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Rybina AA, Glushak RA, Bessonova TA, Dakhnovets AI, Rudenko AY, Ozhiganov RM, Kaznadzey AD, Tutukina MN, Gelfand MS. Phylogeny and structural modeling of the transcription factor CsqR (YihW) from Escherichia coli. Sci Rep 2024; 14:7852. [PMID: 38570624 PMCID: PMC10991401 DOI: 10.1038/s41598-024-58492-y] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/29/2024] [Indexed: 04/05/2024] Open
Abstract
CsqR (YihW) is a local transcription factor that controls expression of yih genes involved in degradation of sulfoquinovose in Escherichia coli. We recently showed that expression of the respective gene cassette might be regulated by lactose. Here, we explore the phylogenetic and functional traits of CsqR. Phylogenetic analysis revealed that CsqR had a conserved Met25. Western blot demonstrated that CsqR was synthesized in the bacterial cell as two protein forms, 28.5 (CsqR-l) and 26 kDa (CsqR-s), the latter corresponding to start of translation at Met25. CsqR-s was dramatically activated during growth with sulfoquinovose as a sole carbon source, and displaced CsqR-l in the stationary phase during growth on rich medium. Molecular dynamic simulations revealed two possible states of the CsqR-s structure, with the interdomain linker being represented by either a disordered loop or an ɑ-helix. This helix allowed the hinge-like motion of the N-terminal domain resulting in a switch of CsqR-s between two conformational states, "open" and "compact". We then modeled the interaction of both CsqR forms with putative effectors sulfoquinovose, sulforhamnose, sulfoquinovosyl glycerol, and lactose, and revealed that they all preferred the same pocket in CsqR-l, while in CsqR-s there were two possible options dependent on the linker structure.
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Affiliation(s)
- Anna A Rybina
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205.
| | - Roman A Glushak
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Tatiana A Bessonova
- Institute of Cell Biophysics RAS (Federal Research Center "Pushchino Scientific Center for Biological Research RAS"), Pushchino, Russia, 142290
| | | | - Alexander Yu Rudenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Ratislav M Ozhiganov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Anna D Kaznadzey
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
| | - Maria N Tutukina
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
- Institute of Cell Biophysics RAS (Federal Research Center "Pushchino Scientific Center for Biological Research RAS"), Pushchino, Russia, 142290
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Semenkov IN, Shelyakin PV, Nikolaeva DD, Tutukina MN, Sharapova AV, Lednev SA, Sarana YV, Gelfand MS, Krechetov PP, Koroleva TV. Data on the temporal changes in soil properties and microbiome composition after a jet-fuel contamination during the pot and field experiments. Data Brief 2022; 46:108860. [PMID: 36632439 PMCID: PMC9826931 DOI: 10.1016/j.dib.2022.108860] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
The soil response to a jet-fuel contamination is uncertain. In this article, original data on the influence of a jet-fuel spillage on the topsoil properties are presented. The data set is obtained during a one-year long pot and field experiments with Dystric Arenosols, Fibric Histosols and Albic Luvisols. Kerosene loads were 1, 5, 10, 25 and 100 g/kg. The data set includes information about temporal changes in kerosene concentration; physicochemical properties, such as рН, moisture, cation exchange capacity, content of soil organic matter, available P and K, exchangeable NH4 +, and water-soluble NO3 -; and biological properties, such as biological consumption of oxygen, and cellulolytic activity. Also, we provide sequencing data on variable regions of 16S ribosomal RNA of microbial communities from the respective soil samples.
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Key Words
- AL, Albic Luvisols
- ASV, amplicon sequence variant
- Bearing capacity
- CA, cellulolytic activity
- CEC, cation exchange capacity
- DA, Dystric Arenosols
- DNA, deoxyribonucleic acid
- EDTA, Ethylenediaminetetraacetic acid
- Ecological indicators
- FH, Fibric Histosols
- Gasoline
- Kav, available potassium
- NH4+, exchangeable ammonium
- NO3–, water-soluble nitrate
- PCR, polymerase chain reaction
- Pav, available phosphorus
- SOM, soil organic matter
- Soil metagenome
- Soil pollution
- Total petroleum hydrocarbons
- WMO, World Meteorological Organization
- Xenobiotic compounds
- qPCR, real-time polymerase chain reaction
- rRNA, ribosomal ribonucleic acid
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Affiliation(s)
- Ivan N. Semenkov
- M.V. Lomonosov Moscow State University, 119991 Moscow, Russia,Correspondence.
| | - Pavel V. Shelyakin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia,Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | | | - Maria N. Tutukina
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia,Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | | | | | - Yuliya V. Sarana
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Mikhail S. Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia,Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
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4
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Bessonova TA, Fando MS, Kostareva OS, Tutukina MN, Ozoline ON, Gelfand MS, Nikulin AD, Tishchenko SV. Differential Impact of Hexuronate Regulators ExuR and UxuR on the Escherichia coli Proteome. Int J Mol Sci 2022; 23:ijms23158379. [PMID: 35955512 PMCID: PMC9369180 DOI: 10.3390/ijms23158379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the Escherichia coli proteome in response to a uxuR or exuR deletion. Our data clearly show that the effects are different: deletion of uxuR resulted in strongly enhanced expression of D-mannonate dehydratase UxuA and flagellar protein FliC, and in a reduced amount of outer membrane porin OmpF, while the absence of ExuR did not significantly alter the spectrum of detected proteins. Consequently, the physiological roles of proteins predicted as homologs seem to be far from identical. Effects of uxuR deletion were largely dependent on the cultivation conditions: during growth with glucose, UxuA and FliC were dramatically altered, while during growth with glucuronate, activation of both was not so prominent. During the growth with glucose, maximal activation was detected for FliC. This was further confirmed by expression analysis and physiological tests, thus suggesting the involvement of UxuR in the regulation of bacterial motility and biofilm formation.
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Affiliation(s)
- Tatiana A. Bessonova
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
| | - Maria S. Fando
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Olga S. Kostareva
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Maria N. Tutukina
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30 Build 1, Moscow 121205, Russia;
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per 19 Build 1, Moscow 127051, Russia
- Correspondence:
| | - Olga N. Ozoline
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
| | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30 Build 1, Moscow 121205, Russia;
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per 19 Build 1, Moscow 127051, Russia
| | - Alexey D. Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Svetlana V. Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
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5
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Shelyakin PV, Semenkov IN, Tutukina MN, Nikolaeva DD, Sharapova AV, Sarana YV, Lednev SA, Smolenkov AD, Gelfand MS, Krechetov PP, Koroleva TV. The Influence of Kerosene on Microbiomes of Diverse Soils. Life (Basel) 2022; 12:life12020221. [PMID: 35207510 PMCID: PMC8878009 DOI: 10.3390/life12020221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 01/04/2023] Open
Abstract
One of the most important challenges for soil science is to determine the limits for the sustainable functioning of contaminated ecosystems. The response of soil microbiomes to kerosene pollution is still poorly understood. Here, we model the impact of kerosene leakage on the composition of the topsoil microbiome in pot and field experiments with different loads of added kerosene (loads up to 100 g/kg; retention time up to 360 days). At four time points we measured kerosene concentration and sequenced variable regions of 16S ribosomal RNA in the microbial communities. Mainly alkaline Dystric Arenosols with low content of available phosphorus and soil organic matter had an increased fraction of Actinobacteriota, Firmicutes, Nitrospirota, Planctomycetota, and, to a lesser extent, Acidobacteriota and Verrucomicobacteriota. In contrast, in highly acidic Fibric Histosols, rich in soil organic matter and available phosphorus, the fraction of Acidobacteriota was higher, while the fraction of Actinobacteriota was lower. Albic Luvisols occupied an intermediate position in terms of both physicochemical properties and microbiome composition. The microbiomes of different soils show similar response to equal kerosene loads. In highly contaminated soils, the proportion of anaerobic bacteria-metabolizing hydrocarbons increased, whereas the proportion of aerobic bacteria decreased. During the field experiment, the soil microbiome recovered much faster than in the pot experiments, possibly due to migration of microorganisms from the polluted area. The microbial community of Fibric Histosols recovered in 6 months after kerosene had been loaded, while microbiomes of Dystric Arenosols and Albic Luvisols did not restore even after a year.
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Affiliation(s)
- Pavel V. Shelyakin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia; (P.V.S.); (M.N.T.); (D.D.N.); (M.S.G.)
- Department of Computational Biology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Ivan N. Semenkov
- Faculty of Geography, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (A.V.S.); (S.A.L.); (P.P.K.); (T.V.K.)
- Correspondence:
| | - Maria N. Tutukina
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia; (P.V.S.); (M.N.T.); (D.D.N.); (M.S.G.)
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, 142290 Moscow, Russia
| | - Daria D. Nikolaeva
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia; (P.V.S.); (M.N.T.); (D.D.N.); (M.S.G.)
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Anna V. Sharapova
- Faculty of Geography, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (A.V.S.); (S.A.L.); (P.P.K.); (T.V.K.)
| | - Yulia V. Sarana
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Sergey A. Lednev
- Faculty of Geography, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (A.V.S.); (S.A.L.); (P.P.K.); (T.V.K.)
| | | | - Mikhail S. Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia; (P.V.S.); (M.N.T.); (D.D.N.); (M.S.G.)
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Pavel P. Krechetov
- Faculty of Geography, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (A.V.S.); (S.A.L.); (P.P.K.); (T.V.K.)
| | - Tatiana V. Koroleva
- Faculty of Geography, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (A.V.S.); (S.A.L.); (P.P.K.); (T.V.K.)
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Bessonova TA, Lekontseva NV, Shvyreva US, Nikulin AD, Tutukina MN, Ozoline ON. Overproduction and purification of the Escherichia coli transcription factors "toxic" to a bacterial cell. Protein Expr Purif 2019; 161:70-77. [PMID: 31054315 DOI: 10.1016/j.pep.2019.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 03/19/2019] [Revised: 04/25/2019] [Accepted: 05/01/2019] [Indexed: 11/28/2022]
Abstract
Transcription factors play a crucial role in control of life of a bacterial cell, working as switchers to a different life style or pathogenicity. To reconstruct the network of regulatory events taking place in changing growth conditions, we need to know regulons of as many transcription factors as possible, and motifs recognized by them. Experimentally this can be attained via ChIP-seq in vivo, SELEX and DNAse I footprinting in vitro. All these approaches require large amounts of purified proteins. However, overproduction of transcription factors leading to their extensive binding to the regulatory elements on the DNA make them toxic to a bacterial cell thus significantly complicating production of a soluble protein. Here, on the example of three regulators from Escherichia coli, UxuR, ExuR, and LeuO, we show that stable production of toxic transcription factors in a soluble fraction can be significantly enhanced by holding the expression of a recombinant protein back at the early stages of bacterial growth. This can be achieved by cloning genes together with their regulatory regions containing repressor sites, with subsequent growth in a very rich media where activity of excessive regulators is not crucial, followed by induction with a very low concentration of an inducer. Schemes of further purification of these proteins were developed, and functional activity was confirmed.
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Affiliation(s)
- Tatiana A Bessonova
- Institute of Cell Biophysics of RAS, Pushchino, Moscow region, 142290, Russia; Institute of Protein Research RAS, Pushchino, Moscow region, 142290, Russia; Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | - Uliana S Shvyreva
- Institute of Cell Biophysics of RAS, Pushchino, Moscow region, 142290, Russia; Institute of Protein Research RAS, Pushchino, Moscow region, 142290, Russia
| | - Alexey D Nikulin
- Institute of Protein Research RAS, Pushchino, Moscow region, 142290, Russia
| | - Maria N Tutukina
- Institute of Cell Biophysics of RAS, Pushchino, Moscow region, 142290, Russia; Kharkevich Institute for Information Transmission Problems RAS, Moscow, 127051, Russia
| | - Olga N Ozoline
- Institute of Cell Biophysics of RAS, Pushchino, Moscow region, 142290, Russia
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7
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Alikina OV, Glazunova OA, Bykov AA, Kiselev SS, Tutukina MN, Shavkunov KS, Ozoline ON. A cohabiting bacterium alters the spectrum of short RNAs secreted by Escherichia coli. FEMS Microbiol Lett 2018; 365:5146451. [PMID: 30376063 DOI: 10.1093/femsle/fny262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/28/2018] [Indexed: 02/07/2023] Open
Abstract
Recently, it has been found that bacteria secrete short RNAs able to affect gene expression in eukaryotic cells, while certain mammalian microRNAs shape the gut microbiome altering bacterial transcriptome. The involvement of bacterial RNAs in communication with other bacteria is also expected, but has not been documented yet. Here, we compared the fractions of extremely short (12-22 nucleotides) RNAs secreted by Escherichia coli grown in a pure culture and jointly with bacteria of the Paenibacillus genus. Besides fragments of rRNAs and tRNAs, abundant in all samples, secreted oligonucleotides (exoRNAs) predominantly contained GC-rich fragments of messenger and antisense RNAs processed from regions with stable secondary structures. They differed in composition from oligonucleotides of intracellular fraction, where fragments of small regulatory RNAs were prevalent. Both fractions contained RNAs capable of forming complementary duplexes, while for exoRNA samples a higher percentage of 3΄-end modified RNAs and different endonuclease cleavage were detected. The presence of a cohabiting bacterium altered the spectrum of E. coli exoRNAs, indicating a population-dependent control over their composition. Possible mechanisms of this effect are discussed.
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MESH Headings
- Biological Transport
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Genome, Bacterial
- Nucleic Acid Conformation
- RNA, Antisense/chemistry
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Olga V Alikina
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Olga A Glazunova
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Alexandr A Bykov
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Sergey S Kiselev
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Maria N Tutukina
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Konstantin S Shavkunov
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Olga N Ozoline
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
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8
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Orlova MV, Tarlachkov SV, Dubinina GA, Belousova EV, Tutukina MN, Grabovich MY. Genomic insights into metabolic versatility of a lithotrophic sulfur-oxidizing diazotrophic AlphaproteobacteriumAzospirillum thiophilum. FEMS Microbiol Ecol 2016; 92:fiw199. [DOI: 10.1093/femsec/fiw199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2016] [Indexed: 11/14/2022] Open
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9
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Tutukina MN, Potapova AV, Cole JA, Ozoline ON. Control of hexuronate metabolism in Escherichia coli by the two interdependent regulators, ExuR and UxuR: derepression by heterodimer formation. Microbiology (Reading) 2016; 162:1220-1231. [DOI: 10.1099/mic.0.000297] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Maria N. Tutukina
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Russia
| | - Anna V. Potapova
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Russia
| | - Jeffrey A. Cole
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Olga N. Ozoline
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Russia
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10
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Tutukina MN, Potapova AV, Vlasov PK, Purtov YA, Ozoline ON. Structural modeling of the ExuR and UxuR transcription factors of E. coli: search for the ligands affecting their regulatory properties. J Biomol Struct Dyn 2016; 34:2296-304. [DOI: 10.1080/07391102.2015.1115779] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Maria N. Tutukina
- Institute of Cell Biophysics Russian Academy of Sciences, Institutskaya str., 3, Pushchino, Moscow Region 142290, Russia
| | - Anna V. Potapova
- Institute of Cell Biophysics Russian Academy of Sciences, Institutskaya str., 3, Pushchino, Moscow Region 142290, Russia
| | - Peter K. Vlasov
- Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), C/Dr. Aiguader, 88, Barcelona 08003, Spain
| | - Yuri A. Purtov
- Institute of Cell Biophysics Russian Academy of Sciences, Institutskaya str., 3, Pushchino, Moscow Region 142290, Russia
| | - Olga N. Ozoline
- Institute of Cell Biophysics Russian Academy of Sciences, Institutskaya str., 3, Pushchino, Moscow Region 142290, Russia
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11
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Melekhov VV, Shvyreva US, Timchenko AA, Tutukina MN, Preobrazhenskaya EV, Burkova DV, Artiukhov VG, Ozoline ON, Antipov SS. Modes of Escherichia coli Dps Interaction with DNA as Revealed by Atomic Force Microscopy. PLoS One 2015; 10:e0126504. [PMID: 25978038 PMCID: PMC4433220 DOI: 10.1371/journal.pone.0126504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/02/2015] [Indexed: 11/18/2022] Open
Abstract
Multifunctional protein Dps plays an important role in iron assimilation and a crucial role in bacterial genome packaging. Its monomers form dodecameric spherical particles accumulating ~400 molecules of oxidized iron ions within the protein cavity and applying a flexible N-terminal ends of each subunit for interaction with DNA. Deposition of iron is a well-studied process by which cells remove toxic Fe2+ ions from the genetic material and store them in an easily accessible form. However, the mode of interaction with linear DNA remained mysterious and binary complexes with Dps have not been characterized so far. It is widely believed that Dps binds DNA without any sequence or structural preferences but several lines of evidence have demonstrated its ability to differentiate gene expression, which assumes certain specificity. Here we show that Dps has a different affinity for the two DNA fragments taken from the dps gene regulatory region. We found by atomic force microscopy that Dps predominantly occupies thermodynamically unstable ends of linear double-stranded DNA fragments and has high affinity to the central part of the branched DNA molecule self-assembled from three single-stranded oligonucleotides. It was proposed that Dps prefers binding to those regions in DNA that provide more contact pads for the triad of its DNA-binding bundle associated with one vertex of the protein globule. To our knowledge, this is the first study revealed the nucleoid protein with an affinity to branched DNA typical for genomic regions with direct and inverted repeats. As a ubiquitous feature of bacterial and eukaryotic genomes, such structural elements should be of particular care, but the protein system evolutionarily adapted for this function is not yet known, and we suggest Dps as a putative component of this system.
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Affiliation(s)
- Vladislav V. Melekhov
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Uliana S. Shvyreva
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Alexander A. Timchenko
- Department of Physics of Nucleoproteids, Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Maria N. Tutukina
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | | | - Diana V. Burkova
- Department of biophysics and biotechnology, Voronezh State University, Voronezh, Russian Federation
| | - Valiriy G. Artiukhov
- Department of biophysics and biotechnology, Voronezh State University, Voronezh, Russian Federation
| | - Olga N. Ozoline
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- * E-mail:
| | - Sergey S. Antipov
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
- Department of biophysics and biotechnology, Voronezh State University, Voronezh, Russian Federation
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Trubitsyn IV, Belousova EV, Tutukina MN, Merkel AY, Dubinina GA, Grabovich MY. Expansion of ability of denitrification within the filamentous colorless sulfur bacteria of the genusThiothrix. FEMS Microbiol Lett 2014; 358:72-80. [DOI: 10.1111/1574-6968.12548] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/20/2014] [Accepted: 07/21/2014] [Indexed: 11/28/2022] Open
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13
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Purtov YA, Glazunova OA, Antipov SS, Pokusaeva VO, Fesenko EE, Preobrazhenskaya EV, Shavkunov KS, Tutukina MN, Lukyanov VI, Ozoline ON. Promoter islands as a platform for interaction with nucleoid proteins and transcription factors. J Bioinform Comput Biol 2014; 12:1441006. [PMID: 24712533 DOI: 10.1142/s0219720014410066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Seventy-eight promoter islands with an extraordinarily high density of potential promoters have been recently found in the genome of Escherichia coli. It has been shown that RNA polymerase binds internal promoters of these islands and produces short oligonucleotides, while the synthesis of normal mRNAs is suppressed. This quenching may be biologically relevant, as most islands are associated with foreign genes, which expression may deplete cellular resources. However, a molecular mechanism of silencing with the participation of these promoter-rich regions remains obscure. It has been demonstrated that all islands interact with histone-like protein H-NS--a specific sentinel of foreign genes. In this study, we demonstrated the inhibitory effect of H-NS using Δhns mutant of Escherichia coli and showed that deletion of dps, encoding another protein of bacterial nucleoid, tended to decrease rather than increase the amount of island-specific transcripts. This observation precluded consideration of promoter islands as sites for targeted heterochromatization only and a computer search for the binding sites of 53 transcription factors (TFs) revealed six proteins, which may specifically regulate their transcriptional output.
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Affiliation(s)
- Yuri A Purtov
- Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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14
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Trubitsyn IV, Andreevskih ZG, Iurevich LI, Belousova EV, Tutukina MN, Merkel' AI, Dubinina GA, Grabovich MI. [Nitrate respiration capacity as a new metabolic aspect of thread-like Thiothrix sulfur bacteria]. Mikrobiologiia 2013; 82:19-26. [PMID: 23718045 DOI: 10.7868/s0026365613010151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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15
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Shvyreva US, Tutukina MN, Ozolin' ON. [Bacterioferritin: properties, structural and functional organization of the dps gene regulatary region]. Biofizika 2011; 56:821-830. [PMID: 22117438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The paper considers the properties of bacterioferritin Dps, which is involved in the sequestering of iron ions, forms the ferrihydrite core inside the protein cavity, and functions as a major nucleoid protein. Experimental evidence on the effect of microwave irradiation on the dps gene expression is presented. The structural and functional organization of its regulatory region is analyzed, and the technological prospects of bacterioferritin application for designing new materials with desired properties are discussed.
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16
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Abstract
Potential promoters in the genome of Escherichia coli were searched by pattern recognition software PlatProm and classified on the basis of positions relative to gene borders. Beside the expected promoters located in front of the coding sequences we found a considerable amount of intragenic promoter-like signals with a putative ability to drive either antisense or alternative transcription and revealed unusual genomic regions with extremely high density of predicted transcription start points (promoter ‘islands’), some of which are located in coding sequences. PlatProm scores converted into probability of RNA polymerase binding demonstrated certain correlation with the enzyme retention registered by ChIP-on-chip technique; however, in ‘dense’ regions the value of correlation coefficient is lower than throughout the entire genome. Experimental verification confirmed the ability of RNA polymerase to interact and form multiple open complexes within promoter ‘island’ associated with appY, yet transcription efficiency was lower than might be expected. Analysis of expression data revealed the same tendency for other promoter ‘islands’, thus assuming functional relevance of non-productive RNA polymerase binding. Our data indicate that genomic DNA of E. coli is enriched by numerous unusual promoter-like sites with biological role yet to be understood.
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Affiliation(s)
- K S Shavkunov
- Institute of Cell Biophysics, of Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
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17
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Tutukina MN, Shavkunov KS, Masulis IS, Ozoline ON. Intragenic promotor-like sites in the genome of Escherichia coli discovery and functional implication. J Bioinform Comput Biol 2007; 5:549-60. [PMID: 17636861 DOI: 10.1142/s0219720007002801] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2006] [Revised: 03/08/2007] [Accepted: 03/08/2007] [Indexed: 11/18/2022]
Abstract
Mapping of putative promoters within the entire genome of Escherichia coli (E. coli) by means of pattern-recognition software PlatProm revealed several thousand of sites having high probability to perform promoter function. Along with the expected promoters located upstream of coding sequences, PlatProm identified more than a thousand potential promoters for antisense transcription and several hundred very similar signals within coding sequences having the same direction with the genes. Since recently developed ChIP-chip technology also testified the presence of intragenic RNA polymerase binding sites, such distribution of putative promoters is likely to be a general biological phenomenon reflecting yet undiscovered regulatory events. Here, we provide experimental evidences that two internal promoters are recognized by bacterial RNA polymerase. One of them is located within the hns coding sequence and may initiate synthesis of RNA from the antisense strand. Another one is found within the overlapping genes htgA/yaaW and may control the production of a shortened mRNA or an RNA-product complementary to mRNA of yaaW. Both RNA-products can form secondary structures with free energies of folding close to those of small regulatory RNAs (sRNAs) of the same length. Folding propensity of known sRNAs was further compared with that of antisense RNAs (aRNAs), predicted in E. coli as well as in Salmonella typhimurium (S. typhimurium). Slightly lower stability observed for aRNAs assumes that their structural compactness may be less significant for biological function.
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Affiliation(s)
- Maria N Tutukina
- Institute of Cell Biophysics Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia.
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