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Bakiyev S, Smekenov I, Zharkova I, Kobegenova S, Sergaliyev N, Absatirov G, Bissenbaev A. Characterization of atypical pathogenic Aeromonas salmonicida isolated from a diseased Siberian sturgeon ( Acipenser baerii). Heliyon 2023; 9:e17775. [PMID: 37483743 PMCID: PMC10359828 DOI: 10.1016/j.heliyon.2023.e17775] [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: 03/07/2023] [Revised: 06/12/2023] [Accepted: 06/28/2023] [Indexed: 07/25/2023] Open
Abstract
Acipenser baerii (Siberian sturgeon) is native to Kazakhstan and is currently endangered and is listed within the first class of protected animals. Sturgeon aquaculture is becoming an important tool for the recovery of this endangered species. Nonetheless, diseases involving typical symptoms of skin ulceration and systemic bacterial hemorrhagic septicemia have occurred in cultured A. baerii on a fish farm located in Western Kazakhstan. In this study, an infectious strain of bacteria isolated from an ulcer of diseased A. baerii was identified as Aeromonas salmonicida (strain AB001). This identification involved analyses of 16S rRNA, gyrB, rpoD, and flaA genes' sequences. Even though strain AB001 belongs to A. salmonicida, it exhibited noticeable mobility and growth at temperatures of ≥37 °C. Profiling of virulence genes uncovered the presence of seven such genes related to pathogenicity. Antibiotic sensitivity testing showed that the strain is sensitive to aminoglycosides, amphenicols, nitrofurans, quinolones, and tetracyclines. Half-lethal doses (LD50) of strain AB001 for Oreochromis mossambicus and A. baerii were determined: respectively 1.7 × 108 and 7.2 × 107 colony-forming units per mL. The experimentally induced infection revealed that strain AB001 causes considerable histological lesions in O. mossambicus, including tissue degeneration, necrosis, and hemorrhages of varied severity.
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Affiliation(s)
- Serik Bakiyev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Izat Smekenov
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Irina Zharkova
- Department of Biodiversity and Bioresources, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Saidina Kobegenova
- Department of Biodiversity and Bioresources, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Nurlan Sergaliyev
- Makhambet Utemisov West Kazakhstan University, Uralsk 090000, Kazakhstan
| | - Gaisa Absatirov
- West Kazakhstan Innovation and Technological University, Uralsk 090000, Kazakhstan
| | - Amangeldy Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
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Smailov B, Alybayev S, Smekenov I, Mursalimov A, Saparbaev M, Sarbassov D, Bissenbaev A. Wheat Germination Is Dependent on Plant Target of Rapamycin Signaling. Front Cell Dev Biol 2020; 8:606685. [PMID: 33330509 PMCID: PMC7719826 DOI: 10.3389/fcell.2020.606685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 09/15/2020] [Accepted: 10/21/2020] [Indexed: 12/21/2022] Open
Abstract
Germination is a process of seed sprouting that facilitates embryo growth. The breakdown of reserved starch in the endosperm into simple sugars is essential for seed germination and subsequent seedling growth. At the early stage of germination, gibberellic acid (GA) activates transcription factor GAMYB to promote de novo synthesis of isoforms of α-amylase in the aleurone layer and scutellar epithelium of the embryo. Here, we demonstrate that wheat germination is regulated by plant target of rapamycin (TOR) signaling. TOR is a central component of the essential-nutrient–dependent pathway controlling cell growth in all eukaryotes. It is known that rapamycin, a highly specific allosteric inhibitor of TOR, is effective in yeast and animal cells but ineffective in most of higher plants likely owing to structural differences in ubiquitous rapamycin receptor FKBP12. The action of rapamycin on wheat growth has not been studied. Our data show that rapamycin inhibits germination of wheat seeds and of their isolated embryos in a dose-dependent manner. The involvement of Triticum aestivum TOR (TaTOR) in wheat germination was consistent with the suppression of wheat embryo growth by specific inhibitors of the TOR kinase: pp242 or torin1. Rapamycin or torin1 interfered with GA function in germination because of a potent inhibitory effect on α-amylase and GAMYB gene expression. The TOR inhibitors selectively targeted the GA-dependent gene expression, whereas expression of the abscisic acid-dependent ABI5 gene was not affected by either rapamycin or torin1. To determine whether the TaTOR kinase activation takes place during wheat germination, we examined phosphorylation of a ribosomal protein, T. aestivum S6 kinase 1 (TaS6K1; a substrate of TOR). The phosphorylation of serine 467 (S467) in a hydrophobic motif on TaS6K1 was induced in a process of germination triggered by GA. Moreover, the germination-induced phosphorylation of TaS6K1 on S467 was dependent on TaTOR and was inhibited by rapamycin or torin1. Besides, a gibberellin biosynthesis inhibitor (paclobutrazol; PBZ) blocked not only α-amylase gene expression but also TaS6K1 phosphorylation in wheat embryos. Thus, a hormonal action of GA turns on the synthesis of α-amylase in wheat germination via activation of the TaTOR–S6K1 signaling pathway.
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Affiliation(s)
- Bauyrzhan Smailov
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Sanzhar Alybayev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Izat Smekenov
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aibek Mursalimov
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Murat Saparbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Sud, Gustave Roussy Cancer Campus, Villejuif, France
| | - Dos Sarbassov
- Department of Biology, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Amangeldy Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Scientific Research Institute of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Smekenov I, Alybayev S, Ayupov T, Rakhmatullaeva G, Bissenbaev A. A polyclonal antibody against a recombinantly expressed Triticum aestivum RHT-D1A protein. J Genet Eng Biotechnol 2020; 18:52. [PMID: 32936364 PMCID: PMC7494718 DOI: 10.1186/s43141-020-00072-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/05/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023]
Abstract
Background Reduced height-1 dwarfing alleles affect DELLA proteins belonging to a family of putative transcriptional regulators that modulate plant growth and development. The Arabidopsis thaliana genome encodes five DELLA proteins, whereas monocot plants, such as rice, barley, and wheat, each have a single DELLA protein. In wheat, wild-type Rht-B1a and Rht-D1a genes encode DELLA proteins and have many alleles that contain lesions. Among them, Rht-B1b and Rht-D1b are the most common mutant dwarfing alleles, which have played a key part in the creation of high-yielding wheat varieties. Despite their fundamental roles in plant biology, until now, DELLA proteins in wheat have been mainly researched regarding the phenotypic effect of defective Rht mutants on yield-related traits, without studies on the underlying mechanisms. The RHT-1 protein has yet to be detected in wheat tissues, owing to a lack of appropriate molecular tools for characterization of RHT function and protein interactions in signal transduction. This study is focused on the production of a polyclonal antibody to the wheat RHT-D1A protein. Results To generate the anti-RHT-D1A antibody, we expressed and purified soluble 6xHis-tagged RHT-D1A. The purified recombinant RHT-D1A was injected into New Zealand white rabbits to generate polyclonal antiserum. The polyclonal anti-RHT-D1A antibody was purified by ammonium sulfate precipitation, followed by affinity chromatography on protein A–agarose beads. The purified polyclonal antibody was demonstrated to be effective in immunoblotting, western blot hybridization, and immunoprecipitation. In wheat seedling extracts, the polyclonal antibody recognized a protein with a molecular mass close to the predicted molecular weight of the endogenous RHT-D1A protein. We also demonstrated that RHT-D1A disappears in response to exogenous and endogenous gibberellic acid. Conclusion The purified polyclonal antibody raised against the recombinant RHT-D1A protein is sufficiently specific and sensitive and could be a useful tool for future insights into upstream and downstream components of DELLA-regulatory mechanisms in wheat plants.
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Affiliation(s)
- Izat Smekenov
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Sanzhar Alybayev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Temurkhan Ayupov
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Guliza Rakhmatullaeva
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Amangeldy Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040. .,Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.
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Bazlekowa-Karaban M, Prorok P, Baconnais S, Taipakova S, Akishev Z, Zembrzuska D, Popov AV, Endutkin AV, Groisman R, Ishchenko AA, Matkarimov BT, Bissenbaev A, Le Cam E, Zharkov DO, Tudek B, Saparbaev M. Mechanism of stimulation of DNA binding of the transcription factors by human apurinic/apyrimidinic endonuclease 1, APE1. DNA Repair (Amst) 2019; 82:102698. [PMID: 31518879 DOI: 10.1016/j.dnarep.2019.102698] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 01/25/2019] [Revised: 08/11/2019] [Accepted: 08/31/2019] [Indexed: 12/22/2022]
Abstract
Aerobic respiration generates reactive oxygen species (ROS), which can damage nucleic acids, proteins and lipids. A number of transcription factors (TFs) contain redox-sensitive cysteine residues at their DNA-binding sites, hence ROS-induced thiol oxidation strongly inhibits their recognition of the cognate DNA sequences. Major human apurinic/apyrimidinic (AP) endonuclease 1 (APE1/APEX1/HAP-1), referred also as a redox factor 1 (Ref-1), stimulates the DNA binding activities of the oxidized TFs such as AP-1 and NF-κB. Also, APE1 participates in the base excision repair (BER) and nucleotide incision repair (NIR) pathways to remove oxidative DNA base damage. At present, the molecular mechanism underlying the TF-stimulating/redox function of APE1 and its biological role remains disputed. Here, we provide evidence that, instead of direct cysteine reduction in TFs by APE1, APE1-catalyzed NIR and TF-stimulating activities may be based on transient cooperative binding of APE1 to DNA and induction of conformational changes in the helix. The structure of DNA duplex strongly influences NIR and TF-stimulating activities. Homologous plant AP endonucleases lacking conserved cysteine residues stimulate DNA binding of the p50 subunit of NF-κB. APE1 acts synergistically with low-molecular-weight reducing agents on TFs. Finally, APE1 stimulates DNA binding of the redox-insensitive p50-C62S mutant protein. Electron microscopy imaging of APE1 complexes with DNA revealed preferential polymerization of APE1 on the gapped and intrinsically curved DNA duplexes. Molecular modeling offers a structural explanation how full-length APE1 can oligomerize on DNA. In conclusion, we propose that DNA-directed APE1 oligomerization can be regarded as a substitute for diffusion of APE1 along the DNA contour to probe for anisotropic flexibility. APE1 oligomers exacerbate pre-existing distortions in DNA and enable both NIR activity and DNA binding by TFs regardless of their oxidation state.
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Affiliation(s)
- Milena Bazlekowa-Karaban
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Paulina Prorok
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Human Genetics, UMR 9002, CNRS - University of Montpellier, Replication and Genome Dynamics, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Sonia Baconnais
- CNRS UMR8126, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Zhiger Akishev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Dominika Zembrzuska
- Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Alexander V Popov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton V Endutkin
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Regina Groisman
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Alexander A Ishchenko
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Bakhyt T Matkarimov
- National laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Amangeldy Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Eric Le Cam
- CNRS UMR8126, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Murat Saparbaev
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France.
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Kuanbay A, Taipakova S, Smekenov I, Saparbaev M, Ishchenko A, Bissenbaev A. Arabidopsis thaliana Poly(ADP-ribose) polymerases ADP-ribosylate DNA oligonucleotides. J Biotechnol 2018. [DOI: 10.1016/j.jbiotec.2018.06.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Smekenov I, Taipakova S, Bissenbaev A. Recombinant industrial Saccharomyces cerevisiae strains for bioconversion of cellobiose. J Biotechnol 2017. [DOI: 10.1016/j.jbiotec.2017.06.1178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bissenbaev A, Taipakova S, Smekenov I. Expression of cellobiohydrolase CEL7A gene from Lentinula edodes in Saccharomyces cerevisiae with use of two different promoters. J Biotechnol 2014. [DOI: 10.1016/j.jbiotec.2014.07.234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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