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Purtov YA, Ozoline ON. Neuromodulators as Interdomain Signaling Molecules Capable of Occupying Effector Binding Sites in Bacterial Transcription Factors. Int J Mol Sci 2023; 24:15863. [PMID: 37958845 PMCID: PMC10647483 DOI: 10.3390/ijms242115863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Hormones and neurotransmitters are important components of inter-kingdom signaling systems that ensure the coexistence of eukaryotes with their microbial community. Their ability to affect bacterial physiology, metabolism, and gene expression was evidenced by various experimental approaches, but direct penetration into bacteria has only recently been reported. This opened the possibility of considering neuromodulators as potential effectors of bacterial ligand-dependent regulatory proteins. Here, we assessed the validity of this assumption for the neurotransmitters epinephrine, dopamine, and norepinephrine and two hormones (melatonin and serotonin). Using flexible molecular docking for transcription factors with ligand-dependent activity, we assessed the ability of neuromodulators to occupy their effector binding sites. For many transcription factors, including the global regulator of carbohydrate metabolism, CRP, and the key regulator of lactose assimilation, LacI, this ability was predicted based on the analysis of several 3D models. By occupying the ligand binding site, neuromodulators can sterically hinder the interaction of the target proteins with the natural effectors or even replace them. The data obtained suggest that the direct modulation of the activity of at least some bacterial transcriptional factors by neuromodulators is possible. Therefore, the natural hormonal background may be a factor that preadapts bacteria to the habitat through direct perception of host signaling molecules.
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Affiliation(s)
- Yuri A. Purtov
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia
| | - Olga N. Ozoline
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia
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Di Somma A, Canè C, Moretta A, Cirillo A, Cemič F, Duilio A. Characterization of the Proteins Involved in the DNA Repair Mechanism in M. smegmatis. Int J Mol Sci 2020; 21:ijms21155391. [PMID: 32751237 PMCID: PMC7432924 DOI: 10.3390/ijms21155391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 11/26/2022] Open
Abstract
Several alkylating agents that either occur in the environment or are self-produced can cause DNA-damaging injuries in bacterial cells. Therefore, all microorganisms have developed repair systems that are able to counteract DNA alkylation damage. The adaptive response to alkylation stress in Escherichia coli consists of the Ada operon, which has been widely described; however, the homologous system in Mycobacterium tuberculosis (MTB) has been shown to have a different genetic organization but it is still largely unknown. In order to describe the defense system of MTB, we first investigated the proteins involved in the repair mechanism in the homologous non-pathogenic mycobacterium M. smegmatis. Ogt, Ada-AlkA and FadE8 proteins were recombinantly produced, purified and characterized. The biological role of Ogt was examined using proteomic experiments to identify its protein partners in vivo under stress conditions. Our results suggested the formation of a functional complex between Ogt and Ada-AlkA, which was confirmed both in silico by docking calculations and by gel filtration chromatography. We propose that this stable association allows the complex to fulfill the biological roles exerted by Ada in the homologous E. coli system. Finally, FadE8 was demonstrated to be structurally and functionally related to its E. coli homologous, AidB.
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Affiliation(s)
- Angela Di Somma
- Department of Chemical Sciences, Università Federico II di, 80126 Naples, Italy; (A.D.S.); (C.C.)
- Istituto Nazionale Biostrutture Biostrumentazioni, INBB, 00136 Rome, Italy
| | - Carolina Canè
- Department of Chemical Sciences, Università Federico II di, 80126 Naples, Italy; (A.D.S.); (C.C.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy;
| | - Antonio Moretta
- Department of Science, Università degli Studi della Basilicata, 85100 Potenza, Italy;
| | | | - Franz Cemič
- Department of Mathematics, Natural Sciences and Computer Science, University of Applied Sciences Giessen, Wiesenstr. 14, 35390 Giessen, Germany;
| | - Angela Duilio
- Department of Chemical Sciences, Università Federico II di, 80126 Naples, Italy; (A.D.S.); (C.C.)
- Correspondence:
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Di Somma A, Caterino M, Soni V, Agarwal M, di Pasquale P, Zanetti S, Molicotti P, Cannas S, Nandicoori VK, Duilio A. The bifunctional protein GlmU is a key factor in biofilm formation induced by alkylating stress in Mycobacterium smegmatis. Res Microbiol 2019; 170:171-181. [DOI: 10.1016/j.resmic.2019.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 10/27/2022]
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Di Pasquale P, Caterino M, Di Somma A, Squillace M, Rossi E, Landini P, Iebba V, Schippa S, Papa R, Selan L, Artini M, Palamara AT, Palamara A, Duilio A. Exposure of E. coli to DNA-Methylating Agents Impairs Biofilm Formation and Invasion of Eukaryotic Cells via Down Regulation of the N-Acetylneuraminate Lyase NanA. Front Microbiol 2016; 7:147. [PMID: 26904018 PMCID: PMC4749703 DOI: 10.3389/fmicb.2016.00147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/26/2016] [Indexed: 12/26/2022] Open
Abstract
DNA methylation damage can be induced by endogenous and exogenous chemical agents, which has led every living organism to develop suitable response strategies. We investigated protein expression profiles of Escherichia coli upon exposure to the alkylating agent methyl-methane sulfonate (MMS) by differential proteomics. Quantitative proteomic data showed a massive downregulation of enzymes belonging to the glycolytic pathway and fatty acids degradation, strongly suggesting a decrease of energy production. A strong reduction in the expression of the N-acetylneuraminate lyases (NanA) involved in the sialic acid metabolism was also observed. Using a null NanA mutant and DANA, a substrate analog acting as competitive inhibitor, we demonstrated that down regulation of NanA affects biofilm formation and adhesion properties of E. coli MV1161. Exposure to alkylating agents also decreased biofilm formation and bacterial adhesion to Caco-2 eukaryotic cell line by the adherent invasive E. coli (AIEC) strain LF82. Our data showed that methylation stress impairs E. coli adhesion properties and suggest a possible role of NanA in biofilm formation and bacteria host interactions.
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Affiliation(s)
- Pamela Di Pasquale
- Department of Chemical Sciences, University of Naples "Federico II" Naples, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II" Naples, Italy
| | - Angela Di Somma
- Department of Chemical Sciences, University of Naples "Federico II" Naples, Italy
| | - Marta Squillace
- Department of Chemical Sciences, University of Naples "Federico II" Naples, Italy
| | - Elio Rossi
- Department of Biosciences, University of Milan Milan, Italy
| | - Paolo Landini
- Department of Biosciences, University of Milan Milan, Italy
| | - Valerio Iebba
- Department of Public Health and Infectious Diseases, Pasteur Institute Cenci, Bolognetti Foundation, Sapienza University of Rome Rome, Italy
| | - Serena Schippa
- Department of Public Health and Infectious Diseases, Sapienza University of Rome Rome, Italy
| | - Rosanna Papa
- Department of Public Health and Infectious Diseases, Sapienza University of Rome Rome, Italy
| | - Laura Selan
- Department of Public Health and Infectious Diseases, Sapienza University of Rome Rome, Italy
| | - Marco Artini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome Rome, Italy
| | - Anna Teresa Palamara
- Department of Public Health and Infectious Diseases, Pasteur Institute Cenci, Bolognetti Foundation, Sapienza University of RomeRome, Italy; IRCCS, San Raffaele Pisana Telematic UniversityRome, Italy
| | | | - Angela Duilio
- Department of Chemical Sciences, University of Naples "Federico II" Naples, Italy
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Kreuzer KN. DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks. Cold Spring Harb Perspect Biol 2013; 5:a012674. [PMID: 24097899 DOI: 10.1101/cshperspect.a012674] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent advances in the area of bacterial DNA damage responses are reviewed here. The SOS pathway is still the major paradigm of bacterial DNA damage response, and recent studies have clarified the mechanisms of SOS induction and key physiological roles of SOS including a very major role in genetic exchange and variation. When considering diverse bacteria, it is clear that SOS is not a uniform pathway with one purpose, but rather a platform that has evolved for differing functions in different bacteria. Relating in part to the SOS response, the field has uncovered multiple apparent cell-cycle checkpoints that assist cell survival after DNA damage and remarkable pathways that induce programmed cell death in bacteria. Bacterial DNA damage responses are also much broader than SOS, and several important examples of LexA-independent regulation will be reviewed. Finally, some recent advances that relate to the replication and repair of damaged DNA will be summarized.
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Affiliation(s)
- Kenneth N Kreuzer
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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Van der Henst C, de Barsy M, Zorreguieta A, Letesson JJ, De Bolle X. The Brucella pathogens are polarized bacteria. Microbes Infect 2013; 15:998-1004. [PMID: 24141086 DOI: 10.1016/j.micinf.2013.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 10/01/2013] [Accepted: 10/03/2013] [Indexed: 11/30/2022]
Abstract
Brucella pathogens are responsible for brucellosis, a worldwide zoonosis. They are facultative intracellular pathogens characterized by their asymmetric division and their unipolar growth. This growth modality generates poles with specialized functions (through polar recruitment of polar adhesins or of cell cycle regulators) and progeny cells with potentially different fates.
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Affiliation(s)
- Charles Van der Henst
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
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Dotreppe D, Mullier C, Letesson JJ, De Bolle X. The alkylation response protein AidB is localized at the new poles and constriction sites in Brucella abortus. BMC Microbiol 2011; 11:257. [PMID: 22111948 PMCID: PMC3236019 DOI: 10.1186/1471-2180-11-257] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 11/23/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brucella abortus is the etiological agent of a worldwide zoonosis called brucellosis. This alpha-proteobacterium is dividing asymmetrically, and PdhS, an essential histidine kinase, was reported to be an old pole marker. RESULTS We were interested to identify functions that could be recruited to bacterial poles. The Brucella ORFeome, a collection of cloned predicted coding sequences, was placed in fusion with yellow fluorescent protein (YFP) coding sequence and screened for polar localizations in B. abortus. We report that AidB-YFP was systematically localized to the new poles and at constrictions sites in B. abortus, either in culture or inside infected HeLa cells or RAW264.7 macrophages. AidB is an acyl-CoA dehydrogenase (ACAD) homolog, similar to E. coli AidB, an enzyme putatively involved in destroying alkylating agents. Accordingly, a B. abortus aidB mutant is more sensitive than the wild-type strain to the lethality induced by methanesulphonic acid ethyl ester (EMS). The exposure to EMS led to a very low frequency of constriction events, suggesting that cell cycle is blocked during alkylation damage. The localization of AidB-YFP at the new poles and at constriction sites seems to be specific for this ACAD homolog since two other ACAD homologs fused to YFP did not show specific localization. The overexpression of aidB, but not the two other ACAD coding sequences, leads to multiple morphological defects. CONCLUSIONS Data reported here suggest that AidB is a marker of new poles and constriction sites, that could be considered as sites of preparation of new poles in the sibling cells originating from cell division. The possible role of AidB in the generation or the function of new poles needs further investigation.
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Affiliation(s)
- Delphine Dotreppe
- URBM, University of Namur (FUNDP), 61 rue de Bruxelles, Namur, 5000, Belgium
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Hamill M, Jost M, Wong C, Elliott SJ, Drennan CL. Flavin-induced oligomerization in Escherichia coli adaptive response protein AidB. Biochemistry 2011; 50:10159-69. [PMID: 22004173 PMCID: PMC3217306 DOI: 10.1021/bi201340t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The process known as "adaptive response" allows Escherichia coli to respond to small doses of DNA-methylating agents by upregulating the expression of four proteins. While the role of three of these proteins in mitigating DNA damage is well understood, the function of AidB is less clear. Although AidB is a flavoprotein, no catalytic role has been established for the bound cofactor. Here we investigate the possibility that flavin plays a structural role in the assembly of the AidB tetramer. We report the generation and biophysical characterization of deflavinated AidB and of an AidB mutant that has greatly reduced affinity for flavin adenine dinucleotide (FAD). Using fluorescence quenching and analytical ultracentrifugation, we find that apo AidB has a high affinity for FAD, as indicated by an apparent dissociation constant of 402.1 ± 35.1 nM, and that binding of substoichiometric amounts of FAD triggers a transition in the AidB oligomeric state. In particular, deflavinated AidB is dimeric, whereas the addition of FAD yields a tetramer. We further investigate the dimerization and tetramerization interfaces of AidB by determining a 2.8 Å resolution crystal structure in space group P3(2) that contains three intact tetramers in the asymmetric unit. Taken together, our findings provide strong evidence that FAD plays a structural role in the formation of tetrameric AidB.
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Affiliation(s)
- Michael
J. Hamill
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States,‡Department
of Chemistry, §Department of Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Environmental Health, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United
States
| | - Marco Jost
- ‡Department
of Chemistry, §Department of Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Environmental Health, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United
States
| | - Cintyu Wong
- ‡Department
of Chemistry, §Department of Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Environmental Health, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United
States
| | - Sean J. Elliott
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States,S.J.E.:
telephone, (617) 358-2816; fax, (617) 353-6466; e-mail, . C.L.D.: telephone, (617) 253-5622; fax, (617) 258-7847; e-mail,
| | - Catherine L. Drennan
- ‡Department
of Chemistry, §Department of Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Environmental Health, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United
States,S.J.E.:
telephone, (617) 358-2816; fax, (617) 353-6466; e-mail, . C.L.D.: telephone, (617) 253-5622; fax, (617) 258-7847; e-mail,
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Rippa V, Duilio A, di Pasquale P, Amoresano A, Landini P, Volkert MR. Preferential DNA damage prevention by the E. coli AidB gene: A new mechanism for the protection of specific genes. DNA Repair (Amst) 2011; 10:934-41. [PMID: 21788159 DOI: 10.1016/j.dnarep.2011.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 06/01/2011] [Accepted: 06/07/2011] [Indexed: 11/19/2022]
Abstract
aidB is one of the four genes of E. coli that is induced by alkylating agents and regulated by Ada protein. Three genes (ada, alkA, and alkB) encode DNA repair proteins that remove or repair alkylated bases. However, the role of AidB remains unclear despite extensive efforts to determine its function in cells exposed to alkylating agents. The E. coli AidB protein was identified as a component of the protein complex that assembles at strong promoters. We demonstrate that AidB protein preferentially binds to UP elements, AT rich transcription enhancer sequences found upstream of many highly expressed genes, several DNA repair genes, and housekeeping genes. AidB allows efficient transcription from promoters containing an UP element upon exposure to a DNA methylating agent and protects downstream genes from DNA damage. The DNA binding domain is required to target AidB to specific genes preferentially protecting them from alkylation damage. However, deletion of AidB's DNA binding domain does not prevent its antimutagenic activity, instead this deletion appears to allow AidB to function as a cytoplasmic alkylation resistance protein. Our studies identify the role of AidB in alkylating agent exposed cells and suggest a new cellular strategy in which a subset of the genome is preferentially protected from damage by alkylating agents.
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Affiliation(s)
- Valentina Rippa
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
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