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Grechishnikova EG, Shemyakina AO, Novikov AD, Lavrov KV, Yanenko AS. Rhodococcus: sequences of genetic parts, analysis of their functionality, and development prospects as a molecular biology platform. Crit Rev Biotechnol 2023; 43:835-850. [PMID: 35786136 DOI: 10.1080/07388551.2022.2091976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/19/2022] [Accepted: 05/12/2022] [Indexed: 12/19/2022]
Abstract
Rhodococcus bacteria are a fast-growing platform for biocatalysis, biodegradation, and biosynthesis, but not a platform for molecular biology. That is, Rhodococcus are not convenient for genetic engineering. One major issue for the engineering of Rhodococcus is the absence of a publicly available, curated, and commented collection of sequences of genetic parts that are functional in biotechnologically relevant species of Rhodococcus (R. erythropolis, R. rhodochrous, R. ruber, and R. jostii). Here, we present a collection of genetic parts for Rhodococcus (vector replicons, promoter regions, regulators, markers, and reporters) supported by a thorough analysis of their functionality. We also highlight and discuss the gaps in Rhodococcus-related genetic parts and techniques, which should be filled in order to make these bacteria a full-fledged molecular biology platform independent of Escherichia coli. We conclude that all major types of required genetic parts for Rhodococcus are available now, except multicopy replicons. As for model Rhodococcus strains, there is a particular shortage of strains with high electrocompetence levels and strains designed for solving specific genetic engineering tasks. We suggest that these obstacles are surmountable in the near future due to an intensification of research work in the field of genetic techniques for non-conventional bacteria.
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Affiliation(s)
- Elena G Grechishnikova
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Anna O Shemyakina
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Andrey D Novikov
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Konstantin V Lavrov
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Alexander S Yanenko
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
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Nazarov PA, Khrulnova SA, Kessenikh AG, Novoyatlova US, Kuznetsova SB, Bazhenov SV, Sorochkina AI, Karakozova MV, Manukhov IV. Observation of Cytotoxicity of Phosphonium Derivatives Is Explained: Metabolism Inhibition and Adhesion Alteration. Antibiotics (Basel) 2023; 12:antibiotics12040720. [PMID: 37107081 PMCID: PMC10135132 DOI: 10.3390/antibiotics12040720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/29/2023] Open
Abstract
The search for new antibiotics, substances that kill prokaryotic cells and do not kill eukaryotic cells, is an urgent need for modern medicine. Among the most promising are derivatives of triphenylphosphonium, which can protect the infected organs of mammals and heal damaged cells as mitochondria-targeted antioxidants. In addition to the antioxidant action, triphenylphosphonium derivatives exhibit antibacterial activity. It has recently been reported that triphenylphosphonium derivatives cause either cytotoxic effects or inhibition of cellular metabolism at submicromolar concentrations. In this work, we analyzed the MTT data using microscopy and compared them with data on changes in the luminescence of bacteria. We have shown that, at submicromolar concentrations, only metabolism is inhibited, while an increase in alkyltriphenylphosphonium (CnTPP) concentration leads to adhesion alteration. Thus, our data on eukaryotic and prokaryotic cells confirm a decrease in the metabolic activity of cells by CnTPPs but do not confirm a cytocidal effect of TPPs at submicromolar concentrations. This allows us to consider CnTPP as a non-toxic antibacterial drug at low concentrations and a relatively safe vector for delivering other antibacterial substances into bacterial cells.
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Affiliation(s)
- Pavel A Nazarov
- Moscow Institute of Physics and Technology,141700 Dolgoprudny, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Svetlana A Khrulnova
- Moscow Institute of Physics and Technology,141700 Dolgoprudny, Russia
- National Research Center for Hematology, 117198 Moscow, Russia
| | - Andrew G Kessenikh
- Moscow Institute of Physics and Technology,141700 Dolgoprudny, Russia
- Laboratory for Microbiology, BIOTECH University, 125080 Moscow, Russia
| | - Uliana S Novoyatlova
- Moscow Institute of Physics and Technology,141700 Dolgoprudny, Russia
- Laboratory for Microbiology, BIOTECH University, 125080 Moscow, Russia
| | | | - Sergey V Bazhenov
- Moscow Institute of Physics and Technology,141700 Dolgoprudny, Russia
- Laboratory for Microbiology, BIOTECH University, 125080 Moscow, Russia
| | - Alexandra I Sorochkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Marina V Karakozova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Ilya V Manukhov
- Moscow Institute of Physics and Technology,141700 Dolgoprudny, Russia
- Laboratory for Microbiology, BIOTECH University, 125080 Moscow, Russia
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Fomin V, Bazhenov S, Kononchuk O, Matveeva V, Zarubina A, Spiridonov S, Manukhov I. Photorhabdus lux-operon heat shock-like regulation. Heliyon 2023; 9:e14527. [PMID: 36950606 PMCID: PMC10025913 DOI: 10.1016/j.heliyon.2023.e14527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/20/2023] [Accepted: 03/09/2023] [Indexed: 03/13/2023] Open
Abstract
For decades, transcription of Photorhabdus luminescens lux-operon was considered being constitutive. Therefore, this lux-operon has been used for measurements in non-specific bacterial luminescent biosensors. Here, the expression of Photorhabdus lux-operon under high temperature was studied. The expression was researched in the natural strain Photorhabdus temperata and in the heterologous system of Escherichia coli. P. temperata FV2201 bacterium was isolated from soil in the Moscow region (growth optimum 28 °C). We showed that its luminescence significantly increases when the temperature rises to 34 °C. The increase in luminescence is associated with an increase in the transcription of luxCDABE genes, which was confirmed by RT-PCR. The promoter of the lux-operon of the related bacterium P. luminescens ZM1 from the forests of Moldova, being cloned in the heterologous system of E. coli, is activated when the temperature rises from room temperature to 42 °C. When heat shock is caused by ethanol addition, transcription of lux-operon increases only in the natural strain of P. temperata, but not in the heterologous system of E. coli cells. In addition, the activation of the lux-operon of P. luminescens persists in E. coli strains deficient in both the rpoH and rpoE genes. These results indicate the presence of sigma 32 and sigma 24 independent heat-shock-like mechanism of regulation of the lux-operon of P. luminescens in the heterologous E. coli system.
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Affiliation(s)
- V.V. Fomin
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, Institutsky Lane 9, Dolgoprudny, Moscow Region, 141700, Russian Federation
- Laboratory of Microbiology, BIOTECH University, Volokolamskoe Highway 11, Moscow 125080, Russian Federation
| | - S.V. Bazhenov
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, Institutsky Lane 9, Dolgoprudny, Moscow Region, 141700, Russian Federation
| | - O.V. Kononchuk
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, Institutsky Lane 9, Dolgoprudny, Moscow Region, 141700, Russian Federation
- Laboratory of Microbiology, BIOTECH University, Volokolamskoe Highway 11, Moscow 125080, Russian Federation
| | - V.O. Matveeva
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, Institutsky Lane 9, Dolgoprudny, Moscow Region, 141700, Russian Federation
| | - A.P. Zarubina
- Biological Faculty, Lomonosov Moscow State University, Vorob’evy Gory, Moscow, 119992, Russian Federation
| | - S.E. Spiridonov
- Centre of Parasitology, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii Prospect, 33, Moscow, 119071, Russian Federation
| | - I.V. Manukhov
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, Institutsky Lane 9, Dolgoprudny, Moscow Region, 141700, Russian Federation
- Corresponding author.
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Burmistrov V, Morisseau C, Babkov DA, Golubeva T, Pitushkin D, Sokolova EV, Vasipov V, Kuznetsov Y, Bazhenov SV, Novoyatlova US, Bondarev NA, Manukhov IV, Osipova V, Berberova N, Spasov AA, Butov GM, Hammock BD. Anti-Inflammatory Activity of Soluble Epoxide Hydrolase Inhibitors Based on Selenoureas Bearing an Adamantane Moiety. Int J Mol Sci 2022; 23:10710. [PMID: 36142611 PMCID: PMC9501280 DOI: 10.3390/ijms231810710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
The inhibitory potency of the series of inhibitors of the soluble epoxide hydrolase (sEH) based on the selenourea moiety and containing adamantane and aromatic lipophilic groups ranges from 34.3 nM to 1.2 μM. The most active compound 5d possesses aliphatic spacers between the selenourea group and lipophilic fragments. Synthesized compounds were tested against the LPS-induced activation of primary murine macrophages. The most prominent anti-inflammatory activity, defined as a suppression of nitric oxide synthesis by LPS-stimulated macrophages, was demonstrated for compounds 4a and 5b. The cytotoxicity of the obtained substances was studied using human neuroblastoma and fibroblast cell cultures. Using these cell assays, the cytotoxic concentration for 4a was 4.7–18.4 times higher than the effective anti-inflammatory concentration. The genotoxicity and the ability to induce oxidative stress was studied using bacterial lux-biosensors. Substance 4a does not exhibit genotoxic properties, but it can cause oxidative stress at concentrations above 50 µM. Put together, the data showed the efficacy and safety of compound 4a.
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Kessenikh AG, Novoyatlova US, Bazhenov SV, Stepanova EA, Khrulnova SA, Gnuchikh EY, Kotova VY, Kudryavtseva AA, Bermeshev MV, Manukhov IV. Constructing of Bacillus subtilis-Based Lux-Biosensors with the Use of Stress-Inducible Promoters. Int J Mol Sci 2021; 22:9571. [PMID: 34502476 DOI: 10.3390/ijms22179571] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Here, we present a new lux-biosensor based on Bacillus subtilis for detecting of DNA-tropic and oxidative stress-causing agents. Hybrid plasmids pNK-DinC, pNK-AlkA, and pNK-MrgA have been constructed, in which the Photorhabdus luminescens reporter genes luxABCDE are transcribed from the stress-inducible promoters of B. subtilis: the SOS promoter PdinC, the methylation-specific response promoter PalkA, and the oxidative stress promoter PmrgA. The luminescence of B. subtilis-based biosensors specifically increases in response to the appearance in the environment of such common toxicants as mitomycin C, methyl methanesulfonate, and H2O2. Comparison with Escherichia coli-based lux-biosensors, where the promoters PdinI, PalkA, and Pdps were used, showed generally similar characteristics. However, for B. subtilis PdinC, a higher response amplitude was observed, and for B. subtilis PalkA, on the contrary, both the amplitude and the range of detectable toxicant concentrations were decreased. B. subtilis PdinC and B. subtilis PmrgA showed increased sensitivity to the genotoxic effects of the 2,2'-bis(bicyclo [2.2.1] heptane) compound, which is a promising propellant, compared to E. coli-based lux-biosensors. The obtained biosensors are applicable for detection of toxicants introduced into soil. Such bacillary biosensors can be used to study the differences in the mechanisms of toxicity against Gram-positive and Gram-negative bacteria.
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Chen J, Wei H, Guo Y, Li Q, Wang H, Liu J. Chaperone-mediated protein folding enhanced D-psicose 3-epimerase expression in engineered Bacillus subtilis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kessenikh A, Gnuchikh E, Bazhenov S, Bermeshev M, Pevgov V, Samoilov V, Shorunov S, Maksimov A, Yaguzhinsky L, Manukhov I. Genotoxic effect of 2,2'-bis(bicyclo[2.2.1] heptane) on bacterial cells. PLoS One 2020; 15:e0228525. [PMID: 32822344 PMCID: PMC7444485 DOI: 10.1371/journal.pone.0228525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/07/2020] [Indexed: 12/30/2022] Open
Abstract
The toxic effect of strained hydrocarbon 2,2'-bis (bicyclo[2.2.1]heptane) (BBH) was studied using whole-cell bacterial lux-biosensors based on Escherichia coli cells in which luciferase genes are transcriptionally fused with stress-inducible promoters. It was shown that BBH has the genotoxic effect causing bacterial SOS response however no alkylating effect has been revealed. In addition to DNA damage, there is an oxidative effect causing the response of OxyR/S and SoxR/S regulons. The most sensitive to BBH lux-biosensor was E. coli pSoxS-lux which reacts to the appearance of superoxide anion radicals in the cell. It is assumed that the oxidation of BBH leads to the generation of reactive oxygen species, which provide the main contribution to the genotoxicity of this substance.
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Affiliation(s)
- A. Kessenikh
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
| | - E. Gnuchikh
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Centre “Kurchatov Institute”, Kurchatov Genomic Center, Moscow, Russia
- NRC “Kurchatov Institute”, Moscow, Russia
| | - S. Bazhenov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
| | - M. Bermeshev
- Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - V. Pevgov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
| | - V. Samoilov
- Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - S. Shorunov
- Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - A. Maksimov
- Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - L. Yaguzhinsky
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
- AN Belozersky Res Inst Physicochem Biol, Moscow MV Lomonosov State Univ, Moscow, Russia
| | - I. Manukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Centre “Kurchatov Institute”, Kurchatov Genomic Center, Moscow, Russia
- * E-mail:
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