead, KY 40351, USA.,Craft Academy for Excellence in Science and Mathematics, Morehead State University, Morehead, KY 40351, USA
| | - Janelle Hare
- Department of Biology and Chemistry, Morehead State University, Morehead, KY 40351, USA
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22
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Antibiotic-induced DNA damage results in a controlled loss of pH homeostasis and genome instability. Sci Rep 2020; 10:19422. [PMID: 33173044 PMCID: PMC7655802 DOI: 10.1038/s41598-020-76426-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/27/2020] [Indexed: 11/08/2022] Open
Abstract
Extracellular pH has been assumed to play little if any role in how bacteria respond to antibiotics and antibiotic resistance development. Here, we show that the intracellular pH of Escherichia coli equilibrates to the environmental pH following treatment with the DNA damaging antibiotic nalidixic acid. We demonstrate that this allows the environmental pH to influence the transcription of various DNA damage response genes and physiological processes such as filamentation. Using purified RecA and a known pH-sensitive mutant variant RecA K250R we show how pH can affect the biochemical activity of a protein central to control of the bacterial DNA damage response system. Finally, two different mutagenesis assays indicate that environmental pH affects antibiotic resistance development. Specifically, at environmental pH's greater than six we find that mutagenesis plays a significant role in producing antibiotic resistant mutants. At pH's less than or equal to 6 the genome appears more stable but extensive filamentation is observed, a phenomenon that has previously been linked to increased survival in the presence of macrophages.
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23
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Myka KK, Marians KJ. Two components of DNA replication-dependent LexA cleavage. J Biol Chem 2020; 295:10368-10379. [PMID: 32513870 PMCID: PMC7383369 DOI: 10.1074/jbc.ra120.014224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/04/2020] [Indexed: 12/19/2022] Open
Abstract
Induction of the SOS response, a cellular system triggered by DNA damage in bacteria, depends on DNA replication for the generation of the SOS signal, ssDNA. RecA binds to ssDNA, forming filaments that stimulate proteolytic cleavage of the LexA transcriptional repressor, allowing expression of > 40 gene products involved in DNA repair and cell cycle regulation. Here, using a DNA replication system reconstituted in vitro in tandem with a LexA cleavage assay, we studied LexA cleavage during DNA replication of both undamaged and base-damaged templates. Only a ssDNA-RecA filament supported LexA cleavage. Surprisingly, replication of an undamaged template supported levels of LexA cleavage like that induced by a template carrying two site-specific cyclobutane pyrimidine dimers. We found that two processes generate ssDNA that could support LexA cleavage. 1) During unperturbed replication, single-stranded regions formed because of stochastic uncoupling of the leading-strand DNA polymerase from the replication fork DNA helicase, and 2) on the damaged template, nascent leading-strand gaps were generated by replisome lesion skipping. The two pathways differed in that RecF stimulated LexA cleavage during replication of the damaged template, but not normal replication. RecF appears to facilitate RecA filament formation on the leading-strand ssDNA gaps generated by replisome lesion skipping.
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Affiliation(s)
- Kamila K Myka
- Molecular Biology Program, Sloan Kettering Institute Memorial Sloan Kettering Cancer Center, New York, New York USA
| | - Kenneth J Marians
- Molecular Biology Program, Sloan Kettering Institute Memorial Sloan Kettering Cancer Center, New York, New York USA
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24
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Hostetler ZM, Cory MB, Jones CM, Petersson EJ, Kohli RM. The Kinetic and Molecular Basis for the Interaction of LexA and Activated RecA Revealed by a Fluorescent Amino Acid Probe. ACS Chem Biol 2020; 15:1127-1133. [PMID: 31999086 DOI: 10.1021/acschembio.9b00886] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The bacterial DNA damage response (the SOS response) is a key pathway involved in antibiotic evasion and a promising target for combating acquired antibiotic resistance. Activation of the SOS response is controlled by two proteins: the repressor LexA and the DNA damage sensor RecA. Following DNA damage, direct interaction between RecA and LexA leads to derepression of the SOS response. However, the exact molecular details of this interaction remain unknown. Here, we employ the fluorescent unnatural amino acid acridonylalanine (Acd) as a minimally perturbing probe of the E. coli RecA:LexA complex. Using LexA labeled with Acd, we report the first kinetic model for the reversible binding of LexA to activated RecA. We also characterize the effects that specific amino acid truncations or substitutions in LexA have on RecA:LexA binding strength and demonstrate that a mobile loop encoding LexA residues 75-84 comprises a key recognition interface for RecA. Beyond insights into SOS activation, our approach also further establishes Acd as a sensitive fluorescent probe for investigating the dynamics of protein-protein interactions in other complex systems.
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Affiliation(s)
- Zachary M. Hostetler
- Graduate Group in Cell and Molecular Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael B. Cory
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chloe M. Jones
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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25
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Yang HW, Yu M, Lee JH, Chatnaparat T, Zhao Y. The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora. BMC Genomics 2020; 21:261. [PMID: 32228459 PMCID: PMC7106674 DOI: 10.1186/s12864-020-6699-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/24/2020] [Indexed: 01/30/2023] Open
Abstract
Background The nucleotide second messengers, i.e., guanosine tetraphosphate and pentaphosphate [collectively referred to as (p) ppGpp], trigger the stringent response under nutrient starvation conditions and play an essential role in virulence in the fire blight pathogen Erwinia amylovora. Here, we present transcriptomic analyses to uncover the overall effect of (p) ppGpp-mediated stringent response in E. amylovora in the hrp-inducing minimal medium (HMM). Results In this study, we investigated the transcriptomic changes of the (p) ppGpp0 mutant under the type III secretion system (T3SS)-inducing condition using RNA-seq. A total of 1314 differentially expressed genes (DEGs) was uncovered, representing more than one third (36.8%) of all genes in the E. amylovora genome. Compared to the wild-type, the (p) ppGpp0 mutant showed down-regulation of genes involved in peptide ATP-binding cassette (ABC) transporters and virulence-related processes, including type III secretion system (T3SS), biofilm, and motility. Interestingly, in contrast to previous reports, the (p) ppGpp0 mutant showed up-regulation of amino acid biosynthesis genes, suggesting that it might be due to that these amino acid biosynthesis genes are indirectly regulated by (p) ppGpp in E. amylovora or represent specific culturing condition used. Furthermore, the (p) ppGpp0 mutant exhibited up-regulation of genes involved in translation, SOS response, DNA replication, chromosome segregation, as well as biosynthesis of nucleotide, fatty acid and lipid. Conclusion These findings suggested that in HMM environment, E. amylovora might use (p) ppGpp as a signal to activate virulence gene expression, and simultaneously mediate the balance between virulence and survival by negatively regulating DNA replication, translation, cell division, as well as biosynthesis of nucleotide, amino acid, fatty acid, and lipid. Therefore, (p) ppGpp could be a promising target for developing novel control measures to fight against this devastating disease of apples and pears.
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Affiliation(s)
- Ho-Wen Yang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Jae Hoon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Tiyakhon Chatnaparat
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA.
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26
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Marx P, Sang Y, Qin H, Wang Q, Guo R, Pfeifer C, Kreth J, Merritt J. Environmental stress perception activates structural remodeling of extant Streptococcus mutans biofilms. NPJ Biofilms Microbiomes 2020; 6:17. [PMID: 32221309 PMCID: PMC7101444 DOI: 10.1038/s41522-020-0128-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/12/2020] [Indexed: 01/28/2023] Open
Abstract
Transcription regulators from the LexA-like Protein Superfamily control a highly diverse assortment of genetic pathways in response to environmental stress. All characterized members of this family modulate their functionality and stability via a strict coordination with the coprotease function of RecA. Using the LexA-like protein IrvR from Streptococcus mutans, we demonstrate an exception to the RecA paradigm and illustrate how this evolutionary innovation has been coopted to diversify the stress responsiveness of S. mutans biofilms. Using a combination of genetics and biophysical measurements, we demonstrate how non-SOS stresses and SOS stresses each trigger separate regulatory mechanisms that stimulate production of a surface lectin responsible for remodeling the viscoelastic properties of extant biofilms during episodes of environmental stress. These studies demonstrate how changes in the external environment or even anti-biofilm therapeutic agents can activate biofilm-specific adaptive mechanisms responsible for bolstering the integrity of established biofilm communities. Such changes in biofilm community structure are likely to play central roles in the notorious recalcitrance of biofilm infections.
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Affiliation(s)
- Patrick Marx
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Yu Sang
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Hua Qin
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Qingjing Wang
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Rongkai Guo
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Carmem Pfeifer
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Jens Kreth
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Justin Merritt
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239 USA
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Phillips R, Belliveau NM, Chure G, Garcia HG, Razo-Mejia M, Scholes C. Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression. Annu Rev Biophys 2020; 48:121-163. [PMID: 31084583 DOI: 10.1146/annurev-biophys-052118-115525] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is tempting to believe that we now own the genome. The ability to read and rewrite it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles' heel exposed by all of the genomic data that has accrued: We still do not know how to interpret them. Many genes are subject to sophisticated programs of transcriptional regulation, mediated by DNA sequences that harbor binding sites for transcription factors, which can up- or down-regulate gene expression depending upon environmental conditions. This gives rise to an input-output function describing how the level of expression depends upon the parameters of the regulated gene-for instance, on the number and type of binding sites in its regulatory sequence. In recent years, the ability to make precision measurements of expression, coupled with the ability to make increasingly sophisticated theoretical predictions, has enabled an explicit dialogue between theory and experiment that holds the promise of covering this genomic Achilles' heel. The goal is to reach a predictive understanding of transcriptional regulation that makes it possible to calculate gene expression levels from DNA regulatory sequence. This review focuses on the canonical simple repression motif to ask how well the models that have been used to characterize it actually work. We consider a hierarchy of increasingly sophisticated experiments in which the minimal parameter set learned at one level is applied to make quantitative predictions at the next. We show that these careful quantitative dissections provide a template for a predictive understanding of the many more complex regulatory arrangements found across all domains of life.
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Affiliation(s)
- Rob Phillips
- Department of Physics, California Institute of Technology, Pasadena, California, USA; .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Nathan M Belliveau
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Department of Biology, University of Washington, Seattle, Washington 98195, USA
| | - Griffin Chure
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Hernan G Garcia
- Department of Molecular & Cell Biology, Department of Physics, Biophysics Graduate Group, and Institute for Quantitative Biosciences-QB3, University of California, Berkeley, California, USA
| | - Manuel Razo-Mejia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Clarissa Scholes
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
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28
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Silpe JE, Bridges AA, Huang X, Coronado DR, Duddy OP, Bassler BL. Separating Functions of the Phage-Encoded Quorum-Sensing-Activated Antirepressor Qtip. Cell Host Microbe 2020; 27:629-641.e4. [PMID: 32101705 DOI: 10.1016/j.chom.2020.01.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/21/2020] [Accepted: 01/28/2020] [Indexed: 01/21/2023]
Abstract
Quorum sensing is a process of chemical communication that bacteria use to track cell density and coordinate gene expression across a population. Bacteria-infecting viruses, called phages, can encode quorum-sensing components that enable them to integrate host cell density information into the lysis-lysogeny decision. Vibriophage VP882 is one such phage, and activation of its quorum-sensing pathway leads to the production of an antirepressor called Qtip. Qtip interferes with the prophage repressor (cIVP882), leading to host-cell lysis. Here, we show that Qtip interacts with the N terminus of cIVP882, inhibiting both cIVP882 DNA binding and cIVP882 autoproteolysis. Qtip also sequesters cIVP882, localizing it to the poles. Qtip can localize to the poles independently of cIVP882. Alanine-scanning mutagenesis of Qtip shows that its localization and interference with cIVP882 activities are separable. Comparison of Qtip to a canonical phage antirepressor reveals that despite both proteins interacting with their partner repressors, only Qtip drives polar localization.
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Affiliation(s)
- Justin E Silpe
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Andrew A Bridges
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xiuliang Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Daniela R Coronado
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Olivia P Duddy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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Himeoka Y, Mitarai N. Modeling slow-processing of toxin messenger RNAs in type-I toxin-antitoxin systems: post-segregational killing and noise filtering. Phys Biol 2019; 16:026001. [PMID: 30523873 DOI: 10.1088/1478-3975/aaf3e3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In type-I toxin-antitoxin (TA) systems, the action of growth-inhibiting toxin proteins is counteracted by the antitoxin small RNAs (sRNAs) that prevent the translation of toxin messenger RNAs (mRNAs). When a TA module is encoded on a plasmid, the short lifetime of antitoxin sRNA compared to toxin mRNAs mediates post-segregational killing (PSK) that contribute the plasmid maintenance, while some of the chromosomal encoded TA loci have been reported to contribute to persister formation in response to a specific upstream signal. Some of the well studied type-I TA systems such as hok/sok are known to have a rather complex regulatory mechanism. Transcribed full-length toxin mRNAs fold such that the ribosome binding site is not accessible and hence cannot be translated. The mRNAs are slowly processed by RNases, and the truncated mRNAs can be either translated or bound by antitoxin sRNA to be quickly degraded. We analyze the role of this extra processing by a mathematical model. We first consider the PSK scenario, and demonstrate that the extra processing compatibly ensures the high toxin expression upon complete plasmid loss, without inducing toxin expression upon acquisition of a plasmid or decrease of plasmid number to a non-zero number. We further show that the extra processing help filtering the transcription noise, avoiding random activation of toxins in transcriptionally regulated TA systems as seen in chromosomal ones. The present model highlights impacts of the slow processing reaction, offering insights on why the slow processing reactions are commonly identified in multiple type-I TA systems.
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Affiliation(s)
- Yusuke Himeoka
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen, 2100-DK, Denmark
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30
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Raychaudhury P, Marians KJ. The recombination mediator proteins RecFOR maintain RecA* levels for maximal DNA polymerase V Mut activity. J Biol Chem 2018; 294:852-860. [PMID: 30482842 DOI: 10.1074/jbc.ra118.005726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/20/2018] [Indexed: 11/06/2022] Open
Abstract
DNA template damage can potentially block DNA replication. Cells have therefore developed different strategies to repair template lesions. Activation of the bacterial lesion bypass DNA polymerase V (Pol V) requires both the cleavage of the UmuD subunit to UmuD' and the acquisition of a monomer of activated RecA recombinase, forming Pol V Mut. Both of these events are mediated by the generation of RecA* via the formation of a RecA-ssDNA filament during the SOS response. Formation of RecA* is itself modulated by competition with the ssDNA-binding protein (SSB) for binding to ssDNA. Previous observations have demonstrated that RecA filament formation on SSB-coated DNA can be favored in the presence of the recombination mediator proteins RecF, RecO, and RecR. We show here using purified proteins that in the presence of SSB and RecA, a stable RecA-ssDNA filament is not formed, although sufficient RecA* is generated to support some activation of Pol V. The presence of RecFOR increased RecA* generation and allowed Pol V to synthesize longer DNA products and to elongate from an unpaired primer terminus opposite template damage, also without the generation of a stable RecA-ssDNA filament.
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Affiliation(s)
- Paromita Raychaudhury
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Kenneth J Marians
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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31
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Otoupal PB, Erickson KE, Escalas-Bordoy A, Chatterjee A. CRISPR Perturbation of Gene Expression Alters Bacterial Fitness under Stress and Reveals Underlying Epistatic Constraints. ACS Synth Biol 2017; 6:94-107. [PMID: 27529436 DOI: 10.1021/acssynbio.6b00050] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The evolution of antibiotic resistance has engendered an impending global health crisis that necessitates a greater understanding of how resistance emerges. The impact of nongenetic factors and how they influence the evolution of resistance is a largely unexplored area of research. Here we present a novel application of CRISPR-Cas9 technology for investigating how gene expression governs the adaptive pathways available to bacteria during the evolution of resistance. We examine the impact of gene expression changes on bacterial adaptation by constructing a library of deactivated CRISPR-Cas9 synthetic devices to tune the expression of a set of stress-response genes in Escherichia coli. We show that artificially inducing perturbations in gene expression imparts significant synthetic control over fitness and growth during stress exposure. We present evidence that these impacts are reversible; strains with synthetically perturbed gene expression regained wild-type growth phenotypes upon stress removal, while maintaining divergent growth characteristics under stress. Furthermore, we demonstrate a prevailing trend toward negative epistatic interactions when multiple gene perturbations are combined simultaneously, thereby posing an intrinsic constraint on gene expression underlying adaptive trajectories. Together, these results emphasize how CRISPR-Cas9 can be employed to engineer gene expression changes that shape bacterial adaptation, and present a novel approach to synthetically control the evolution of antimicrobial resistance.
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Affiliation(s)
- Peter B. Otoupal
- Department
of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Keesha E. Erickson
- Department
of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Antoni Escalas-Bordoy
- Department
of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Anushree Chatterjee
- Department
of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
- BioFrontiers
Institute, University of Colorado at Boulder, Boulder, Colorado 80309, United States
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Sergeeva S, Demidova E, Sinitsyna O, Goryachkovskaya T, Bryanskaya A, Semenov A, Meshcheryakova I, Dianov G, Popik V, Peltek S. 2.3THz radiation: Absence of genotoxicity/mutagenicity in Escherichia coli and Salmonella typhimurium. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2016; 803-804:34-8. [PMID: 27265378 DOI: 10.1016/j.mrgentox.2016.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 05/06/2016] [Accepted: 05/12/2016] [Indexed: 11/18/2022]
Abstract
The mutagenicity and genotoxicity in bacteria of 2.3THz radiation (THz) produced by a free-electron laser (NovoFEL) were evaluated; exposures were 5, 10, or 15min at average power 1.4W/cm(2). Two Ames mutagenicity test strains of Salmonella typhimurium, TA98 and TA102, were used. For the genotoxicity test, we measured SOS induction in Escherichia coli PQ37. No significant differences were found between exposed and control cells, indicating that THz radiation is neither mutagenic nor genotoxic under these conditions. Nevertheless, a small increase in total cell number of S. typhimurium after 15min exposure, and an increase in β-galactosidase and alkaline phosphatase activities in E.coli PQ37, were observed, indicating some effect of THz radiation on cell metabolism. We also examined the combined effect of 4-NQO (8μM; positive control) and THz exposure (5min) on genotoxicity in E.coli PQ37. Unexpectedly, THz radiation decreased 4-NQO genotoxicity.
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Affiliation(s)
- Svetlana Sergeeva
- Institute of Cytology and Genetics RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Elisaveta Demidova
- Institute of Cytology and Genetics RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Olga Sinitsyna
- Institute of Cytology and Genetics RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Tatiana Goryachkovskaya
- Institute of Cytology and Genetics RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Alla Bryanskaya
- Institute of Cytology and Genetics RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Artem Semenov
- Budker Institute of Nucleic Physics SB RAS, Prospekt Lavrentyeva 11, Novosibirsk, 630090, Russia
| | - Irina Meshcheryakova
- Institute of Cytology and Genetics RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Grigory Dianov
- Oxford Institute for Radiation Oncology, University of Oxford, Department of Oncology, Roosevelt Drive, OX37DQ Oxford, UK
| | - Vasiliy Popik
- Budker Institute of Nucleic Physics SB RAS, Prospekt Lavrentyeva 11, Novosibirsk, 630090, Russia
| | - Sergey Peltek
- Institute of Cytology and Genetics RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
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Witkowski TA, Grice AN, Stinnett DB, Wells WK, Peterson MA, Hare JM. UmuDAb: An Error-Prone Polymerase Accessory Homolog Whose N-Terminal Domain Is Required for Repression of DNA Damage Inducible Gene Expression in Acinetobacter baylyi. PLoS One 2016; 11:e0152013. [PMID: 27010837 PMCID: PMC4807011 DOI: 10.1371/journal.pone.0152013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 03/08/2016] [Indexed: 12/01/2022] Open
Abstract
In many bacteria, the DNA damage response induces genes (SOS genes) that were repressed by LexA. LexA represses transcription by binding to SOS promoters via a helix-turn-helix motif in its N-terminal domain (NTD). Upon DNA damage, LexA cleaves itself and allows induction of transcription. In Acinetobacter baumannii and Acinetobacter baylyi, multiple genes are induced by DNA damage, and although the Acinetobacter genus lacks LexA, a homolog of the error-prone polymerase subunit UmuD, called UmuDAb, regulates some DNA damage-induced genes. The mechanism of UmuDAb regulation has not been determined. We constructed UmuDAb mutant strains of A. baylyi to test whether UmuDAb mediates gene regulation through LexA-like repressor actions consisting of relief of repression through self-cleavage after DNA damage. Real-time quantitative PCR experiments in both a null umuDAb mutant and an NTD mutant showed that the DNA damage-inducible, UmuDAb-regulated gene ddrR was highly expressed even in the absence of DNA damage. Protein modeling identified a potential LexA-like helix-turn-helix structure in the UmuDAb NTD, which when disrupted, also relieved ddrR and umuDAb repression under non-inducing conditions. Mutations in a putative SOS box in the shared umuDAb-ddrR promoter region similarly relieved these genes’ repression under non-inducing conditions. Conversely, cells possessing a cleavage-deficient UmuDAb were unable to induce gene expression after MMC-mediated DNA damage. This evidence of a UmuDAb repressor mechanism was contrasted with the failure of umuDAb to complement an Escherichia coli umuD mutant for UmuD error-prone DNA replication activity. Similarly, A. baumannii null umuDAb mutant cells did not have a reduced UmuDˊ2UmuC-mediated mutation rate after DNA damage, suggesting that although this UmuDAb protein may have evolved from a umuDC operon in this genus, it now performs a LexA-like repressor function for a sub-set of DNA damage-induced genes.
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Affiliation(s)
- Travis A. Witkowski
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States of America
| | - Alison N. Grice
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States of America
| | - DeAnna B. Stinnett
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States of America
| | - Whitney K. Wells
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States of America
| | - Megan A. Peterson
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States of America
| | - Janelle M. Hare
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States of America
- * E-mail:
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Fornelos N, Browning DF, Butala M. The Use and Abuse of LexA by Mobile Genetic Elements. Trends Microbiol 2016; 24:391-401. [PMID: 26970840 DOI: 10.1016/j.tim.2016.02.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/12/2016] [Accepted: 02/18/2016] [Indexed: 11/15/2022]
Abstract
The SOS response is an essential process for responding to DNA damage in bacteria. The expression of SOS genes is under the control of LexA, a global transcription factor that undergoes self-cleavage during stress to allow the expression of DNA repair functions and delay cell division until the damage is rectified. LexA also regulates genes that are not part of this cell rescue program, and the induction of bacteriophages, the movement of pathogenicity islands, and the expression of virulence factors and bacteriocins are all controlled by this important transcription factor. Recently it has emerged that when regulating the expression of genes from mobile genetic elements (MGEs), LexA often does so in concert with a corepressor. This accessory regulator can either be a host-encoded global transcription factor, which responds to various metabolic changes, or a factor that is encoded for by the MGE itself. Thus, the coupling of LexA-mediated regulation to a secondary transcription factor not only detaches LexA from its primary SOS role, but also fine-tunes gene expression from the MGE, enabling it to respond to multiple stresses. Here we discuss the mechanisms of such coordinated regulation and its implications for cells carrying such MGEs.
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Affiliation(s)
- Nadine Fornelos
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, PO Box 35, F-40014 Jyvaskyla, Finland.
| | - Douglas F Browning
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia.
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Khodursky A, Guzmán EC, Hanawalt PC. Thymineless Death Lives On: New Insights into a Classic Phenomenon. Annu Rev Microbiol 2015; 69:247-63. [PMID: 26253395 DOI: 10.1146/annurev-micro-092412-155749] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The primary mechanisms by which bacteria lose viability when deprived of thymine have been elusive for over half a century. Early research focused on stalled replication forks and the deleterious effects of uracil incorporation into DNA from thymidine-deficient nucleotide pools. The initiation of the replication cycle and origin-proximal DNA degradation during thymine starvation have now been quantified via whole-genome microarrays and other approaches. These advances have fostered innovative models and informative experiments in bacteria since this topic was last reviewed. Given that thymineless death is similar in mammalian cells and that certain antibacterial and chemotherapeutic drugs elicit thymine deficiency, a mechanistic understanding of this phenomenon might have valuable biomedical applications.
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Affiliation(s)
- Arkady Khodursky
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108;
| | - Elena C Guzmán
- Departamento de Bioquímica Biología Molecular y Genética, Universidad de Extremadura, 06071 Badajoz, Spain;
| | - Philip C Hanawalt
- Department of Biology, Stanford University, Stanford, California 94305;
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36
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Asplund-Samuelsson J. The art of destruction: revealing the proteolytic capacity of bacterial caspase homologs. Mol Microbiol 2015; 98:1-6. [PMID: 26123017 DOI: 10.1111/mmi.13111] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2015] [Indexed: 12/29/2022]
Abstract
Caspases are proteases that initiate and execute programmed cell death in animal tissues, thereby facilitating multicellular development and survival. While caspases are unique to metazoans and specifically cleave substrates at aspartic acid residues, homologs are found in protozoa, plants, algae, fungi, bacteria and archaea, and show specificity for basic residues. In this issue of Molecular Microbiology, Klemenčič and colleagues present the first biochemical characterization of a bacterial caspase homolog, classified as an orthocaspase. By expressing the gene MaOC1 from the cyanobacterium Microcystis aeruginosa PCC 7806 in Escherichia coli, the authors discovered specificity for substrates with arginine in the P1 position. The protein requires autocatalytic processing to become active and is dependent on an intact histidine-cysteine dyad. These results significantly extend our knowledge of the specificities of bacterial caspase homologs, which are known to be highly diverse in protein domain architectures and active site mutations. Although bacterial programmed cell death is one possible area of action, the function of most bacterial caspase homologs remains unexplored. Cyanobacteria represent the best studied group in terms of prokaryotic caspase-like proteins both genomically and experimentally, and thereby provide a suitable platform for further investigations into activation, regulation and physiological roles of orthocaspases.
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Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University, P-Box 1031, 171 21, Solna, Sweden
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Fornelos N, Butala M, Hodnik V, Anderluh G, Bamford JK, Salas M. Bacteriophage GIL01 gp7 interacts with host LexA repressor to enhance DNA binding and inhibit RecA-mediated auto-cleavage. Nucleic Acids Res 2015; 43:7315-29. [PMID: 26138485 PMCID: PMC4551915 DOI: 10.1093/nar/gkv634] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/05/2015] [Indexed: 01/22/2023] Open
Abstract
The SOS response in Eubacteria is a global response to DNA damage and its activation is increasingly associated with the movement of mobile genetic elements. The temperate phage GIL01 is induced into lytic growth using the host's SOS response to genomic stress. LexA, the SOS transcription factor, represses bacteriophage transcription by binding to a set of SOS boxes in the lysogenic promoter P1. However, LexA is unable to efficiently repress GIL01 transcription unless the small phage-encoded protein gp7 is also present. We found that gp7 forms a stable complex with LexA that enhances LexA binding to phage and cellular SOS sites and interferes with RecA-mediated auto-cleavage of LexA, the key step in the initiation of the SOS response. Gp7 did not bind DNA, alone or when complexed with LexA. Our findings suggest that gp7 induces a LexA conformation that favors DNA binding but disfavors LexA auto-cleavage, thereby altering the dynamics of the cellular SOS response. This is the first account of an accessory factor interacting with LexA to regulate transcription.
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Affiliation(s)
- Nadine Fornelos
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Centre of Excellence in Biological Interactions, PO Box 35, F-40014 Jyvaskyla, Finland Instituto de Biología Molecular 'Eladio Viñuela' (CSIC), Centro de Biología Molecular 'Severo Ochoa' (CSIC-Universidad Autónoma de Madrid), Cantoblanco, 28049 Madrid, Spain
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Vesna Hodnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Jaana K Bamford
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Centre of Excellence in Biological Interactions, PO Box 35, F-40014 Jyvaskyla, Finland
| | - Margarita Salas
- Instituto de Biología Molecular 'Eladio Viñuela' (CSIC), Centro de Biología Molecular 'Severo Ochoa' (CSIC-Universidad Autónoma de Madrid), Cantoblanco, 28049 Madrid, Spain
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LexA protein of cyanobacterium Anabaena sp. strain PCC7120 exhibits in vitro pH-dependent and RecA-independent autoproteolytic activity. Int J Biochem Cell Biol 2015; 59:84-93. [DOI: 10.1016/j.biocel.2014.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/27/2014] [Accepted: 12/08/2014] [Indexed: 02/04/2023]
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Bugay AN, Krasavin EA, Parkhomenko AY, Vasilyeva MA. Modeling nucleotide excision repair and its impact on UV-induced mutagenesis during SOS-response in bacterial cells. J Theor Biol 2015; 364:7-20. [DOI: 10.1016/j.jtbi.2014.08.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/31/2014] [Accepted: 08/22/2014] [Indexed: 02/01/2023]
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Mo CY, Birdwell LD, Kohli RM. Specificity determinants for autoproteolysis of LexA, a key regulator of bacterial SOS mutagenesis. Biochemistry 2014; 53:3158-68. [PMID: 24779472 PMCID: PMC4030785 DOI: 10.1021/bi500026e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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Bacteria utilize the tightly regulated
stress response (SOS) pathway
to respond to a variety of genotoxic agents, including antimicrobials.
Activation of the SOS response is regulated by a key repressor-protease,
LexA, which undergoes autoproteolysis in the setting of stress, resulting
in derepression of SOS genes. Remarkably, genetic inactivation of
LexA’s self-cleavage activity significantly decreases acquired
antibiotic resistance in infection models and renders bacteria hypersensitive
to traditional antibiotics, suggesting that a mechanistic study of
LexA could help inform its viability as a novel target for combating
acquired drug resistance. Despite structural insights into LexA, a
detailed knowledge of the enzyme’s protease specificity is
lacking. Here, we employ saturation and positional scanning mutagenesis
on LexA’s internal cleavage region to analyze >140 mutants
and generate a comprehensive specificity profile of LexA from the
human pathogen Pseudomonas aeruginosa (LexAPa). We find that the LexAPa active site possesses a unique mode of substrate recognition.
Positions P1–P3 prefer small hydrophobic residues that suggest
specific contacts with the active site, while positions P5 and P1′
show a preference for flexible glycine residues that may facilitate
the conformational change that permits autoproteolysis. We further
show that stabilizing the β-turn within the cleavage region
enhances LexA autoproteolytic activity. Finally, we identify permissive
positions flanking the scissile bond (P4 and P2′) that are
tolerant to extensive mutagenesis. Our studies shed light on the active
site architecture of the LexA autoprotease and provide insights that
may inform the design of probes of the SOS pathway.
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Affiliation(s)
- Charlie Y Mo
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania , 3610 Hamilton Walk, Philadelphia, Pennsylvania 19014, United States
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41
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The LexA regulated genes of the Clostridium difficile. BMC Microbiol 2014; 14:88. [PMID: 24713082 PMCID: PMC4234289 DOI: 10.1186/1471-2180-14-88] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/27/2014] [Indexed: 01/05/2023] Open
Abstract
Background The SOS response including two main proteins LexA and RecA, maintains the integrity of bacterial genomes after DNA damage due to metabolic or environmental assaults. Additionally, derepression of LexA-regulated genes can result in mutations, genetic exchange and expression of virulence factors. Here we describe the first comprehensive description of the in silico LexA regulon in Clostridium difficile, an important human pathogen. Results We grouped thirty C. difficile strains from different ribotypes and toxinotypes into three clusters according to lexA gene/protein variability. We applied in silico analysis coupled to surface plasmon resonance spectroscopy (SPR) and determined 16 LexA binding sites in C. difficile. Our data indicate that strains within the cluster, as defined by LexA variability, harbour several specific LexA regulon genes. In addition to core SOS genes: lexA, recA, ruvCA and uvrBA, we identified a LexA binding site on the pathogenicity locus (PaLoc) and in the putative promoter region of several genes involved in housekeeping, sporulation and antibiotic resistance. Conclusions Results presented here suggest that in C. difficile LexA is not merely a regulator of the DNA damage response genes but also controls the expression of dozen genes involved in various other biological functions. Our in vitro results indicate that in C. difficile inactivation of LexA repressor depends on repressor`s dissociation from the operators. We report that the repressor`s dissociation rates from operators differentiate, thus the determined LexA-DNA dissociation constants imply on the timing of SOS gene expression in C. difficile.
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Bellio P, Brisdelli F, Perilli M, Sabatini A, Bottoni C, Segatore B, Setacci D, Amicosante G, Celenza G. Curcumin inhibits the SOS response induced by levofloxacin in Escherichia coli. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2014; 21:430-434. [PMID: 24252336 DOI: 10.1016/j.phymed.2013.10.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/04/2013] [Accepted: 10/05/2013] [Indexed: 06/02/2023]
Abstract
The role of RecA protein in bacterial resistance to antibiotics makes this protein attractive from a pharmacological point of view. In this study we demonstrate that curcumin is able to inhibit the SOS response in Escherichia coli induced by levofloxacin. The blaTEM-1 gene has been placed under the control of the LexA-binding box and used as reporter gene. The expression of TEM-1 β-lactamase enzyme was increased in the presence of ssDNA induced by levofloxacin, while, the presence of curcumin at 8μg/ml, reduced dramatically the expression of the reporter gene. Moreover a simple microplate assay suitable for high-throughput screening has been developed.
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Affiliation(s)
- Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Italy
| | - Fabrizia Brisdelli
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Italy
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Italy
| | - Alessia Sabatini
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Italy
| | - Carlo Bottoni
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Italy
| | - Bernardetta Segatore
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Italy
| | - Domenico Setacci
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Italy
| | - Gianfranco Amicosante
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Italy
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Italy.
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Fonseca LS, da Silva JB, Milanez JS, Monteiro-Vitorello CB, Momo L, de Morais ZM, Vasconcellos SA, Marques MV, Ho PL, da Costa RMA. Leptospira interrogans serovar copenhageni harbors two lexA genes involved in SOS response. PLoS One 2013; 8:e76419. [PMID: 24098496 PMCID: PMC3789691 DOI: 10.1371/journal.pone.0076419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 08/28/2013] [Indexed: 11/24/2022] Open
Abstract
Bacteria activate a regulatory network in response to the challenges imposed by DNA damage to genetic material, known as the SOS response. This system is regulated by the RecA recombinase and by the transcriptional repressor lexA. Leptospira interrogans is a pathogen capable of surviving in the environment for weeks, being exposed to a great variety of stress agents and yet retaining its ability to infect the host. This study aims to investigate the behavior of L. interrogans serovar Copenhageni after the stress induced by DNA damage. We show that L. interrogans serovar Copenhageni genome contains two genes encoding putative LexA proteins (lexA1 and lexA2) one of them being potentially acquired by lateral gene transfer. Both genes are induced after DNA damage, but the steady state levels of both LexA proteins drop, probably due to auto-proteolytic activity triggered in this condition. In addition, seven other genes were up-regulated following UV-C irradiation, recA, recN, dinP, and four genes encoding hypothetical proteins. This set of genes is potentially regulated by LexA1, as it showed binding to their promoter regions. All these regions contain degenerated sequences in relation to the previously described SOS box, TTTGN 5CAAA. On the other hand, LexA2 was able to bind to the palindrome TTGTAN10TACAA, found in its own promoter region, but not in the others. Therefore, the L. interrogans serovar Copenhageni SOS regulon may be even more complex, as a result of LexA1 and LexA2 binding to divergent motifs. New possibilities for DNA damage response in Leptospira are expected, with potential influence in other biological responses such as virulence.
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Affiliation(s)
- Luciane S Fonseca
- Centro de Biotecnologia, Instituto Butantan, São Paulo, Brazil ; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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Kovačič L, Paulič N, Leonardi A, Hodnik V, Anderluh G, Podlesek Z, Žgur-Bertok D, Križaj I, Butala M. Structural insight into LexA-RecA* interaction. Nucleic Acids Res 2013; 41:9901-10. [PMID: 23965307 PMCID: PMC3834820 DOI: 10.1093/nar/gkt744] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RecA protein is a hallmark for the bacterial response to insults inflicted on DNA. It catalyzes the strand exchange step of homologous recombination and stimulates self-inactivation of the LexA transcriptional repressor. Importantly, by these activities, RecA contributes to the antibiotic resistance of bacteria. An original way to decrease the acquisition of antibiotic resistance would be to block RecA association with LexA. To engineer inhibitors of LexA–RecA complex formation, we have mapped the interaction area between LexA and active RecA–ssDNA filament (RecA*) and generated a three-dimensional model of the complex. The model revealed that one subunit of the LexA dimer wedges into a deep helical groove of RecA*, forming multiple interaction sites along seven consecutive RecA protomers. Based on the model, we predicted that LexA in its DNA-binding conformation also forms a complex with RecA* and that the operator DNA sterically precludes interaction with RecA*, which guides the induction of SOS gene expression. Moreover, the model shows that besides the catalytic C-terminal domain of LexA, its N-terminal DNA-binding domain also interacts with RecA*. Because all the model-based predictions have been confirmed experimentally, the presented model offers a validated insight into the critical step of the bacterial DNA damage response.
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Affiliation(s)
- Lidija Kovačič
- Department of Molecular and Biomedical Sciences, JoŽef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia, Department of Biology, University of Ljubljana, Biotechnical Faculty, Večna pot 111, 1000 Ljubljana, Slovenia, National Institute of Chemistry, 1000 Ljubljana, Slovenia, Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia and Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
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45
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Role of cis-acting sites in stimulation of the phage λ P(RM) promoter by CI-mediated looping. J Bacteriol 2013; 195:3401-11. [PMID: 23708136 DOI: 10.1128/jb.02148-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The lysogenic state of phage λ is maintained by the CI repressor. CI binds to three operators each in the right operator (O(R)) and left operator (O(L)) regions, which lie 2.4 kb apart. At moderate CI levels, the predominant binding pattern is two dimers of CI bound cooperatively at each regulatory region. The resulting tetramers can then interact, forming an octamer and a loop of the intervening DNA. CI is expressed from the P(RM) promoter, which lies in the O(R) region and is subjected to multiple regulatory controls. Of these, the most recently discovered is stimulation by loop formation. In this work, we have investigated the mechanism by which looping stimulates P(RM). We find that two cis-acting sites lying in the O(L) region are involved. One site, an UP element, is required for stimulation. Based on the behavior of other promoters with UP elements located upstream of the -35 region, we suggest that a subunit of RNA polymerase (RNAP) bound at P(RM) binds to the UP element located in the O(L) region. In addition, adjacent to the UP element lies a binding site for integration host factor (IHF); this site plays a less critical role but is required for stimulation of the weak prm240 allele. A loop with CI at the O(L)2 and O(L)3 operators does not stimulate P(RM), while one with CI only at O(L)2 provides some stimulation. We discuss possible mechanisms for stimulation.
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46
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Steffen SE, Bryant FR. Altered nucleotide cofactor-dependent properties of the mutant [S240K]RecA protein. Biochem Biophys Res Commun 2012; 421:527-31. [PMID: 22521886 DOI: 10.1016/j.bbrc.2012.04.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 04/06/2012] [Indexed: 10/28/2022]
Abstract
Two mutant Escherichia coli RecA proteins were prepared in which the ATP active site residue, Ser240, was replaced with asparagine and lysine (these amino acids are found in the corresponding positions in other bacterial RecA proteins). The S240N mutation had no discernible effect on the ATP-dependent activities of the RecA protein, indicating that serine and asparagine are functionally interchangeable at position 240. The S240K mutation, in contrast, essentially eliminated the ability of the RecA protein to utilize ATP as a nucleotide cofactor. The [S240K]RecA protein was able to catalyze the hydrolysis of dATP, however, suggesting that the absence of the 2'-hydroxyl group reduced an inhibitory interaction with the Lys240 side chain. Interestingly, the [S240K]RecA protein was able to promote an efficient LexA cleavage reaction but exhibited no strand exchange activity when dATP was provided as the nucleotide cofactor. This apparent separation of function may be attributable to the elevated S(0.5) value for dATP for the [S240K]RecA protein (490 μM, compared to 20-30 μM for the wild type and [S240N]RecA proteins), and may reflect a differential dependence of the LexA co-protease and DNA strand exchange activities on the nucleotide cofactor-mediated stabilization of the functionally-active state of the RecA-ssDNA complex.
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Affiliation(s)
- Scott E Steffen
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21205, United States
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47
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Etoh H, Yasuda M, Akimoto T. Signal enhancement by a multi-layered substrate for mutagen detection using an SOS response-induced green fluorescent protein in genetically modified Escherichia coli. ANAL SCI 2011; 27:1179-83. [PMID: 22156243 DOI: 10.2116/analsci.27.1179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this paper, we describe a method to enhance the fluorescence signal of mutagen detection using SOS response-induced green fluorescence protein (GFP) in genetically modified Escherichia coli using a multi-layered substrate. To generate E. coli that express SOS response-induced GFP, we constructed a plasmid carrying the RecA promoter located upstream of the GFP gene and used it to transform E. coli BL21. The transformed strain was incubated with mitomycin C (MMC), a typical mutagen, and then immobilized on a multi-layered substrate with Ag and a thin Al(2)O(3) layer on a glass slide. Since the multi-layered substrate technique is an optical technique with potential to enhance the fluorescence of fluorophore placed on top of the substrate, the multi-layered substrate was expected to improve the fluorescence signal of mutagen detection. We obtained an average 14-fold fluorescence enhancement of MMC-induced GFP in the concentration range 1 to 1000 ng/ml. In addition, the lower detection limit of MMC was improved using this technique, and was estimated to be 1 ng/ml because of an enlargement of the difference between the blank and the signal of 1 ng/ml of MMC.
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Affiliation(s)
- Hiroki Etoh
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachiouji, Tokyo 192–0982, Japan
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48
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Göhler AK, Kökpinar Ö, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K, Kaleta C. More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli. BMC SYSTEMS BIOLOGY 2011; 5:197. [PMID: 22168595 PMCID: PMC3265435 DOI: 10.1186/1752-0509-5-197] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 12/14/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND The pyruvate dehydrogenase regulator protein (PdhR) of Escherichia coli acts as a transcriptional regulator in a pyruvate dependent manner to control central metabolic fluxes. However, the complete PdhR regulon has not yet been uncovered. To achieve an extended understanding of its gene regulatory network, we combined large-scale network inference and experimental verification of results obtained by a systems biology approach. RESULTS 22 new genes contained in two operons controlled by PdhR (previously only 20 regulatory targets in eight operons were known) were identified by analysing a large-scale dataset of E. coli from the Many Microbes Microarray Database and novel expression data from a pdhR knockout strain, as well as a PdhR overproducing strain. We identified a regulation of the glycolate utilization operon glcDEFGBA using chromatin immunoprecipitation and gel shift assays. We show that this regulation could be part of a cross-induction between genes necessary for acetate and pyruvate utilisation controlled through PdhR. Moreover, a link of PdhR regulation to the replication machinery of the cell via control of the transcription of the dcw-cluster was verified in experiments. This augments our knowledge of the functions of the PdhR-regulon and demonstrates its central importance for further cellular processes in E. coli. CONCLUSIONS We extended the PdhR regulon by 22 new genes contained in two operons and validated the regulation of the glcDEFGBA operon for glycolate utilisation and the dcw-cluster for cell division proteins experimentally. Our results provide, for the first time, a plausible regulatory link between the nutritional status of the cell and cell replication mediated by PdhR.
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Butala M, Klose D, Hodnik V, Rems A, Podlesek Z, Klare JP, Anderluh G, Busby SJW, Steinhoff HJ, Zgur-Bertok D. Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response. Nucleic Acids Res 2011; 39:6546-57. [PMID: 21576225 PMCID: PMC3159453 DOI: 10.1093/nar/gkr265] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The bacterial SOS response is essential for the maintenance of genomes, and also modulates antibiotic resistance and controls multidrug tolerance in subpopulations of cells known as persisters. In Escherichia coli, the SOS system is controlled by the interplay of the dimeric LexA transcriptional repressor with an inducer, the active RecA filament, which forms at sites of DNA damage and activates LexA for self-cleavage. Our aim was to understand how RecA filament formation at any chromosomal location can induce the SOS system, which could explain the mechanism for precise timing of induction of SOS genes. Here, we show that stimulated self-cleavage of the LexA repressor is prevented by binding to specific DNA operator targets. Distance measurements using pulse electron paramagnetic resonance spectroscopy reveal that in unbound LexA, the DNA-binding domains sample different conformations. One of these conformations is captured when LexA is bound to operator targets and this precludes interaction by RecA. Hence, the conformational flexibility of unbound LexA is the key element in establishing a co-ordinated SOS response. We show that, while LexA exhibits diverse dissociation rates from operators, it interacts extremely rapidly with DNA target sites. Modulation of LexA activity changes the occurrence of persister cells in bacterial populations.
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Affiliation(s)
- Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia.
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50
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Little JW, Michalowski CB. Stability and instability in the lysogenic state of phage lambda. J Bacteriol 2010; 192:6064-76. [PMID: 20870769 PMCID: PMC2976446 DOI: 10.1128/jb.00726-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/11/2010] [Indexed: 12/26/2022] Open
Abstract
Complex gene regulatory circuits exhibit emergent properties that are difficult to predict from the behavior of the components. One such property is the stability of regulatory states. Here we analyze the stability of the lysogenic state of phage λ. In this state, the virus maintains a stable association with the host, and the lytic functions of the virus are repressed by the viral CI repressor. This state readily switches to the lytic pathway when the host SOS system is induced. A low level of SOS-dependent switching occurs without an overt stimulus. We found that the intrinsic rate of switching to the lytic pathway, measured in a host lacking the SOS response, was almost undetectably low, probably less than 10(-8)/generation. We surmise that this low rate has not been selected directly during evolution but results from optimizing the rate of switching in a wild-type host over the natural range of SOS-inducing conditions. We also analyzed a mutant, λprm240, in which the promoter controlling CI expression was weakened, rendering lysogens unstable. Strikingly, the intrinsic stability of λprm240 lysogens depended markedly on the growth conditions; lysogens grown in minimal medium were nearly stable but switched at high rates when grown in rich medium. These effects on stability likely reflect corresponding effects on the strength of the prm240 promoter, measured in an uncoupled assay system. Several derivatives of λprm240 with altered stabilities were characterized. This mutant and its derivatives afford a model system for further analysis of stability.
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Affiliation(s)
- John W Little
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA.
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