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Rodionova IA, Gao Y, Monk J, Hefner Y, Wong N, Szubin R, Lim HG, Rodionov DA, Zhang Z, Saier MH, Palsson BO. A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli. Sci Rep 2022; 12:7274. [PMID: 35508583 PMCID: PMC9068703 DOI: 10.1038/s41598-022-11134-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/14/2022] [Indexed: 11/24/2022] Open
Abstract
Although Escherichia coli K-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs in E. coli BW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on the E. coli K-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YcaN, YbhD, YgfI, YiaU, YneJ. We show that: (1) YbdO (tentatively re-named CitR) regulation has an effect on bacterial growth at low pH with citrate supplementation. CitR is a repressor of the ybdNM operon and is implicated in the regulation of citrate lyase genes (citCDEFG); (2) YgfI (tentatively re-named DhfA) activates the dhaKLM operon that encodes the phosphotransferase system, DhfA is involved in formate, glycerol and dihydroxyacetone utilization; (3) YiaU (tentatively re-named LpsR) regulates the yiaT gene encoding an outer membrane protein, and waaPSBOJYZU operon is also important in determining cell density at the stationary phase and resistance to oxacillin microaerobically; (4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator of fnrS (a small RNA molecule). PtrR is important for bacterial growth in the presence of l-glutamate and putrescine as nitrogen/energy sources; and (5) YbhD and YcaN regulate adjacent y-genes on the genome. We have thus established the functions for four LTFs and identified the target genes for three LTFs.
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Affiliation(s)
- Irina A Rodionova
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA. .,Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA.
| | - Ye Gao
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA.,Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Jonathan Monk
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Ying Hefner
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Nicholas Wong
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Dmitry A Rodionov
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Zhongge Zhang
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Milton H Saier
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA. .,Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
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Navakoudis E, Kotzabasis K. Polyamines: Α bioenergetic smart switch for plant protection and development. JOURNAL OF PLANT PHYSIOLOGY 2022; 270:153618. [PMID: 35051689 DOI: 10.1016/j.jplph.2022.153618] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 05/27/2023]
Abstract
The present review highlights the bioenergetic role of polyamines in plant protection and development and proposes a universal model for describing polyamine-mediated stress responses. Any stress condition induces an excitation pressure on photosystem II by reforming the photosynthetic apparatus. To control this phenomenon, polyamines act directly on the molecular structure and function of the photosynthetic apparatus as well as on the components of the chemiosmotic proton-motive force (ΔpH/Δψ), thus regulating photochemical (qP) and non-photochemical quenching (NPQ) of energy. The review presents the mechanistic characteristics that underline the key role of polyamines in the structure, function, and bioenergetics of the photosynthetic apparatus upon light adaptation and/or under stress conditions. By following this mechanism, it is feasible to make stress-sensitive plants to be tolerant by simply altering their polyamine composition (especially the ratio of putrescine to spermine), either chemically or by light regulation.
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Affiliation(s)
- Eleni Navakoudis
- Department of Biology, University of Crete, Voutes University Campus, 70013, Heraklion, Greece; Department of Chemical Engineering, Cyprus University of Technology, 3603, Limassol, Cyprus
| | - Kiriakos Kotzabasis
- Department of Biology, University of Crete, Voutes University Campus, 70013, Heraklion, Greece.
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N1, N12-Diacetylspermine Is Elevated in Colorectal Cancer and Promotes Proliferation through the miR-559/CBS Axis in Cancer Cell Lines. JOURNAL OF ONCOLOGY 2021; 2021:6665704. [PMID: 34603448 PMCID: PMC8486517 DOI: 10.1155/2021/6665704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 08/06/2021] [Accepted: 08/15/2021] [Indexed: 01/05/2023]
Abstract
N1, N12-Diacetylspermine (DiAcSpm) has been reported to be upregulated in the urine of cancer patients. Mass spectrometry has shown elevated DiAcSpm expressions in colorectal cancer (CRC) tissues. However, the diagnostic application of DiAcSpm is not available due to a lack of diagnostic grade antibodies. Also, its biological roles in CRC cells remain unexplored. In the present study, we developed an antibody that directly detected DiAcSpm expression in paraffin-embedded tissues. We also characterized its biological characteristics and underlying mechanisms. Polyclonal antibodies were generated by immunizing animals with a synthetic product of DiAcSpm. Antibody DAS AB016 showed strong sensitivity against DiAcSpm in CRC tissues. Immunohistochemistry results showed that DiAcSpm expression was significantly elevated in CRC tissues. High levels of DiAcSpm correlated with the clinical stage and Ki67 index. DiAcSpm treatment increased levels of proliferation, cell cycle progression, and cyclin D1 and cyclin E proteins in CRC cell lines, SW480 and Caco-2. DiAcSpm also upregulated ATP production in these two cell lines. RNA-sequencing showed that DiAcSpm downregulated miR-559, which was confirmed using RT-qPCR. The luciferase reporter assay, western blotting, and RT-qPCR showed that cystathionine β-synthase (CBS) was the target of miR-559. miR-559 inhibited, while CBS accelerated, CRC proliferation. In addition, CBS siRNA knockdown blocked the biological effects of DiAcSpm on CRC cells. In conclusion, DiAcSpm was found to be increased in CRC tissues using a newly developed antibody. DiAcSpm accelerated CRC proliferation by regulating the miR-559/CBS axis.
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Bazoni RF, Moura TA, Rocha MS. Hydroxychloroquine Exhibits a Strong Complex Interaction with DNA: Unraveling the Mechanism of Action. J Phys Chem Lett 2020; 11:9528-9534. [PMID: 33115235 DOI: 10.1021/acs.jpclett.0c02590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In the past months, the use of the drug hydroxychloroquine has considerably increased in many countries, associated with a proposed treatment for the COVID-19 disease. Although there is no conclusive evidence about the efficacy of the drug for this purpose, surprisingly there are no conclusive studies in the literature concerning its mechanism of action inside cells, which is related to its interaction with nucleic acids. Here, we performed a robust characterization of the interaction between hydroxychloroquine and double-stranded DNA using single-molecule force spectroscopy and gel electrophoresis. Two different binding modes were identified, namely, minor groove binding for low drug concentrations and intercalation for high drug concentrations, and the sets of binding parameters were determined for each of these modes. Such results have unraveled in detail the molecular mechanism of action of the drug as a DNA ligand.
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Affiliation(s)
- R F Bazoni
- Departamento de Ciências Naturais, Universidade Federal do Espírito Santo, São Mateus, Espírito Santo 29.932-540, Brazil
| | - T A Moura
- Departamento de Física, Universidade Federal de Viçosa. Viçosa, Minas Gerais 36.570-900, Brazil
| | - M S Rocha
- Departamento de Física, Universidade Federal de Viçosa. Viçosa, Minas Gerais 36.570-900, Brazil
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Freeland J, Zhang L, Wang ST, Ruiz M, Wang Y. Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules. SENSORS (BASEL, SWITZERLAND) 2020; 20:E3112. [PMID: 32486417 PMCID: PMC7309149 DOI: 10.3390/s20113112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/23/2020] [Accepted: 05/29/2020] [Indexed: 01/20/2023]
Abstract
Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.
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Affiliation(s)
- Jack Freeland
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA; (J.F.); (M.R.)
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Lihua Zhang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA; (L.Z.); (S.-T.W.)
| | - Shih-Ting Wang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA; (L.Z.); (S.-T.W.)
| | - Mason Ruiz
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA; (J.F.); (M.R.)
- Department of Biology, University of Arkansas, Fayetteville, AR 72701, USA
| | - Yong Wang
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA; (J.F.); (M.R.)
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
- Microelectronics-Photonics Program, University of Arkansas, Fayetteville, AR 72701, USA
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Alves PS, Mesquita ON, Rocha MS. Model for DNA Interactions with Proteins and Other Large Ligands: Extracting Physical Chemistry from Pure Mechanical Measurements. J Phys Chem B 2020; 124:1020-1024. [DOI: 10.1021/acs.jpcb.0c00155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. S. Alves
- Instituto Federal de Educaçào, Ciência e Tecnologia de Minas Gerais, Santa Luzia, Minas Gerais 30575-180, Brazil
- Departamento de Fı́sica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901 Brazil
| | - O. N. Mesquita
- Departamento de Fı́sica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901 Brazil
| | - M. S. Rocha
- Departamento de Fı́sica, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900 Brazil
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