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Li CY, Liao LJ, Yang SX, Wang LY, Chen H, Luo P, Huang GR, Huang YQ. Cinnamaldehyde: An effective component of Cinnamomum cassia inhibiting Helicobacter pylori. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118222. [PMID: 38663778 DOI: 10.1016/j.jep.2024.118222] [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: 02/07/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Cinnamomum cassia Presl (Cinnamomum cassia) is a common traditional Chinese medicine, which can promote the secretion and digestion of gastric juice, improve the function of gastrointestinal tract. Cinnamaldehyde (CA) is a synthetic food flavoring in the Chinese Pharmacopoeia. AIM OF THE STUDY This study aimed to search for the active ingredient (CA) of inhibiting H. pylori from Cinnamomum cassia, and elucidate mechanism of action, so as to provide the experimental basis for the treatment of H. pylori infection with Cinnamomum cassia. MATERIALS AND METHODS It's in vitro and in vivo pharmacological properties were evaluated based on minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and an acute gastric inflammation model in mice infected with H. pylori. Drug safety was evaluated using the CCK8 method and high-dose administration in mice. The advantageous characteristics of CA in inhibiting H. pylori were confirmed using acidic conditions and in combination with the antibiotics. The mechanism underlying the action of CA on H. pylori was explored using scanning electron microscopy (SEM), adhesion experiments, biofilm inhibition tests, ATP and ROS release experiments, and drug affinity responsive target stability (DARTS) screening of target proteins. The protein function and target genes were verified by molecular docking and Real-Time quantitative reverse transcription PCR (qRT-PCR). RESULTS The results demonstrated that CA was found to be the main active ingredient against H. pylori in Cinnamomum cassia in-vitro tests, with a MIC of 8-16 μg/mL. Moreover, CA effectively inhibited both sensitive and resistant H. pylori strains. The dual therapy of PPI + CA exhibited remarkable in vivo efficacy in the acute gastritis mouse model, superior to the standard triple therapy. DARTS, molecular docking, and qRT-PCR results suggested that the target sites of action were closely associated with GyrA, GyrB, AtpA, and TopA, which made DNA replication and transcription impossible, then leading to inhibition of bacterial adhesion and colonization, suppression of biofilm formation, and inhibition ATP and enhancing ROS. CONCLUSIONS This study demonstrated the suitability of CA as a promising lead drug against H. pylori, The main mechanisms can target GyrA ect, leading to reduce ATP and produce ROS, which induces the apoptosis of bacterial.
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Affiliation(s)
- Chen-Yan Li
- Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes With Drug Resistance, Youjiang Medical University for Nationalities, Baise, 533000, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Clinical Prevention and Control Technology and Leading Drug for Microorganisms with Drug Resistance in Border Ethnic Areasn, Baise, 533000, China; Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Education Department of Guangxi Zhuang Autonomous Region, Baise, 533000, China; Graduate School of Youjiang Medical University for Nationalities, Baise, 533000, China
| | - Li-Juan Liao
- Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes With Drug Resistance, Youjiang Medical University for Nationalities, Baise, 533000, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Clinical Prevention and Control Technology and Leading Drug for Microorganisms with Drug Resistance in Border Ethnic Areasn, Baise, 533000, China; Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Education Department of Guangxi Zhuang Autonomous Region, Baise, 533000, China
| | - Shi-Xian Yang
- Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes With Drug Resistance, Youjiang Medical University for Nationalities, Baise, 533000, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Clinical Prevention and Control Technology and Leading Drug for Microorganisms with Drug Resistance in Border Ethnic Areasn, Baise, 533000, China; Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Education Department of Guangxi Zhuang Autonomous Region, Baise, 533000, China
| | - Lu-Yao Wang
- Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes With Drug Resistance, Youjiang Medical University for Nationalities, Baise, 533000, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Clinical Prevention and Control Technology and Leading Drug for Microorganisms with Drug Resistance in Border Ethnic Areasn, Baise, 533000, China; Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Education Department of Guangxi Zhuang Autonomous Region, Baise, 533000, China
| | - Hao Chen
- Department of Pathology, Wannan Medical College, Wuhu, 241002, Anhui Province, China
| | - Peipei Luo
- Department of Gastroenterology, Wujin People's Hospital affiliated to Jiangsu University, Changzhou, 213004, Jiangsu Province, China
| | - Gan-Rong Huang
- Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes With Drug Resistance, Youjiang Medical University for Nationalities, Baise, 533000, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Clinical Prevention and Control Technology and Leading Drug for Microorganisms with Drug Resistance in Border Ethnic Areasn, Baise, 533000, China; Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Education Department of Guangxi Zhuang Autonomous Region, Baise, 533000, China.
| | - Yan-Qiang Huang
- Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes With Drug Resistance, Youjiang Medical University for Nationalities, Baise, 533000, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Clinical Prevention and Control Technology and Leading Drug for Microorganisms with Drug Resistance in Border Ethnic Areasn, Baise, 533000, China; Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Education Department of Guangxi Zhuang Autonomous Region, Baise, 533000, China.
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Effects of Sub-Minimum Inhibitory Concentrations of Imipenem and Colistin on Expression of Biofilm-Specific Antibiotic Resistance and Virulence Genes in Acinetobacter baumannii Sequence Type 1894. Int J Mol Sci 2022; 23:ijms232012705. [PMID: 36293559 PMCID: PMC9603859 DOI: 10.3390/ijms232012705] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotics at suboptimal doses promote biofilm formation and the development of antibiotic resistance. The underlying molecular mechanisms, however, were not investigated. Here, we report the effects of sub-minimum inhibitory concentrations (sub-MICs) of imipenem and colistin on genes associated with biofilm formation and biofilm-specific antibiotic resistance in a multidrug-tolerant clinical strain of Acinetobacter baumannii Sequence Type (ST) 1894. Comparative transcriptome analysis was performed in untreated biofilm and biofilm treated with sub-MIC doses of imipenem and colistin. RNA sequencing data showed that 78 and 285 genes were differentially expressed in imipenem and colistin-treated biofilm cells, respectively. Among the differentially expressed genes (DEGs), 48 and 197 genes were upregulated exclusively in imipenem and colistin-treated biofilm cells, respectively. The upregulated genes included those encoding matrix synthesis (pgaB), multidrug efflux pump (novel00738), fimbrial proteins, and homoserine lactone synthase (AbaI). Upregulation of biofilm-associated genes might enhance biofilm formation when treated with sub-MICs of antibiotics. The downregulated genes include those encoding DNA gyrase (novel00171), 30S ribosomal protein S20 (novel00584), and ribosome releasing factor (RRF) were downregulated when the biofilm cells were treated with imipenem and colistin. Downregulation of these genes affects protein synthesis, which in turn slows down cell metabolism and makes biofilm cells more tolerant to antibiotics. In this investigation, we also found that 5 of 138 small RNAs (sRNAs) were differentially expressed in biofilm regardless of antibiotic treatment or not. Of these, sRNA00203 showed the highest expression levels in biofilm. sRNAs regulate gene expression and are associated with biofilm formation, which may in turn affect the expression of biofilm-specific antibiotic resistance. In summary, when biofilm cells were exposed to sub-MIC doses of colistin and imipenem, coordinated gene responses result in increased biofilm production, multidrug efflux pump expression, and the slowdown of metabolism, which leads to drug tolerance in biofilm. Targeting antibiotic-induced or repressed biofilm-specific genes represents a new strategy for the development of innovative and effective treatments for biofilm-associated infections caused by A. baumannii.
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Inducible knockdown of Mycobacterium smegmatis MSMEG_2975 (glyoxalase II) affected bacterial growth, antibiotic susceptibility, biofilm, and transcriptome. Arch Microbiol 2021; 204:97. [DOI: 10.1007/s00203-021-02652-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 10/19/2022]
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Kever L, Hünnefeld M, Brehm J, Heermann R, Frunzke J. Identification of Gip as a novel phage-encoded gyrase inhibitor protein of Corynebacterium glutamicum. Mol Microbiol 2021; 116:1268-1280. [PMID: 34536319 DOI: 10.1111/mmi.14813] [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: 04/09/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/30/2022]
Abstract
By targeting key regulatory hubs of their host, bacteriophages represent a powerful source for the identification of novel antimicrobial proteins. Here, a screening of small cytoplasmic proteins encoded by the CGP3 prophage of Corynebacterium glutamicum resulted in the identification of the gyrase-inhibiting protein Cg1978, termed Gip. Pull-down assays and surface plasmon resonance revealed a direct interaction of Gip with the gyrase subunit A (GyrA). The inhibitory activity of Gip was shown to be specific to the DNA gyrase of its bacterial host C. glutamicum. Overproduction of Gip in C. glutamicum resulted in a severe growth defect as well as an induction of the SOS response. Furthermore, reporter assays revealed an RecA-independent induction of the cryptic CGP3 prophage, most likely caused by topological alterations. Overexpression of gip was counteracted by an increased expression of gyrAB and a reduction of topA expression at the same time, reflecting the homeostatic control of DNA topology. We postulate that the prophage-encoded Gip protein plays a role in modulating gyrase activity to enable efficient phage DNA replication. A detailed elucidation of the mechanism of action will provide novel directions for the design of drugs targeting DNA gyrase.
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Affiliation(s)
- Larissa Kever
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Max Hünnefeld
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Jannis Brehm
- Institut für Molekulare Physiologie, Biozentrum II, Mikrobiologie und Weinforschung, Johannes-Gutenberg-Universität Mainz, Mainz, Germany
| | - Ralf Heermann
- Institut für Molekulare Physiologie, Biozentrum II, Mikrobiologie und Weinforschung, Johannes-Gutenberg-Universität Mainz, Mainz, Germany
| | - Julia Frunzke
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
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Hinzke T, Kleiner M, Meister M, Schlüter R, Hentschker C, Pané-Farré J, Hildebrandt P, Felbeck H, Sievert SM, Bonn F, Völker U, Becher D, Schweder T, Markert S. Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. eLife 2021; 10:58371. [PMID: 33404502 PMCID: PMC7787665 DOI: 10.7554/elife.58371] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/05/2020] [Indexed: 12/13/2022] Open
Abstract
The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.
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Affiliation(s)
- Tjorven Hinzke
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany.,Energy Bioengineering Group, University of Calgary, Calgary, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Mareike Meister
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.,Leibniz Institute for Plasma Science and Technology, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Christian Hentschker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Petra Hildebrandt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Horst Felbeck
- Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, United States
| | - Florian Bonn
- Institute of Biochemistry, University Hospital, Goethe University School of Medicine Frankfurt, Frankfurt, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
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Sutormin DA, Galivondzhyan AK, Polkhovskiy AV, Kamalyan SO, Severinov KV, Dubiley SA. Diversity and Functions of Type II Topoisomerases. Acta Naturae 2021; 13:59-75. [PMID: 33959387 PMCID: PMC8084294 DOI: 10.32607/actanaturae.11058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/09/2020] [Indexed: 11/29/2022] Open
Abstract
The DNA double helix provides a simple and elegant way to store and copy genetic information. However, the processes requiring the DNA helix strands separation, such as transcription and replication, induce a topological side-effect - supercoiling of the molecule. Topoisomerases comprise a specific group of enzymes that disentangle the topological challenges associated with DNA supercoiling. They relax DNA supercoils and resolve catenanes and knots. Here, we review the catalytic cycles, evolution, diversity, and functional roles of type II topoisomerases in organisms from all domains of life, as well as viruses and other mobile genetic elements.
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Affiliation(s)
- D. A. Sutormin
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - A. K. Galivondzhyan
- Lomonosov Moscow State University, Moscow, 119991 Russia
- Institute of Molecular Genetics RAS, Moscow, 123182 Russia
| | - A. V. Polkhovskiy
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - S. O. Kamalyan
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - K. V. Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Centre for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
- Waksman Institute for Microbiology, Piscataway, New Jersey, 08854 USA
| | - S. A. Dubiley
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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Stokes SS, Vemula R, Pucci MJ. Advancement of GyrB Inhibitors for Treatment of Infections Caused by Mycobacterium tuberculosis and Non-tuberculous Mycobacteria. ACS Infect Dis 2020; 6:1323-1331. [PMID: 32183511 DOI: 10.1021/acsinfecdis.0c00025] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The prospect of ever increasing antibiotic resistance eroding currently available treatment options for bacterial infections underscores the need to continue to identify new antibiotics, preferably those that act on novel targets or with novel mechanisms of action. Bacterial gyrase B subunit (GyrB), an essential component of bacterial gyrase required for successful DNA replication, represents such a target. We describe recent examples of GyrB inhibitors and point out their potential utility for treatment of mycobacterial diseases caused by Mycobacterium tuberculosis (TB) and non-tuberculous mycobacteria (NTM). Current therapeutic options for these diseases are often suboptimal due to resistance to current standard of care antibiotics. A future GyrB inhibitor-based antibiotic could offer a new and effective addition to the armamentarium for treatment of mycobacterial diseases and possibly for infections caused by other bacterial pathogens. One GyrB inhibitor, SPR720, has recently completed a first-in-human clinical trial and is in clinical development for the treatment of NTM and TB infections.
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Affiliation(s)
- Suzanne S. Stokes
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rajender Vemula
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael J. Pucci
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Możejko-Ciesielska J, Serafim LS. Proteomic Response of Pseudomonas putida KT2440 to Dual Carbon-Phosphorus Limitation during mcl-PHAs Synthesis. Biomolecules 2019; 9:E796. [PMID: 31795154 PMCID: PMC6995625 DOI: 10.3390/biom9120796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/19/2019] [Accepted: 11/24/2019] [Indexed: 01/01/2023] Open
Abstract
Pseudomonas putida KT2440, one of the best characterized pseudomonads, is a metabolically versatile producer of medium-chain-length polyhydroxyalkanoates (mcl-PHAs) that serves as a model bacterium for molecular studies. The synthesis of mcl-PHAs is of great interest due to their commercial potential. Carbon and phosphorus are the essential nutrients for growth and their limitation can trigger mcl-PHAs' production in microorganisms. However, the specific molecular mechanisms that drive this synthesis in Pseudomonas species under unfavorable growth conditions remain poorly understood. Therefore, the proteomic responses of Pseudomonas putida KT2440 to the limited carbon and phosphorus levels in the different growth phases during mcl-PHAs synthesis were investigated. The data indicated that biopolymers' production was associated with the cell growth of P. putida KT2440 under carbon- and phosphorus-limiting conditions. The protein expression pattern changed during mcl-PHAs synthesis and accumulation, and during the different physiological states of the microorganism. The data suggested that the majority of metabolic activities ceased under carbon and phosphorus limitation. The abundance of polyhydroxyalkanoate granule-associated protein (PhaF) involved in PHA synthesis increased significantly at 24 and 48 h of the cultivations. The activation of proteins belonging to the phosphate regulon was also detected. Moreover, these results indicated changes in the protein profiles related to amino acids metabolism, replication, transcription, translation, stress response mechanisms, transport or signal transduction. The presented data allowed the investigation of time-course proteome alterations in response to carbon and phosphorus limitation, and PHAs synthesis. This study provided information about proteins that can be potential targets in improving the efficiency of mcl-PHAs synthesis.
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Affiliation(s)
- Justyna Możejko-Ciesielska
- Department of Microbiology and Mycology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10719 Olsztyn, Poland
- Chemistry Department, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal;
| | - Luísa S. Serafim
- Chemistry Department, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal;
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Szafran MJ, Strzałka A, Jakimowicz D. A highly processive actinobacterial topoisomerase I - thoughts on Streptomyces' demand for an enzyme with a unique C-terminal domain. MICROBIOLOGY-SGM 2019; 166:120-128. [PMID: 31390324 PMCID: PMC7398561 DOI: 10.1099/mic.0.000841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Topoisomerase I (TopA) is an essential enzyme that is required to remove excess negative supercoils from chromosomal DNA. Actinobacteria encode unusual TopA homologues with a unique C-terminal domain that contains lysine repeats and confers high enzyme processivity. Interestingly, the longest stretch of lysine repeats was identified in TopA from Streptomyces, environmental bacteria that undergo complex differentiation and produce a plethora of secondary metabolites. In this review, we aim to discuss potential advantages of the lysine repeats in Streptomyces TopA. We speculate that the chromosome organization, transcriptional regulation and lifestyle of these species demand a highly processive but also fine-tuneable relaxase. We hypothesize that the unique TopA provides flexible control of chromosomal topology and globally regulates gene expression.
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Affiliation(s)
- Marcin J Szafran
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Agnieszka Strzałka
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Dagmara Jakimowicz
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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Szafran MJ, Gongerowska M, Małecki T, Elliot M, Jakimowicz D. Transcriptional Response of Streptomyces coelicolor to Rapid Chromosome Relaxation or Long-Term Supercoiling Imbalance. Front Microbiol 2019; 10:1605. [PMID: 31354687 PMCID: PMC6637917 DOI: 10.3389/fmicb.2019.01605] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022] Open
Abstract
Negative DNA supercoiling allows chromosome condensation and facilitates DNA unwinding, which is required for the occurrence of DNA transaction processes, i.e., DNA replication, transcription and recombination. In bacteria, changes in chromosome supercoiling impact global gene expression; however, the limited studies on the global transcriptional response have focused mostly on pathogenic species and have reported various fractions of affected genes. Furthermore, the transcriptional response to long-term supercoiling imbalance is still poorly understood. Here, we address the transcriptional response to both novobiocin-induced rapid chromosome relaxation or long-term topological imbalance, both increased and decreased supercoiling, in environmental antibiotic-producing bacteria belonging to the Streptomyces genus. During the Streptomyces complex developmental cycle, multiple copies of GC-rich linear chromosomes present in hyphal cells undergo profound topological changes, from being loosely condensed in vegetative hyphae, to being highly compacted in spores. Moreover, changes in chromosomal supercoiling have been suggested to be associated with the control of antibiotic production and environmental stress response. Remarkably, in S. coelicolor, a model Streptomyces species, topoisomerase I (TopA) is solely responsible for the removal of negative DNA supercoils. Using a S. coelicolor strain in which topA transcription is under the control of an inducible promoter, we identified genes involved in the transcriptional response to long-term supercoiling imbalance. The affected genes are preferentially organized in several clusters, and a supercoiling-hypersensitive cluster (SHC) was found to be located in the core of the S. coelicolor chromosome. The transcripts affected by long-term topological imbalance encompassed genes encoding nucleoid-associated proteins, DNA repair proteins and transcriptional regulators, including multiple developmental regulators. Moreover, using a gyrase inhibitor, we identified those genes that were directly affected by novobiocin, and found this was correlated with increased AT content in their promoter regions. In contrast to the genes affected by long-term supercoiling changes, among the novobiocin-sensitive genes, a significant fraction encoded for proteins associated with membrane transport or secondary metabolite synthesis. Collectively, our results show that long-term supercoiling imbalance globally regulates gene transcription and has the potential to impact development, secondary metabolism and DNA repair, amongst others.
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Affiliation(s)
- Marcin Jan Szafran
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Martyna Gongerowska
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Tomasz Małecki
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Marie Elliot
- Department of Biology, M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Dagmara Jakimowicz
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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