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Bystritskaya E, Chernysheva N, Stenkova A, Guzev K, Rakin A, Isaeva M. Differential Expression of Yersinia pseudotuberculosis General Porin Genes during Short- and Long-Term Antibiotic Stresses. Molecules 2021; 26:3956. [PMID: 34203552 PMCID: PMC8272246 DOI: 10.3390/molecules26133956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/25/2022] Open
Abstract
Here, we investigated general porin regulation in Yersinia pseudotuberculosis 488, the causative agent of Far Eastern scarlet-like fever, in response to sublethal concentrations of antibiotics. We chose four antibiotics of different classes and measured gene expression using qRT-PCR and GFP reporter systems. Our data showed temporal regulation of the general porin genes ompF and ompC caused by antibiotic stress. The porin transcription initially decreased, providing early defensive response of the bacterium, while it returned to that of the untreated cells on prolonged antibiotic exposure. Unlike the major porin genes, the transcription of the alternative porin genes ompX and lamB was increased. Moreover, a short-term ompR- and marA-mediated porin regulation was observed. The main finding was a phenotypic heterogeneity of Y. pseudotuberculosis population manifested in variable porin gene expression under carbenicillin exposure. This may offer adaptive fitness advantages for a particular bacterial subpopulation.
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Affiliation(s)
- Evgeniya Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 Let Vladivostoku, 690022 Vladivostok, Russia; (E.B.); (N.C.); (K.G.)
| | - Nadezhda Chernysheva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 Let Vladivostoku, 690022 Vladivostok, Russia; (E.B.); (N.C.); (K.G.)
| | - Anna Stenkova
- School of Biomedicine, Far Eastern Federal University, 8 Sukhanova St., 690090 Vladivostok, Russia;
| | - Konstantin Guzev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 Let Vladivostoku, 690022 Vladivostok, Russia; (E.B.); (N.C.); (K.G.)
| | - Alexander Rakin
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Bacterial Infections and Zoonoses, Naumburger Str. 96a, D-07743 Jena, Germany;
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 Let Vladivostoku, 690022 Vladivostok, Russia; (E.B.); (N.C.); (K.G.)
- School of Biomedicine, Far Eastern Federal University, 8 Sukhanova St., 690090 Vladivostok, Russia;
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Lopes-Rodrigues M, Puiggalí-Jou A, Martí-Balleste D, del Valle LJ, Michaux C, Perpète EA, Alemán C. Thermomechanical Response of a Representative Porin for Biomimetics. ACS OMEGA 2018; 3:7856-7867. [PMID: 31458928 PMCID: PMC6644815 DOI: 10.1021/acsomega.8b00463] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/02/2018] [Indexed: 06/09/2023]
Abstract
The thermomechanical response of Omp2a, a representative porin used for the fabrication of smart biomimetic nanomembranes, has been characterized using microcantilever technology and compared with standard proteins. For this purpose, thermally induced transitions involving the conversion of stable trimers to bigger aggregates, local reorganizations based on the strengthening or weakening of intermolecular interactions, and protein denaturation have been detected by the microcantilever resonance frequency and deflection as a function of the temperature. Measurements have been carried out on arrays of 8-microcantilevers functionalized with proteins (Omp2a, lysozyme and bovine serum albumin). To interpret the measured nanofeatures, the response of proteins to temperature has been also examined using other characterization techniques, including real time wide angle X-ray diffraction. Results not only demonstrate the complex behavior of porins, which exhibit multiple local thermal transitions before undergoing denaturation at temperatures higher than 105 °C, but also suggest a posttreatment to control the orientation of immobilized Omp2a molecules in functionalized biomimetic nanomembranes and, thus, increase their efficacy in ion transport.
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Affiliation(s)
- Maximilien Lopes-Rodrigues
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
- Laboratoire
de Chimie Physique des Biomolécules, Unité de Chimie
Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Anna Puiggalí-Jou
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Didac Martí-Balleste
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Luis J. del Valle
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Catherine Michaux
- Laboratoire
de Chimie Physique des Biomolécules, Unité de Chimie
Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Eric A. Perpète
- Laboratoire
de Chimie Physique des Biomolécules, Unité de Chimie
Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Carlos Alemán
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
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Solov'eva T, Likhatskaya G, Khomenko V, Guzev K, Kim N, Bystritskaya E, Novikova O, Stenkova A, Rakin A, Isaeva M. The impact of length variations in the L2 loop on the structure and thermal stability of non-specific porins: The case of OmpCs from the Yersinia pseudotuberculosis complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:515-525. [PMID: 29038023 DOI: 10.1016/j.bbamem.2017.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 09/25/2017] [Accepted: 10/11/2017] [Indexed: 10/18/2022]
Abstract
Porins are integral proteins of the outer membranes of gram-negative bacteria. In membranes, they exist as homotrimers and the L2 loops contribute to their stability. Comparison of OmpC porins of the Yersinia pseudotuberculosis complex with other enterobacterial porins demonstrated L2 loop length diversity, which is caused by varying numbers of dipeptide/tripeptide repeats. The OmpC porins are highly homologous to each other, and they can be subdivided into five isoforms based on their L2 loop structure. Optical spectroscopy and SDS-PAGE experiments revealed that particularities of the L2 loops affected the structure and thermal stability of the porins. Thermal denaturation studies showed that porins with shorter loops, compared to porins with longer loops, had more stable tertiary and less stable secondary and quaternary structures. According to our comparative modeling results, the L2 loops differ in their structure by adopting different spatial positions and forming different polar bonds with a neighbor monomer. The replacement of asparagine with arginine at the C-terminus of the L2 loop shifts the loop upwards and causes the loss of contacts with the arginine clusters within the pores. The increase in the length of these loops ensures that they shift down toward the pore and restore their contacts with arginines on the channel wall, as is the case in classical nonspecific porins. Despite the fact that the surface charge density varies considerably among the OmpC porins, the L2 loops form a typical negatively charged region in the center of the trimer.
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Affiliation(s)
- T Solov'eva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - G Likhatskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - V Khomenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - K Guzev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - N Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - E Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - O Novikova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - A Stenkova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - A Rakin
- Institute for Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Naumburger Str. 96 a, 07743 Jena, Germany
| | - M Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia.
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Shaban H, Na I, Kislichkina AA, Dentovskaya SV, Anisimov AP, Uversky VN. Effect of natural polymorphism on structure and function of the Yersinia pestis outer membrane porin F (OmpF protein): a computational study. J Biomol Struct Dyn 2016; 35:2588-2603. [PMID: 27593697 DOI: 10.1080/07391102.2016.1224734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The Yersinia pestis outer membrane porin F (OmpF) is a transmembrane protein located in the outer membrane of this Gram-negative bacterium which is the causative agent of plague, where it plays a significant role in controlling the selective permeability of the membrane. The amino acid sequences of OmpF proteins from 48 Y. pestis strains representing all currently available phylogenetic groups of this Gram-negative bacterium were recently deduced. Comparison of these amino acid sequences revealed that the OmpF can be present in four isoforms, the pestis-pestis type, and the pestis-microtus types I, II, and III. OmpF of the most recent pestis-pestis type has an alanine residue at the position 148, where all the pestis-microtus types have threonine there (T148A polymorphism). The variability of different pestis-microtus types is caused by an additional polymorphism at the 193rd position, where the OmpFs of the pestis-microtus type II and type III have isoleucine-glycine (IG+193) or isoleucine-glycine-isoleucine-glycine (IGIG+193) insertions, respectively (IG+193 and IGIG+193 polymorphism). To investigate potential effects of these sequence polymorphisms on the structural properties of the OmpF protein, we conducted multi-level computational analysis of its isoforms. Analysis of the I-TASSER-generated 3D-models revealed that the Yersinia OmpF is very similar to other non-specific enterobacterial porins. The T148A polymorphism affected a loop located in the external vestibule of the OmpF channel, whereas IG+193 and IGIG+193 polymorphisms affected one of its β-strands. Our analysis also suggested that polymorphism has moderate effect on the predicted local intrinsic disorder predisposition of OmpF, but might have some functional implementations.
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Affiliation(s)
- Hiba Shaban
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA
| | - Insing Na
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA
| | - Angelina A Kislichkina
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Svetlana V Dentovskaya
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Andrey P Anisimov
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Vladimir N Uversky
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA.,c USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine, University of South Florida , Tampa 33612 , FL , USA.,d Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg 194064 , Russia
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Bystritskaya E, Stenkova A, Chistuylin D, Chernysheva N, Khomenko V, Anastyuk S, Novikova O, Rakin A, Isaeva M. Adaptive responses of outer membrane porin balance of Yersinia ruckeri under different incubation temperature, osmolarity, and oxygen availability. Microbiologyopen 2016; 5:597-603. [PMID: 27038237 PMCID: PMC4985593 DOI: 10.1002/mbo3.354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 02/18/2016] [Accepted: 02/25/2016] [Indexed: 11/10/2022] Open
Abstract
The capability of Yersinia ruckeri to survive in the aquatic systems reflects its adaptation (most importantly through the alteration of membrane permeability) to the unfavorable environments. The nonspecific porins are a key factor contributing to the permeability. Here we studied the influence of the stimuli, such as temperature, osmolarity, and oxygen availability on regulation of Y. ruckeri porins. Using qRT-PCR and SDS-PAGE methods we found that major porins are tightly controlled by temperature. Hyperosmosis did not repress OmpF production. The limitation of oxygen availability led to decreased expression of both major porins and increased transcription of the minor porin OmpY. Regulation of the porin balance in Y. ruckeri, in spite of some similarities, diverges from that system in Escherichia coli. The changes in porin regulation can be adapted in Y. ruckeri in a species-specific manner determined by its aquatic habitats.
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Affiliation(s)
- Evgeniya Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS690022 Prospect 100‐let Vladivostoku 159VladivostokRussia
- The School of BiomedicineFar Eastern Federal University690950 Suchanova str. 8VladivostokRussia
| | - Anna Stenkova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS690022 Prospect 100‐let Vladivostoku 159VladivostokRussia
- The School of BiomedicineFar Eastern Federal University690950 Suchanova str. 8VladivostokRussia
| | - Dmitriy Chistuylin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS690022 Prospect 100‐let Vladivostoku 159VladivostokRussia
| | - Nadezhda Chernysheva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS690022 Prospect 100‐let Vladivostoku 159VladivostokRussia
- The School of BiomedicineFar Eastern Federal University690950 Suchanova str. 8VladivostokRussia
| | - Valentina Khomenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS690022 Prospect 100‐let Vladivostoku 159VladivostokRussia
| | - Stanislav Anastyuk
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS690022 Prospect 100‐let Vladivostoku 159VladivostokRussia
| | - Olga Novikova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS690022 Prospect 100‐let Vladivostoku 159VladivostokRussia
| | - Alexander Rakin
- Max von Pettenkofer Institute for Hygiene and Clinical Microbiology of Ludwig Maximilians‐University80336 Pettenkofer str. 9aMunichGermany
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS690022 Prospect 100‐let Vladivostoku 159VladivostokRussia
- The School of BiomedicineFar Eastern Federal University690950 Suchanova str. 8VladivostokRussia
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Solov'eva TF, Tischenko NM, Khomenko VA, Portnyagina OY, Kim NY, Likhatskaya GN, Novikova OD, Isaeva MP. Study of effect of substitution of the penultimate amino acid residue on expression, structure, and functional properties of Yersinia pseudotuberculosis OmpY porin. BIOCHEMISTRY (MOSCOW) 2014; 79:694-705. [PMID: 25108332 DOI: 10.1134/s0006297914070116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The purpose of the study was to compare the expression of two Yersinia pseudotuberculosis proteins, wild-type porin OmpY and the mutant porin OmpY designated as OmpY-Q having the uncharged amino acid residue Gln instead of positively charged Arg at the penultimate position in the same heterologous host. According to the literature, a similar substitution (Lys to Gln) of the penultimate amino acid residue in Neisseria meningitidis porin PorA drastically improved the assembly of the protein in the E. coli outer membrane in vivo. Site-directed mutagenesis was used to replace Arg by Gln (R338Q) in OmpY, and the conditions for optimal expression and maturation of OmpY-Q were selected. It was found that the growth rates of E. coli strains producing OmpY and OmpY-Q and the expression levels of the porins were approximately equal. Comparative analysis of recombinant OmpY and OmpY-Q did not show significant differences in structure, antigenic, and functional properties of the porins, or any noticeable effect of the R338Q substitution in OmpY on its assembly in the E. coli outer membrane in vivo. The probable causes of discrepancies between our results and the previous data on porin PorA are discussed considering the known mechanisms of biogenesis of porins at the periplasmic stage.
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Affiliation(s)
- T F Solov'eva
- Elyakov Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia.
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Mutant OmpF porins of Yersinia pseudotuberculosis with deletions of external loops: structure-functional and immunochemical properties. Biochem Biophys Res Commun 2014; 445:428-32. [PMID: 24530904 DOI: 10.1016/j.bbrc.2014.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 02/05/2014] [Indexed: 11/20/2022]
Abstract
Recombinant mutant OmpF porins from Yersinia pseudotuberculosis outer membrane were obtained using site-directed mutagenesis. Here we used four OmpF mutants where single extracellular loops L1, L4, L6, and L8 were deleted one at a time. The proteins were expressed in Escherichia coli at levels comparable to full-sized recombinant OmpF porin and isolated from the inclusion bodies. Purified trimers of the mutant porins were obtained after dialysis and consequent ion-exchange chromatography. Changes in molecular and spatial structure of the mutants obtained were studied using SDS-PAGE and optical spectroscopy (circular dichroism and intrinsic protein fluorescence). Secondary and tertiary structure of the mutant proteins was found to have some features in comparison with that of the full-sized recombinant OmpF. As shown by bilayer lipid membrane technique, the pore-forming activity of purified mutant porins was identical to OmpF porin isolated from the bacterial outer membrane. Lacking of the external loops mentioned above influenced significantly upon the antigenic structure of the porin as demonstrated using ELISA.
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Chistyulin DK, Novikova OD, Portnyagina OY, Khomenko VA, Vakorina TI, Kim NY, Isaeva MP, Likhatskaya GN, Solov’eva TF. Isolation and characterization of OmpF-like porin from Yersinia ruckeri. BIOCHEMISTRY MOSCOW SUPPLEMENT SERIES A-MEMBRANE AND CELL BIOLOGY 2012. [DOI: 10.1134/s1990747812030038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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