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Li L, Guo B, Dai L, Liu C, Lin Z. Ebselen and TPI-1, as RecG helicase inhibitors, potently enhance the susceptibility of Pseudomonas aeruginosa to DNA damage agents. Biochem Pharmacol 2024; 222:116051. [PMID: 38354956 DOI: 10.1016/j.bcp.2024.116051] [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: 11/03/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
Holliday junction (HJ) is a four-way structured DNA intermediate in processes of homologous recombination and DNA double-stranded break (DSB) repair. In bacteria, HJs are processed via either the RuvABC or RecG-dependent pathways. In addition, RecG also plays a critical role in the reactivation of stalled replication forks, making it an attractive target for antibacterial drug development. Here, we conducted a high-throughput screening targeting the RecG helicase from a common opportunistic pathogen Pseudomonas aeruginosa (Pa). From a library containing 7920 compounds, we identified Ebselen and TPI-1 (2',5'-Dichloro-[1,1'-biphenyl]-2,5-dione) as two potent PaRecG inhibitors, with IC50 values of 0.31 ± 0.02 μM and 1.16 ± 0.06 μM, respectively. Further biochemical analyses suggested that both Ebselen and TPI-1 inhibited the ATPase activity of PaRecG, and hindered its binding to HJ DNA with high selectivity. These compounds, when combined with our previously reported RuvAB inhibitors, resulted in more severe DNA repair defects than the individual treatment, and potently enhanced the susceptibility of P. aeruginosa to the DNA damage agents. This work reports novel small molecule inhibitors of RecG, offering valuable chemical tools for advancing our understanding of RecG's function and mechanism. Additionally, these inhibitors might be further developed as promising antibacterial agents in the fight against P. aeruginosa infections.
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Affiliation(s)
- Longheng Li
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Binbin Guo
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Lin Dai
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Chun Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China.
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, Fuzhou 350108, China.
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Zerouki C, Bensalah F, Kuittinen S, Pappinen A, Turunen O. Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara. BMC Genomics 2021; 22:578. [PMID: 34315408 PMCID: PMC8317367 DOI: 10.1186/s12864-021-07866-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sahara is one of the largest deserts in the world. The harsh climatic conditions, especially high temperature and aridity lead to unique adaptation of organisms, which could be a potential source of new metabolites. In this respect, two Saharan soils from El Oued Souf and Beni Abbes in Algeria were collected. The bacterial isolates were selected by screening for antibacterial, antifungal, and enzymatic activities. The whole genomes of the two native Saharan strains were sequenced to study desert Streptomyces microbiology and ecology from a genomic perspective. RESULTS Strains Babs14 (from Beni Abbes, Algeria) and Osf17 (from El Oued Souf, Algeria) were initially identified by 16S rRNA sequencing as belonging to the Streptomyces genus. The whole genome sequencing of the two strains was performed using Pacific Biosciences Sequel II technology (PacBio), which showed that Babs14 and Osf17 have a linear chromosome of 8.00 Mb and 7.97 Mb, respectively. The number of identified protein coding genes was 6910 in Babs14 and 6894 in Osf17. No plasmids were found in Babs14, whereas three plasmids were detected in Osf17. Although the strains have different phenotypes and are from different regions, they showed very high similarities at the DNA level. The two strains are more similar to each other than either is to the closest database strain. The search for potential secondary metabolites was performed using antiSMASH and predicted 29 biosynthetic gene clusters (BGCs). Several BGCs and proteins were related to the biosynthesis of factors needed in response to environmental stress in temperature, UV light and osmolarity. CONCLUSION The genome sequencing of Saharan Streptomyces strains revealed factors that are related to their adaptation to an extreme environment and stress conditions. The genome information provides tools to study ecological adaptation in a desert environment and to explore the bioactive compounds of these microorganisms. The two whole genome sequences are among the first to be sequenced for the Streptomyces genus of Algerian Sahara. The present research was undertaken as a first step to more profoundly explore the desert microbiome.
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Affiliation(s)
- Chahira Zerouki
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland.
- Laboratory of Microbial Genetics, Department of Biology, University ORAN 1, 31000, Oran, Algeria.
| | - Farid Bensalah
- Laboratory of Microbial Genetics, Department of Biology, University ORAN 1, 31000, Oran, Algeria
| | - Suvi Kuittinen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland
| | - Ari Pappinen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland
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Najah S, Saulnier C, Pernodet JL, Bury-Moné S. Design of a generic CRISPR-Cas9 approach using the same sgRNA to perform gene editing at distinct loci. BMC Biotechnol 2019; 19:18. [PMID: 30894153 PMCID: PMC6425556 DOI: 10.1186/s12896-019-0509-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CRISPR/Cas (clustered regularly interspaced short palindromic repeat and CRISPR-associated nucleases) based technologies have revolutionized genome engineering. While their use for prokaryotic genome editing is expanding, some limitations remain such as possible off-target effects and design constraints. These are compounded when performing systematic genome editing at distinct loci or when targeting repeated sequences (e.g. multicopy genes or mobile genetic elements). To overcome these limitations, we designed an approach using the same sgRNA and CRISPR-Cas9 system to independently perform gene editing at different loci. RESULTS We developed a two-step procedure based on the introduction by homologous recombination of 'bait' DNA at the vicinity of a gene copy of interest before inducing CRISPR-Cas9 activity. The introduction of a genetic tool encoding a CRISPR-Cas9 complex targeting this 'bait' DNA induces a double strand break near the copy of interest. Its repair by homologous recombination can lead either to reversion or gene copy-specific editing. The relative frequencies of these events are linked to the impact of gene editing on cell fitness. In our study, we used this technology to successfully delete the native copies of two xenogeneic silencers lsr2 paralogs in Streptomyces ambofaciens. We observed that one of these paralogs is a candidate-essential gene since its native locus can be deleted only in the presence of an extra copy. CONCLUSION By targeting 'bait' DNA, we designed a 'generic' CRISPR-Cas9 toolkit that can be used to edit different loci. The differential action of this CRISPR-Cas9 system is exclusively based on the specific recombination between regions surrounding the gene copy of interest. This approach is suitable to edit multicopy genes. One such particular example corresponds to the mutagenesis of candidate-essential genes that requires the presence of an extra copy of the gene before gene disruption. This opens new insights to explore gene essentiality in bacteria and to limit off-target effects during systematic CRISPR-Cas9 based approaches.
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Affiliation(s)
- Soumaya Najah
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Corinne Saulnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Stéphanie Bury-Moné
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-Sur-Yvette, France
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Wlodek A, Kendrew SG, Coates NJ, Hold A, Pogwizd J, Rudder S, Sheehan LS, Higginbotham SJ, Stanley-Smith AE, Warneck T, Nur-E-Alam M, Radzom M, Martin CJ, Overvoorde L, Samborskyy M, Alt S, Heine D, Carter GT, Graziani EI, Koehn FE, McDonald L, Alanine A, Rodríguez Sarmiento RM, Chao SK, Ratni H, Steward L, Norville IH, Sarkar-Tyson M, Moss SJ, Leadlay PF, Wilkinson B, Gregory MA. Diversity oriented biosynthesis via accelerated evolution of modular gene clusters. Nat Commun 2017; 8:1206. [PMID: 29089518 PMCID: PMC5663706 DOI: 10.1038/s41467-017-01344-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/08/2017] [Indexed: 11/09/2022] Open
Abstract
Erythromycin, avermectin and rapamycin are clinically useful polyketide natural products produced on modular polyketide synthase multienzymes by an assembly-line process in which each module of enzymes in turn specifies attachment of a particular chemical unit. Although polyketide synthase encoding genes have been successfully engineered to produce novel analogues, the process can be relatively slow, inefficient, and frequently low-yielding. We now describe a method for rapidly recombining polyketide synthase gene clusters to replace, add or remove modules that, with high frequency, generates diverse and highly productive assembly lines. The method is exemplified in the rapamycin biosynthetic gene cluster where, in a single experiment, multiple strains were isolated producing new members of a rapamycin-related family of polyketides. The process mimics, but significantly accelerates, a plausible mechanism of natural evolution for modular polyketide synthases. Detailed sequence analysis of the recombinant genes provides unique insight into the design principles for constructing useful synthetic assembly-line multienzymes. Reengineering polyketide synthase encoding genes to produce analogues of natural products can be slow and low-yielding. Here the authors use accelerated evolution to recombine the gene cluster for rapid production of rapamycin-related products.
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Affiliation(s)
- Aleksandra Wlodek
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Steve G Kendrew
- Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Engineered Biodesign Limited, Cambridge, CB22 3GN, UK
| | - Nigel J Coates
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Adam Hold
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Joanna Pogwizd
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Steven Rudder
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Lesley S Sheehan
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | | | - Anna E Stanley-Smith
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Tony Warneck
- Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Mohammad Nur-E-Alam
- Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 12372, Saudi Arabia
| | - Markus Radzom
- Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,BASF SE, Speyerer Str. 2, Limburgerhof, 67117, Germany
| | - Christine J Martin
- Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Lois Overvoorde
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Markiyan Samborskyy
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Silke Alt
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Guy T Carter
- Chemical and Screening Sciences, Wyeth Pharmaceuticals, 401 North Middletown Road, Pearl River, NY, 10965, USA
| | - Edmund I Graziani
- Chemical and Screening Sciences, Wyeth Pharmaceuticals, 401 North Middletown Road, Pearl River, NY, 10965, USA.,Medicine Discovery Network-Synthetic Biology, Pfizer Worldwide R&D, 445 Eastern Point Rd., Groton, CT, 06340, USA
| | - Frank E Koehn
- Chemical and Screening Sciences, Wyeth Pharmaceuticals, 401 North Middletown Road, Pearl River, NY, 10965, USA
| | - Leonard McDonald
- Chemical and Screening Sciences, Wyeth Pharmaceuticals, 401 North Middletown Road, Pearl River, NY, 10965, USA
| | - Alexander Alanine
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development (PRED), Basel, CH-4070, Switzerland
| | | | - Suzan Keen Chao
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development (PRED), Basel, CH-4070, Switzerland
| | - Hasane Ratni
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development (PRED), Basel, CH-4070, Switzerland
| | - Lucinda Steward
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development (PRED), Basel, CH-4070, Switzerland
| | - Isobel H Norville
- Defence Science and Technology Laboratory, Porton Down, PO17 6AD, UK
| | - Mitali Sarkar-Tyson
- Defence Science and Technology Laboratory, Porton Down, PO17 6AD, UK.,Marshall Centre for Infectious Diseases, School of Biomedical Sciences, University of Western Australia, Monash Avenue, Nedlands, WA, 6009, Australia
| | - Steven J Moss
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Barrie Wilkinson
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK. .,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK. .,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Matthew A Gregory
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK. .,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.
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Hoff G, Bertrand C, Zhang L, Piotrowski E, Chipot L, Bontemps C, Confalonieri F, McGovern S, Lecointe F, Thibessard A, Leblond P. Multiple and Variable NHEJ-Like Genes Are Involved in Resistance to DNA Damage in Streptomyces ambofaciens. Front Microbiol 2016; 7:1901. [PMID: 27965636 PMCID: PMC5124664 DOI: 10.3389/fmicb.2016.01901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/14/2016] [Indexed: 11/26/2022] Open
Abstract
Non-homologous end-joining (NHEJ) is a double strand break (DSB) repair pathway which does not require any homologous template and can ligate two DNA ends together. The basic bacterial NHEJ machinery involves two partners: the Ku protein, a DNA end binding protein for DSB recognition and the multifunctional LigD protein composed a ligase, a nuclease and a polymerase domain, for end processing and ligation of the broken ends. In silico analyses performed in the 38 sequenced genomes of Streptomyces species revealed the existence of a large panel of NHEJ-like genes. Indeed, ku genes or ligD domain homologues are scattered throughout the genome in multiple copies and can be distinguished in two categories: the “core” NHEJ gene set constituted of conserved loci and the “variable” NHEJ gene set constituted of NHEJ-like genes present in only a part of the species. In Streptomyces ambofaciens ATCC23877, not only the deletion of “core” genes but also that of “variable” genes led to an increased sensitivity to DNA damage induced by electron beam irradiation. Multiple mutants of ku, ligase or polymerase encoding genes showed an aggravated phenotype compared to single mutants. Biochemical assays revealed the ability of Ku-like proteins to protect and to stimulate ligation of DNA ends. RT-qPCR and GFP fusion experiments suggested that ku-like genes show a growth phase dependent expression profile consistent with their involvement in DNA repair during spores formation and/or germination.
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Affiliation(s)
- Grégory Hoff
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Claire Bertrand
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Lingli Zhang
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Emilie Piotrowski
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Ludovic Chipot
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Cyril Bontemps
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Fabrice Confalonieri
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud Orsay, France
| | - Stephen McGovern
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - François Lecointe
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - Annabelle Thibessard
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
| | - Pierre Leblond
- UMR 1128, Dynamique des Génomes et Adaptation Microbienne, Université de LorraineVandœuvre-lès-Nancy, France; UMR 1128, Institut National de la Recherche Agronomique, Dynamique des Génomes et Adaptation MicrobienneVandœuvre-lès-Nancy, France
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