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Çöl B, Kürkçü MS, Di Bek E. Genome-Wide Screens Identify Genes Responsible for Intrinsic Boric Acid Resistance in Escherichia coli. Biol Trace Elem Res 2024; 202:5771-5793. [PMID: 38466471 PMCID: PMC11502571 DOI: 10.1007/s12011-024-04129-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/24/2024] [Indexed: 03/13/2024]
Abstract
Boric acid (BA) has antimicrobial properties and is used to combat bacterial infections, including Enterobacteria. However, the molecular mechanisms and cellular responses to BA are still unknown. This genomics study aims to provide new information on the genes and molecular mechanisms related to the antimicrobial effect of BA in Escherichia coli. The Keio collection of E. coli was used to screen 3985 single-gene knockout strains in order to identify mutant strains that were sensitive or hypersensitive to BA at certain concentrations. The mutant strains were exposed to different concentrations of BA ranging from 0 to 120 mM in LB media. Through genome-wide screens, 92 mutants were identified that were relatively sensitive to BA at least at one concentration tested. The related biological processes in the particular cellular system were listed. This study demonstrates that intrinsic BA resistance is the result of various mechanisms acting together. Additionally, we identified eighteen out of ninety-two mutant strains (Delta_aceF, aroK, cheZ, dinJ, galS, garP, glxK, nohA, talB, torR, trmU, trpR, yddE, yfeS, ygaV, ylaC, yoaC, yohN) that exhibited sensitivity using other methods. To increase sensitivity to BA, we constructed double and triple knockout mutants of the selected sensitive mutants. In certain instances, engineered double and triple mutants exhibited significantly amplified effects. Overall, our analysis of these findings offers further understanding of the mechanisms behind BA toxicity and intrinsic resistance in E. coli.
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Affiliation(s)
- Bekir Çöl
- Faculty of Science, Department of Biology, Mugla Sitki Kocman University, Mugla, Turkey.
- Research Laboratories Center, Biotechnology Research Center, Mugla Sitki Kocman University, Mugla, Turkey.
| | - Merve Sezer Kürkçü
- Research Laboratories Center, Biotechnology Research Center, Mugla Sitki Kocman University, Mugla, Turkey
- Research and Application Center For Research Laboratories, Mugla Sitki Kocman University, Mugla, Turkey
| | - Esra Di Bek
- Research Laboratories Center, Biotechnology Research Center, Mugla Sitki Kocman University, Mugla, Turkey
- Köyceğiz Vocational School of Health Services, Department of Pharmacy Services, Mugla Sitki Kocman University, Mugla, Turkey
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2
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Yao Y, Sun H, Wurihan, Gegeheng, Gezi, Skarstad K, Fan L, Morigen. A DnaA-dependent riboswitch for transcription attenuation of the his operon. MLIFE 2023; 2:126-140. [PMID: 38817620 PMCID: PMC10989985 DOI: 10.1002/mlf2.12075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/04/2023] [Indexed: 06/01/2024]
Abstract
Transcription attenuation in response to the availability of a specific amino acid is believed to be controlled by alternative configurations of RNA secondary structures that lead to the arrest of translation or the release of the arrested ribosome from the leader mRNA molecule. In this study, we first report a possible example of the DnaA-dependent riboswitch for transcription attenuation in Escherichia coli. We show that (i) DnaA regulates the transcription of the structural genes but not that of the leader hisL gene; (ii) DnaA might bind to rDnaA boxes present in the HisL-SL RNA, and subsequently attenuate the transcription of the operon; (iii) the HisL-SL RNA and rDnaA boxes are phylogenetically conserved and evolutionarily important; and (iv) the translating ribosome is required for deattenuation of the his operon, whereas tRNAHis strengthens attenuation. This mechanism seems to be phylogenetically conserved in Gram-negative bacteria and evolutionarily important.
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Affiliation(s)
- Yuan Yao
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Hongwei Sun
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Wurihan
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Gegeheng
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Gezi
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Kirsten Skarstad
- Department of Molecular Cell Biology and Department of MicrobiologyOslo University HospitalOsloNorway
| | - Lifei Fan
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Morigen
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
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3
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Sano K, Kobayashi H, Chuta H, Matsuyoshi N, Kato Y, Ogasawara H. CsgI (YccT) Is a Novel Inhibitor of Curli Fimbriae Formation in Escherichia coli Preventing CsgA Polymerization and Curli Gene Expression. Int J Mol Sci 2023; 24:ijms24054357. [PMID: 36901788 PMCID: PMC10002515 DOI: 10.3390/ijms24054357] [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: 12/31/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Curli fimbriae are amyloids-found in bacteria (Escherichia coli)-that are involved in solid-surface adhesion and bacterial aggregation during biofilm formation. The curli protein CsgA is coded by a csgBAC operon gene, and the transcription factor CsgD is essential to induce its curli protein expression. However, the complete mechanism underlying curli fimbriae formation requires elucidation. Herein, we noted that curli fimbriae formation was inhibited by yccT-i.e., a gene that encodes a periplasmic protein of unknown function regulated by CsgD. Furthermore, curli fimbriae formation was strongly repressed by CsgD overexpression caused by a multicopy plasmid in BW25113-the non-cellulose-producing strain. YccT deficiency prevented these CsgD effects. YccT overexpression led to intracellular YccT accumulation and reduced CsgA expression. These effects were addressed by deleting the N-terminal signal peptide of YccT. Localization, gene expression, and phenotypic analyses revealed that YccT-dependent inhibition of curli fimbriae formation and curli protein expression was mediated by the two-component regulatory system EnvZ/OmpR. Purified YccT inhibited CsgA polymerization; however, no intracytoplasmic interaction between YccT and CsgA was detected. Thus, YccT-renamed CsgI (curli synthesis inhibitor)-is a novel inhibitor of curli fimbriae formation and has a dual role as an OmpR phosphorylation modulator and CsgA polymerization inhibitor.
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Affiliation(s)
- Kotaro Sano
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Hiroaki Kobayashi
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Hirotaka Chuta
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Nozomi Matsuyoshi
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Yuki Kato
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Hiroshi Ogasawara
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Academic Assembly School of Humanities and Social Sciences Institute of Humanities, Shinshu University, Matsumoto 390-8621, Japan
- Institute for Fiber Engineering (IFES), Interdisciplinary Cluster for Cutting Edge Research (ICCER), Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan
- Renaissance Center for Applied Microbiology, Shinshu University, Nagano-shi, Nagano 380-8553, Japan
- Correspondence: ; Tel.: +81-268-21-5803
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4
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Li G, Yao Y. TorR/TorS Two-Component system resists extreme acid environment by regulating the key response factor RpoS in Escherichia coli. Gene 2022; 821:146295. [PMID: 35181503 DOI: 10.1016/j.gene.2022.146295] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/26/2021] [Accepted: 02/04/2022] [Indexed: 01/23/2023]
Abstract
Response to acid stress is critical for Escherichia coli to successfully complete its life-cycle. Acid resistance is an indispensable mechanism that allows neutralophilic bacteria, such as E. coli, to survive in the gastrointestinal tract. Escherichia coli acid tolerance has been extensively studied over the past decades, and most studies have focused on mechanisms of gene regulation. Bacterial two-component signal transduction systems sense and respond to external environmental changes through regulating genes expression. However, there has been little research on the mechanism of the TorR/TorS system in acid resistance, and how TorR/TorS regulate the expression ofacid-resistantgenes is still unclear. We found that TorR/TorS deletion in E. coli cells led to a growth defect in extreme acid conditions,andthis defectmightdepend on the nutritional conditionsand growth phase.TorS/TorR sensed an extremely acidic environment, and this TorR phosphorylation process might not be entirely dependent on TorS.RNA-seqand RT-qPCR results suggested that TorR regulated expressions of gadB, gadC, hdeA, gadE, mdtE, mdtF, gadX, and slp acid-resistant genes. Compared with wild-type cells, the stress response factor RpoSlevels and itsexpressions were significantly decreased in Δ torR cellsstimulated by extreme acid. And under these circumstances, the expression of iraM was significantly reduced to 0.6-fold inΔ torR cells. Electrophoreticmobility shift assay showed that TorR-His6 could interact with the rpoS promoter sequence in vitro. β-galactosidase activity assayresultsapprovedthat TorR might bind the rpoS promoter region in vivo. After the mutation of the TorR-box in the rpoS promoter region, these interactions were no longer observed. Taken together, we propose thatTorS and potential Hanks model Ser/Thr kinase received an external acid stress signal and then phosphorylated TorR, which guided the expressions of a variety of acid resistance genes. Moreover,TorRcoped with extreme acid environmentsthroughRpoS, levels of which might be maintained byIraM. Finally,TorR may confer E. coli with the abilityto resist gastric acid, allowing the bacterium to reach the surface of the terminal ileum and large intestine mucosal epithelial cells through the gastric acid barrier, andestablishcolonization and pathogenicity.
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Affiliation(s)
- Guotao Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Yuan Yao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China; Department of Neurology, Inner Mongolia People's Hospital, Hohhot, China.
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5
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GeZi G, Liu R, Du D, Wu N, Bao N, Fan L, Morigen M. YfiF, an unknown protein, affects initiation timing of chromosome replication in Escherichia coli. J Basic Microbiol 2021; 61:883-899. [PMID: 34486756 DOI: 10.1002/jobm.202100265] [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: 06/05/2021] [Revised: 08/03/2021] [Accepted: 08/21/2021] [Indexed: 11/09/2022]
Abstract
The Escherichia coli YfiF protein is functionally unknown, being predicted as a transfer RNA/ribosomal RNA (tRNA/rRNA) methyltransferase. We find that absence of the yfiF gene delays initiation of chromosome replication and the delay is reversed by ectopic expression of YfiF, whereas excess YfiF causes an early initiation. A slight decrease in both cell size and number of origin per mass is observed in ΔyfiF cells. YfiF does not genetically interact with replication proteins such as DnaA, DnaB, and DnaC. Interestingly, YfiF is associated with ribosome modulation factor (RMF), hibernation promotion factor (HPF), and the tRNA methyltransferase TrmL. Defects in replication initiation of Δrmf, Δhpf, and ΔtrmL can be rescued by overexpression of YfiF, indicating that YfiF is functionally identical to RMF, HPF, and TrmL in terms of replication initiation. Also, YfiF interacts with the rRNA methyltransferase RsmC. Moreover, the total amount of proteins and DnaA content per cell decreases or increases in the absence of YfiF or the presence of excess YfiF. These facts suggest that YfiF is a ribosomal dormancy-like factor, affecting ribosome function. Thus, we propose that YfiF is involved in the correct timing of chromosome replication by changing the DnaA content per cell as a result of affecting ribosome function.
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Affiliation(s)
- GeZi GeZi
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Rui Liu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Dongdong Du
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Nier Wu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Narisu Bao
- Institute of Mongolian Medicinal Chemistry, School of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, China
| | - Lifei Fan
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Morigen Morigen
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
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6
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Shastri MD, Chong WC, Dua K, Peterson GM, Patel RP, Mahmood MQ, Tambuwala M, Chellappan DK, Hansbro NG, Shukla SD, Hansbro PM. Emerging concepts and directed therapeutics for the management of asthma: regulating the regulators. Inflammopharmacology 2020; 29:15-33. [PMID: 33152094 DOI: 10.1007/s10787-020-00770-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/17/2020] [Indexed: 12/19/2022]
Abstract
Asthma is a common, heterogeneous and serious disease, its prevalence has steadily risen in most parts of the world, and the condition is often inadequately controlled in many patients. Hence, there is a major need for new therapeutic approaches. Mild-to-moderate asthma is considered a T-helper cell type-2-mediated inflammatory disorder that develops due to abnormal immune responses to otherwise innocuous allergens. Prolonged exposure to allergens and persistent inflammation results in myofibroblast infiltration and airway remodelling with mucus hypersecretion, airway smooth muscle hypertrophy, and excess collagen deposition. The airways become hyper-responsive to provocation resulting in the characteristic wheezing and obstructed airflow experienced by patients. Extensive research has progressed the understanding of the underlying mechanisms and the development of new treatments for the management of asthma. Here, we review the basis of the disease, covering new areas such as the role of vascularisation and microRNAs, as well as associated potential therapeutic interventions utilising reports from animal and human studies. We also cover novel drug delivery strategies that are being developed to enhance therapeutic efficacy and patient compliance. Potential avenues to explore to improve the future of asthma management are highlighted.
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Affiliation(s)
- Madhur D Shastri
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, Australia
| | - Wai Chin Chong
- Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, Australia.,Priority Research Centre for Healthy Lungs, School of Medicine and Public Health, The University of Newcastle, Callaghan, Australia.,Centre for Inflammation, Centenary Institute, Sydney, NSW, 2050, Australia.,Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Gregory M Peterson
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, Australia
| | - Rahul P Patel
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, Australia
| | - Malik Q Mahmood
- Faculty of Health, School of Medicine, Deakin University, Melbourne, Australia
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Belfast, Northern Ireland, UK
| | - Dinesh K Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Nicole G Hansbro
- Priority Research Centre for Healthy Lungs, School of Medicine and Public Health, The University of Newcastle, Callaghan, Australia.,Centre for Inflammation, Centenary Institute, Sydney, NSW, 2050, Australia.,Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Shakti D Shukla
- Priority Research Centre for Healthy Lungs, School of Medicine and Public Health, The University of Newcastle, Callaghan, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, School of Medicine and Public Health, The University of Newcastle, Callaghan, Australia. .,Centre for Inflammation, Centenary Institute, Sydney, NSW, 2050, Australia. .,Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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7
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Rajpoot K. Lipid-based Nanoplatforms in Cancer Therapy: Recent Advances and Applications. Curr Cancer Drug Targets 2020; 20:271-287. [PMID: 31951180 DOI: 10.2174/1568009620666200115160805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022]
Abstract
Though modern available cancer therapies are effective, they possess major adverse effects, causing non-compliance to patients. Furthermore, the majority of the polymeric-based medication platforms are certainly not universally acceptable, due to their several restrictions. With this juxtaposition, lipid-based medication delivery systems have appeared as promising drug nanocarriers to replace the majority of the polymer-based products because they are in a position to reverse polymer as well as, drug-associated restrictions. Furthermore, the amalgamation of the basic principle of nanotechnology in designing lipid nanocarriers, which are the latest form of lipid carriers, has tremendous chemotherapeutic possibilities as tumor-targeted drug-delivery pertaining to tumor therapy. Apart from this, it is reported that nearly 40% of the modern medication entities are lipophilic. Moreover, research continues to be efficient in attaining a significant understanding of the absorption and bioavailability of the developed lipids systems.
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Affiliation(s)
- Kuldeep Rajpoot
- Institute of Pharmaceutical Sciences, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh- 495009, India
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8
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Wang Y, Yao Y, Liu J, Wu L, Liu T, Cui J, Lee DYW. Synthesis and Biological Activity of Piperine Derivatives as Potential PPARγ Agonists. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:2069-2078. [PMID: 32546971 PMCID: PMC7266110 DOI: 10.2147/dddt.s238245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Introduction Peroxisome proliferator-activated receptor γ (PPARγ) plays a key role in glucose, which is a ligand-mediated transcription factor. The lipid homeostasis often serves as a pharmacological target for new drug discovery and development. Materials and Methods In the research, we synthesized a series of piperine derivatives and then used a fluorescence polarization-based PPARγ ligand screening assay to evaluate the agonistic activity of PPARγ. Then, we cultured human normal hepatocytes, which were treated with 100μM compounds 2a, 2t or 3d. Then, the levels of PPARγ gene were determined so as to show whether the compounds could activate or inhibit the expression of PPARγ. Results A total of 30 piperine derivatives were synthesized and evaluated. Compound 2a was identified as a potential PPARγ agonist with IC50 at 2.43 μM, which is 2 times more potent than the positive control rosiglitazone with IC50 at 5.61μM. The human hepatocytes cells were cultured and treated with compounds 2a, 2t or 3d as described in the "Materials and Methods" section. We found that compounds 2a, 2t and 3d could activate PPARγ by 11.8, 1.9 and 7.0 times compared with the "blank", with compound 2a activation being the most significant. Molecular docking studies indicated that the piperine derivative 2a stably interacts with the amino acid residues of the PPARγ complex active site, which is consistent with the results of the in vitro PPARγ ligand screening assay.
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Affiliation(s)
- Yanli Wang
- School of Pharmacy, Minzu University of China, Beijing 100081, People's Republic of China.,Bio-Organic and Natural Products Laboratory, McLean Hospital, Harvard Medical School, Boston, MA 02478, USA.,Key Laboratory of Plant Molecular Biology, Inner Mongolia Autonomous Region Institute of Biotechnology, Hohhot 010010, Inner Mongolia, People's Republic of China
| | - Yuan Yao
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, People's Republic of China.,Department of Neurology, Inner Mongolia People's Hospital, Hohhot 010017, Inner Mongolia, People's Republic of China
| | - Jing Liu
- Bio-Organic and Natural Products Laboratory, McLean Hospital, Harvard Medical School, Boston, MA 02478, USA.,Natural Pharmacia International Inc., Burlington, MA 01803, USA
| | - Lili Wu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, People's Republic of China
| | - Tonghua Liu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, People's Republic of China
| | - Jian Cui
- School of Pharmacy, Minzu University of China, Beijing 100081, People's Republic of China
| | - David Yue-Wei Lee
- Bio-Organic and Natural Products Laboratory, McLean Hospital, Harvard Medical School, Boston, MA 02478, USA
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9
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Huang T, Yuan H, Fan L, Moregen M. H-NS, IHF, and DnaA lead to changes in nucleoid organizations, replication initiation, and cell division. J Basic Microbiol 2019; 60:136-148. [PMID: 32011760 DOI: 10.1002/jobm.201900497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/08/2019] [Accepted: 10/18/2019] [Indexed: 12/29/2022]
Abstract
Histone-like nucleoid-structuring protein (H-NS) and integration host factor (IHF) are major nucleoid-associated proteins, and DnaA, a replication initiator, may also be related with nucleoid compaction. It has been shown that protein-dependent DNA compaction is related with many aspects of bacterial physiology, including transcription, DNA replication, and site-specific recombination. However, the mechanism of bacterial physiology resulting from nucleoid compaction remains unknown. Here, we show that H-NS is important for correct nucleoid compaction in a medium-independent manner. H-NS-mediated nucleoid compaction is not required for correct cell division, but the latter is dependent on H-NS in rich medium. Further, it is found that the IHFα-mediated nucleoid compaction is needed for correct cell division, and the effect is dependent on medium. Also, we show that the effects of H-NS and IHF on nucleoid compaction are cumulative. Interestingly, DnaA also plays an important role in nucleoid compaction, and the effect of DnaA on nucleoid compaction appears to be related to cell division in a medium-dependent manner. The results presented here suggest that scrambled initiation of replication, improper cell division, and slow growth is likely associated with disturbances in nucleoid organization directly or indirectly.
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Affiliation(s)
- Tingting Huang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.,Daban No. 1 Middle School, Chifeng, China
| | - Hong Yuan
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.,Basic Medical College, Inner Mongolia Medical University, Hohhot, China
| | - Lifei Fan
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Morigen Moregen
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
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10
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Zhang S, Wunier W, Yao Y, Morigen M. Defects in ribosome function delay the initiation of chromosome replication in Escherichia coli. J Basic Microbiol 2018; 58:1091-1099. [PMID: 30211949 DOI: 10.1002/jobm.201800295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/14/2018] [Accepted: 08/25/2018] [Indexed: 01/14/2023]
Abstract
The Sra protein is a component of the 30S ribosomal subunit while RimJ is a ribosome-associated protein that plays a role in the maturation of the 30S ribosomal subunit. Here we found that Δsra and ΔrimJ cells showed a delayed initiation of DNA replication, prolonged doubling time, decreased cell size, and decreased amounts of total protein and DnaA per cell compared with these observed for wild-type cells. A temperature sensitivity test demonstrated that absence of the Sra or RimJ protein did not change the temperature sensitivity of the dnaA46, dnaB252, or dnaC2 mutants. Moreover, ectopic expression of Sra reversed the mutant phenotype while cells carrying the pACYC177-rimJ plasmid did not reverse the rimJ mutant phenotype. The results indicate that deletion of sra or rimJ cause defects in ribosomal function and affect the translation process, leading to a decrease in synthesis of proteins including DnaA. Therefore, we conclude that Sra- and RimJ-mediated ribosomal function is required for precise timing of initiation of chromosome replication.
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Affiliation(s)
- Shujun Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.,School of Life Sciences, Inner Mongolia University for Nationalities, Tongliao, China
| | - Wunier Wunier
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yuan Yao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.,Department of Neurology, Inner Mongolia People's Hospital, Hohhot, China
| | - Morigen Morigen
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
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11
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Absence of RstA results in delayed initiation of DNA replication in Escherichia coli. PLoS One 2018; 13:e0200688. [PMID: 30011323 PMCID: PMC6047807 DOI: 10.1371/journal.pone.0200688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022] Open
Abstract
RstB/RstA is an uncharacterized Escherichia coli two-component system, the regulatory effects of which on the E. coli cell cycle remain unclear. We found that the doubling time and average number of replication origins per cell in an ΔrstB mutant were the same as the wild-type, and the average number of replication origins in an ΔrstA mutant was 18.2% lower than in wild-type cells. The doubling times were 34 min, 35 min, and 40 min for the wild-type, ΔrstB, and ΔrstA strains, respectively. Ectopic expression of RstA from plasmid pACYC-rstA partly reversed the ΔrstA mutant phenotypes. The amount of initiator protein DnaA per cell was reduced by 40% in the ΔrstA mutant compared with the wild-type, but the concentration of DnaA did not change as the total amount of cellular protein was also reduced in these cells. Deletion or overproduction of RstA does not change the temperature sensitivity of dnaA46, dnaB252 and dnaC2. The expression of hupA was decreased by 0.53-fold in ΔrstA. RstA interacted with Topoisomerase I weakly in vivo and increased its activity of relaxing the negative supercoiled plasmid. Our data suggest that deletion of RstA leads to delayed initiation of DNA replication, and RstA may affect initiation of replication by controlling expression of dnaA or hupA. Furthermore, the delayed initiation may by caused by the decreased activity of topoisomerase I in RstA mutant.
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Yao Y, Enkhtsetseg S, Odsbu I, Fan L, Morigen M. Mutations of DnaA-boxes in the oriR region increase replication frequency of the MiniR1-1 plasmid. BMC Microbiol 2018; 18:27. [PMID: 29614952 PMCID: PMC5883639 DOI: 10.1186/s12866-018-1162-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/02/2018] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The MiniR1-1 plasmid is a derivative of the R1 plasmid, a low copy cloning vector. RESULTS Nucleotide sequencing analysis shows that the MiniR1-1 plasmid is a 6316 bp circular double-stranded DNA molecule with an oriR1 (origin for replication). The plasmid carries the repA, tap, copA and bla genes, and genes for ORF1 and ORF2. MiniR1-1 contains eight DnaA-binding sites (DnaA-boxes). DnaA-box1 is in the oriR1 region and fully matched to the DnaA-box consensus sequence, and DnaA-box8, with one mismatch, is close to the copA gene. The presence of the MiniR1-1 plasmid leads to an accumulation of the D-period cells and an increase in cell size of slowly growing Escherichia coli cells, suggesting that the presence of MiniR1-1 delays cell division. Mutations in the MiniR1-1 DnaA-box1 and DnaA-box8 significantly increase the copy number of the plasmid and the mutations in DnaA-box1 also affect cell size. It is likely that titration of DnaA to DnaA-boxes negatively controls replication of the MiniR1-1 plasmid and delays cell division. Interestingly, DnaA weakly interacts with the initiator protein RepA in vivo. CONCLUSION DnaA regulates the copy number of MiniR1-1 as a negative factor through interacting with the RepA protein.
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Affiliation(s)
- Yuan Yao
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock,School of Life Sciences, Inner Mongolia University, Hohhot, 010070 China
| | - Sukhbold Enkhtsetseg
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock,School of Life Sciences, Inner Mongolia University, Hohhot, 010070 China
| | - Ingvild Odsbu
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Lifei Fan
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock,School of Life Sciences, Inner Mongolia University, Hohhot, 010070 China
| | - Morigen Morigen
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock,School of Life Sciences, Inner Mongolia University, Hohhot, 010070 China
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