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Zhou N, Xu X, Jiang H, Liang Z, Wang S. Exposure pattern of triclosan and tetracycline change their impacts on methanogenic digestion microbiomes. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135604. [PMID: 39197282 DOI: 10.1016/j.jhazmat.2024.135604] [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: 04/17/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024]
Abstract
Triclosan (TCS) and tetracycline (TC) as common antibacterial agents are frequently detected in the influent of wastewater treatment plants. The TCS and TC exposure patterns may determine their impacts on wastewater treatment microbiomes, on which information remains unknown. In this study, the impacts of sequential exposure of TCS and TC on methanogenic digestion microbiomes in upflow anaerobic sludge blanket (UASB) reactors were analyzed and compared with that of the same microbiomes being simultaneously exposed to TCS and TC. Results indicated that the UASB reactor 2 (MD2) with sequential TCS-TC exposure consistently demonstrated higher chemical oxygen demand (COD) removal efficiency (94.7 %). In contrast, in the MD1 reactor, COD removal efficiency decreased from 94.4 % to 82.7 % upon simultaneous exposure to TCS and TC. Accordingly, a 1.8 times higher enrichment of total antibiotic resistance genes (ARGs) was observed in MD1 relative to MD2. Using a dissimilarity-overlap approach, the MD2 microbiome with sequential exposure was predominantly mediated by deterministic factors in their community assembly (largely contributed by abundant and intermediate biospheres), resulting in microbial interaction networks with higher average clustering coefficients and shorter average path lengths, compared to the MD1 microbiomes. Our results could support sustainable management of TCS and TC contamination in wastewater treatment plants.
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Affiliation(s)
- Na Zhou
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiangping Xu
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Haihong Jiang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhiwei Liang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
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Ericksen B. Enhancement of the activity of the antimicrobial peptides HNP1 and LL-37 by bovine pancreatic ribonuclease A. F1000Res 2023; 11:933. [PMID: 37360940 PMCID: PMC10285323 DOI: 10.12688/f1000research.123044.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2023] [Indexed: 03/24/2024] Open
Abstract
Background: HNP1, LL-37, and HBD1 are antimicrobial against Escherichia coli ATCC 25922 at the standard inoculum but less active at higher inocula. Methods: The virtual colony count (VCC) microbiological assay was adapted for high inocula and the addition of yeast tRNA and bovine pancreatic ribonuclease A (RNase). 96-well plates were read for 12 hours in a Tecan Infinite M1000 plate reader and photographed under 10x magnification. Results: Adding tRNA 1:1 wt/wt to HNP1 at the standard inoculum almost completely abrogated activity. Adding RNase 1:1 to HNP1 at the standard inoculum of 5x10 5 CFU/mL did not enhance activity. Increasing the inoculum to 6.25x10 7 CFU/mL almost abrogated HNP1 activity. However, adding RNase 25:1 to HNP1 enhanced activity at the highest tested concentration of HNP1. Adding both tRNA and RNase resulted in enhanced activity, indicating that the enhancement effect of RNase overwhelms the inhibiting effect of tRNA when both are present. HBD1 activity at the standard inoculum was almost completely abrogated by the addition of tRNA, but LL-37 activity was only slightly inhibited by tRNA. At the high inoculum, LL-37 activity was enhanced by RNase. HBD1 activity was not enhanced by RNase. RNase was not antimicrobial in the absence of antimicrobial peptides. Cell clumps were observed at the high inoculum in the presence of all three antimicrobial peptides and at the standard inoculum in the presence of HNP1+tRNA and HBD1+tRNA. Conclusions: Antimicrobial peptide-ribonuclease combinations have the potential to be active against high cell concentrations, conditions where the antimicrobial agent alone is relatively ineffective.
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Affiliation(s)
- Bryan Ericksen
- School of Medicine Institute of Human Virology, University of Maryland, Baltimore, Baltimore, Maryland, 21201, USA
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Tutukina MN, Dakhnovets AI, Kaznadzey AD, Gelfand MS, Ozoline ON. Sense and antisense RNA products of the uxuR gene can affect motility and chemotaxis acting independent of the UxuR protein. Front Mol Biosci 2023; 10:1121376. [PMID: 36936992 PMCID: PMC10016265 DOI: 10.3389/fmolb.2023.1121376] [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: 12/11/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Small non-coding and antisense RNAs are widespread in all kingdoms of life, however, the diversity of their functions in bacteria is largely unknown. Here, we study RNAs synthesised from divergent promoters located in the 3'-end of the uxuR gene, encoding transcription factor regulating hexuronate metabolism in Escherichia coli. These overlapping promoters were predicted in silico with rather high scores, effectively bound RNA polymerase in vitro and in vivo and were capable of initiating transcription in sense and antisense directions. The genome-wide correlation between in silico promoter scores and RNA polymerase binding in vitro and in vivo was higher for promoters located on the antisense strands of the genes, however, sense promoters within the uxuR gene were more active. Both regulatory RNAs synthesised from the divergent promoters inhibited expression of genes associated with the E. coli motility and chemotaxis independent of a carbon source on which bacteria had been grown. Direct effects of these RNAs were confirmed for the fliA gene encoding σ28 subunit of RNA polymerase. In addition to intracellular sRNAs, promoters located within the uxuR gene could initiate synthesis of transcripts found in the fraction of RNAs secreted in the extracellular medium. Their profile was also carbon-independent suggesting that intragenic uxuR transcripts have a specific regulatory role not directly related to the function of the protein in which gene they are encoded.
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Affiliation(s)
- Maria N. Tutukina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, FRC PRCBR, Pushchino, Russia
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
- *Correspondence: Maria N. Tutukina, , Olga N. Ozoline,
| | - Artemiy I. Dakhnovets
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Biotechnology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Anna D. Kaznadzey
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Mikhail S. Gelfand
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Olga N. Ozoline
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, FRC PRCBR, Pushchino, Russia
- *Correspondence: Maria N. Tutukina, , Olga N. Ozoline,
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Lan L, Liu J, Xing M, Smith AR, Wang J, Wu X, Appelman C, Li K, Roy A, Gowthaman R, Karanicolas J, Somoza AD, Wang CCC, Miao Y, De Guzman R, Oakley BR, Neufeld KL, Xu L. Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction. Cancers (Basel) 2020; 12:cancers12082221. [PMID: 32784494 PMCID: PMC7463734 DOI: 10.3390/cancers12082221] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/01/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
RNA-binding protein Musashi-1 (MSI1) is a key regulator of several stem cell populations. MSI1 is involved in tumor proliferation and maintenance, and it regulates target mRNAs at the translational level. The known mRNA targets of MSI1 include Numb, APC, and P21WAF-1, key regulators of Notch/Wnt signaling and cell cycle progression, respectively. In this study, we aim to identify small molecule inhibitors of MSI1-mRNA interactions, which could block the growth of cancer cells with high levels of MSI1. Using a fluorescence polarization (FP) assay, we screened small molecules from several chemical libraries for those that disrupt the binding of MSI1 to its consensus RNA. One cluster of hit compounds is the derivatives of secondary metabolites from Aspergillus nidulans. One of the top hits, Aza-9, from this cluster was further validated by surface plasmon resonance and nuclear magnetic resonance spectroscopy, which demonstrated that Aza-9 binds directly to MSI1, and the binding is at the RNA binding pocket. We also show that Aza-9 binds to Musashi-2 (MSI2) as well. To test whether Aza-9 has anti-cancer potential, we used liposomes to facilitate Aza-9 cellular uptake. Aza-9-liposome inhibits proliferation, induces apoptosis and autophagy, and down-regulates Notch and Wnt signaling in colon cancer cell lines. In conclusion, we identified a series of potential lead compounds for inhibiting MSI1/2 function, while establishing a framework for identifying small molecule inhibitors of RNA binding proteins using FP-based screening methodology.
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Affiliation(s)
- Lan Lan
- Departments of Molecular Biosciences, the University of Kansas, Lawrence, KS 66045, USA; (L.L.); (J.L.); (A.R.S.); (X.W.); (C.A.); (K.L.); (R.D.G.); (B.R.O.); (K.L.N.)
| | - Jiajun Liu
- Departments of Molecular Biosciences, the University of Kansas, Lawrence, KS 66045, USA; (L.L.); (J.L.); (A.R.S.); (X.W.); (C.A.); (K.L.); (R.D.G.); (B.R.O.); (K.L.N.)
| | - Minli Xing
- Bio-NMR Core Facility, the University of Kansas, Lawrence, KS 66045, USA;
| | - Amber R. Smith
- Departments of Molecular Biosciences, the University of Kansas, Lawrence, KS 66045, USA; (L.L.); (J.L.); (A.R.S.); (X.W.); (C.A.); (K.L.); (R.D.G.); (B.R.O.); (K.L.N.)
| | - Jinan Wang
- Center for Computational Biology, the University of Kansas, Lawrence, KS 66045, USA; (J.W.); (R.G.); (Y.M.)
| | - Xiaoqing Wu
- Departments of Molecular Biosciences, the University of Kansas, Lawrence, KS 66045, USA; (L.L.); (J.L.); (A.R.S.); (X.W.); (C.A.); (K.L.); (R.D.G.); (B.R.O.); (K.L.N.)
| | - Carl Appelman
- Departments of Molecular Biosciences, the University of Kansas, Lawrence, KS 66045, USA; (L.L.); (J.L.); (A.R.S.); (X.W.); (C.A.); (K.L.); (R.D.G.); (B.R.O.); (K.L.N.)
| | - Ke Li
- Departments of Molecular Biosciences, the University of Kansas, Lawrence, KS 66045, USA; (L.L.); (J.L.); (A.R.S.); (X.W.); (C.A.); (K.L.); (R.D.G.); (B.R.O.); (K.L.N.)
| | - Anuradha Roy
- High Throughput Screening Laboratory, the University of Kansas, Lawrence, KS 66045, USA;
| | - Ragul Gowthaman
- Center for Computational Biology, the University of Kansas, Lawrence, KS 66045, USA; (J.W.); (R.G.); (Y.M.)
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA;
| | - Amber D. Somoza
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007, USA; (A.D.S.); (C.C.C.W.)
| | - Clay C. C. Wang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007, USA; (A.D.S.); (C.C.C.W.)
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90007, USA
| | - Yinglong Miao
- Center for Computational Biology, the University of Kansas, Lawrence, KS 66045, USA; (J.W.); (R.G.); (Y.M.)
| | - Roberto De Guzman
- Departments of Molecular Biosciences, the University of Kansas, Lawrence, KS 66045, USA; (L.L.); (J.L.); (A.R.S.); (X.W.); (C.A.); (K.L.); (R.D.G.); (B.R.O.); (K.L.N.)
| | - Berl R. Oakley
- Departments of Molecular Biosciences, the University of Kansas, Lawrence, KS 66045, USA; (L.L.); (J.L.); (A.R.S.); (X.W.); (C.A.); (K.L.); (R.D.G.); (B.R.O.); (K.L.N.)
| | - Kristi L. Neufeld
- Departments of Molecular Biosciences, the University of Kansas, Lawrence, KS 66045, USA; (L.L.); (J.L.); (A.R.S.); (X.W.); (C.A.); (K.L.); (R.D.G.); (B.R.O.); (K.L.N.)
- Department of Cancer Biology, the University of Kansas Cancer Center, Kansas City, KS 66160, USA
| | - Liang Xu
- Departments of Molecular Biosciences, the University of Kansas, Lawrence, KS 66045, USA; (L.L.); (J.L.); (A.R.S.); (X.W.); (C.A.); (K.L.); (R.D.G.); (B.R.O.); (K.L.N.)
- Department of Radiation Oncology, the University of Kansas Cancer Center, Kansas City, KS 66160, USA
- Correspondence:
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Bateman A. Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells. Biol Direct 2020; 15:8. [PMID: 32345370 PMCID: PMC7187495 DOI: 10.1186/s13062-020-00260-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Abstract Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the second model, two prokaryotes, probably an archaeon and a bacterial cell, engaged in prokaryotic endosymbiosis, with the species resident within the host becoming the mitochondrial progenitor. Both models have limitations. A search was therefore undertaken for alternative routes towards the origin of eukaryotic cells. The question was addressed by considering classes of potential pathways from prokaryotic to eukaryotic cells based on considerations of cellular topology. Among the solutions identified, one, called here the “third-space model”, has not been widely explored. A version is presented in which an extracellular space (the third-space), serves as a proxy cytoplasm for mixed populations of archaea and bacteria to “merge” as a transitionary complex without obligatory endosymbiosis or phagocytosis and to form a precursor cell. Incipient nuclei and mitochondria diverge by division of labour. The third-space model can accommodate the reorganization of prokaryote-like genomes to a more eukaryote-like genome structure. Nuclei with multiple chromosomes and mitosis emerge as a natural feature of the model. The model is compatible with the loss of archaeal lipid biochemistry while retaining archaeal genes and provides a route for the development of membranous organelles such as the Golgi apparatus and endoplasmic reticulum. Advantages, limitations and variations of the “third-space” models are discussed. Reviewers This article was reviewed by Damien Devos, Buzz Baum and Michael Gray.
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Affiliation(s)
- Andrew Bateman
- Division of Experimental Medicine, Department of Medicine, McGill University, Glen Site Pavilion E, 1001 Boulevard Decarie, Montreal, Quebec, H4A 3J1, Canada. .,Centre for Translational Biology, Research Institute of McGill University Health Centre, Glen Site Pavilion E, 1001 Boulevard Decarie, Montreal, Quebec, H4A 3J1, Canada.
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