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Gantsova EA, Serova OV, Eladari D, Bobrovskiy DM, Petrenko AG, Elchaninov AV, Deyev IE. A Comparative Kidney Transcriptome Analysis of Bicarbonate-Loaded insrr-Null Mice. Curr Issues Mol Biol 2023; 45:9709-9722. [PMID: 38132452 PMCID: PMC10742211 DOI: 10.3390/cimb45120606] [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: 10/19/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
The maintenance of plasma pH is critical for life in all organisms. The kidney plays a critical role in acid-base regulation in vertebrates by controlling the plasma concentration of bicarbonate. The receptor tyrosine kinase IRR (insulin receptor-related receptor) is expressed in renal β-intercalated cells and is involved in alkali sensing due to its ability to autophosphorylate under alkalization of extracellular medium (pH > 7.9). In mice with a knockout of the insrr gene, which encodes for IRR, urinary bicarbonate secretion in response to alkali loading is impaired. The specific regulatory mechanisms in the kidney that are under the control of IRR remain unknown. To address this issue, we analyzed and compared the kidney transcriptomes of wild-type and insrr knockout mice under basal or bicarbonate-loaded conditions. Transcriptomic analyses revealed a differential regulation of a number of genes in the kidney. Using TaqMan real-time PCR, we confirmed different expressions of the slc26a4, rps7, slc5a2, aqp6, plcd1, gapdh, rny3, kcnk5, slc6a6 and atp6v1g3 genes in IRR knockout mice. Also, we found that the expression of the kcnk5 gene is increased in wild-type mice after bicarbonate loading but not in knockout mice. Gene set enrichment analysis between the IRR knockout and wild-type samples identified that insrr knockout causes alterations in expression of genes related mostly to the ATP metabolic and electron transport chain processes.
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Affiliation(s)
- E. A. Gantsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow 117997, Russia; (E.A.G.); (O.V.S.); (A.G.P.)
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution “Petrovsky National Research Centre of Surgery”, Moscow 117418, Russia;
| | - O. V. Serova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow 117997, Russia; (E.A.G.); (O.V.S.); (A.G.P.)
| | - D. Eladari
- Service de Médecine de Précision des Maladies Métaboliques et Rénales, CHU Amiens-Picardie, Université de Picardie Jules Verne, 80054 Amiens, France
| | - D. M. Bobrovskiy
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - A. G. Petrenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow 117997, Russia; (E.A.G.); (O.V.S.); (A.G.P.)
| | - A. V. Elchaninov
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution “Petrovsky National Research Centre of Surgery”, Moscow 117418, Russia;
| | - I. E. Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow 117997, Russia; (E.A.G.); (O.V.S.); (A.G.P.)
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Gantsova EA, Gavrilenkova AA, Serova OV, Deyev IE. Changes in the Expression of the gapdh Gene in the Organs of insrr Knockout Mice. Dokl Biol Sci 2022; 505:113-118. [PMID: 36038798 DOI: 10.1134/s0012496622040056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
The most important property of a living organism is the maintenance of optimal acid-base balance and the ionic composition of the internal environment. The kidneys are one of the main pH-regulating organs in the body. Receptor tyrosine kinase IRR (an insulin receptor-related receptor) is an alkaline pH-sensor. In mice (Mus Musculus) with a knockout of the insrr gene encoding the IRR receptor, bicarbonate secretion is impaired under the conditions of alkaline loading, which indicates the role of the receptor tyrosine kinase IRR in the regulation of acid-base balance in the body. In order to search for proteins functionally associated with the receptor tyrosine kinase IRR, we performed a large-scale sequencing of the mouse kidney transcriptome of wild type and insrr knockout mice kept under normal conditions and under alkaline conditions. As a result, we found a decrease in the gapdh gene expression in the kidneys of insrr knockout mice compared to wild type mice. RNA sequencing data were confirmed by TaqMan real-time PCR and Western blotting. Using the TaqMan real-time PCR method, we revealed a decrease in the level of gapdh expression not only in the kidneys, but also in the liver and brain of insrr knockout mice. Thus, the changes in the gapdh gene expression in the kidneys of insrr knockout mice may indicate a functional relationship between genes and a possible role of GAPDH in previously undescribed molecular mechanisms of regulation of acid-base balance in the body.
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Affiliation(s)
- E A Gantsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia.
| | - A A Gavrilenkova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudnyi, Moscov oblast, Russia
| | - O V Serova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia
| | - I E Deyev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia
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Serova OV, Gantsova EA, Deyev IE, Petrenko AG. Tissue-Specific Expression of Neurexin-1α Isoforms in Rat Organs. Russ J Bioorg Chem 2022. [DOI: 10.1134/s1068162022020194] [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] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract—
Neurexins are a family of synaptic adhesion proteins that play a key role in synapse formation and maintenance. Neurexins undergo extensive alternative splicing at six sites (SS1–SS6) resulting in expression of multiplicity of different isoforms. Alternative splicing regulates the functional activity of neurexins in different types of tissues and cells and presumably plays a key role in determining the specificity of the interaction of various neurons. In this study, we have investigated the pattern of tissue expression of neurexin-1α mRNA isoforms including an insert in the recently discovered splice site SS6 using TaqMan Real-Time PCR in different organs of Wistar rats. The isoform containing the insert in the SS6 site was found only in neural tissues suggesting its potential functional importance. Position of the SS6 insert in the hinge region between the LNS5 and LNS6 domains increases variability of possible conformations of the molecule which may represent an additional mechanism for regulating functional activity of the neurexin-1α in the brain.
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Orsa AN, Goryashchenko AS, Serova OV, Mozhaev AA, Martynov VI, Pakhomov AA, Svirshchevskaya EV, Petrenko AG, Deyev IE. Generation and Characteristics of Genetically Encoded Fluorescent Sensors of Extracellular pH. Russ J Bioorg Chem 2021. [DOI: 10.1134/s1068162021040178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Serova OV, Gantsova EA, Deyev IE, Petrenko AG. The Value of pH Sensors in Maintaining Homeostasis of the Nervous System. Russ J Bioorg Chem 2020. [DOI: 10.1134/s1068162020040196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Mozhaev AA, Serova OV, Orsa AN, Boyko AA, Goryashchenko AS, Deyev IE, Petrenko AG. The Hybrid Protein of the Alkaline Sensor IRR and the Fluorescent Protein GFP Retains the Functional Activity of the Receptor. Russ J Bioorg Chem 2019. [DOI: 10.1134/s1068162019020080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kudzhaev AM, Dubovtseva ES, Serova OV, Andrianova AG, Rotanova TV. Effect of the Deletion of the (173–280) Fragment of the Inserted α-Helical Domain on the Functional Properties of АТР-Dependent Lon Protease from E. coli. Russ J Bioorg Chem 2018. [DOI: 10.1134/s1068162018050084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zinchenko AA, Kotelnikova OV, Gordeeva EA, Prokopenko YA, Razgulyaeva OA, Serova OV, Melikhova TD, Nokel EA, Zhigis LS, Zueva VS, Alliluev AP, Rumsh LD. Immunogenic and Protective Properties of Neisseria meningitidis IgA1 Protease and of Its Truncated Fragments. Russ J Bioorg Chem 2018. [DOI: 10.1134/s1068162018010193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Mozhaev AA, Erokhina TN, Serova OV, Deyev IE, Petrenko AG. Production and immunochemical characterization of monoclonal antibody to IRR ectodomain. Russ J Bioorg Chem 2018. [DOI: 10.1134/s1068162017060097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kudzhaev AM, Andrianova AG, Dubovtseva ES, Serova OV, Rotanova TV. Role of the Inserted α-Helical Domain in E. coli ATP-Dependent Lon Protease Function. Acta Naturae 2017. [DOI: 10.32607/20758251-2017-9-2-75-81] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidomain ATP-dependent Lon protease of E. coli (Ec-Lon) is one of the key enzymes of the quality control system of the cellular proteome. A recombinant form of Ec-Lon with deletion of the inserted characteristic -helical HI(CC) domain (Lon-dHI(CC)) has been prepared and investigated to understand the role of this domain. A comparative study of the ATPase, proteolytic, and peptidase activities of the intact Lon protease and Lon-dHI(CC) has been carried out. The ability of the enzymes to undergo autolysis and their ability to bind DNA have been studied as well. It has been shown that the HI(CC) domain of Ec-Lon protease is required for the formation of a functionally active enzyme structure and for the implementation of protein-protein interactions.
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Kudzhaev AM, Andrianova AG, Dubovtseva ES, Serova OV, Rotanova TV. Role of the Inserted α-Helical Domain in E. coli ATP-Dependent Lon Protease Function. Acta Naturae 2017; 9:75-81. [PMID: 28740729 PMCID: PMC5509003] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Indexed: 11/02/2022] Open
Abstract
Multidomain ATP-dependent Lon protease of E. coli (Ec-Lon) is one of the key enzymes of the quality control system of the cellular proteome. A recombinant form of Ec-Lon with deletion of the inserted characteristic α-helical HI(CC) domain (Lon-dHI(CC)) has been prepared and investigated to understand the role of this domain. A comparative study of the ATPase, proteolytic, and peptidase activities of the intact Lon protease and Lon-dHI(CC) has been carried out. The ability of the enzymes to undergo autolysis and their ability to bind DNA have been studied as well. It has been shown that the HI(CC) domain of Ec-Lon protease is required for the formation of a functionally active enzyme structure and for the implementation of protein-protein interactions.
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Affiliation(s)
- A. M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, 117997, Russia
| | - A. G. Andrianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, 117997, Russia
| | - E. S. Dubovtseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, 117997, Russia
| | - O. V. Serova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, 117997, Russia
| | - T. V. Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, 117997, Russia
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Kudzhaev AM, Dubovtseva ES, Serova OV, Andrianova AG, Rotanova TV. Influence of the (1–106) fragment of Escherichia coli Lon protease on the enzyme function and DNA binding. Russ J Bioorg Chem 2016. [DOI: 10.1134/s1068162016040142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kudzhaev AM, Andrianova AG, Serova OV, Arkhipova VA, Dubovtseva ES, Rotanova TV. [The Effect of Mutations in the Inserted Domain of ATP-Dependent Lon Protease from E. coli on the Enzyme Function]. Bioorg Khim 2016; 41:579-86. [PMID: 26762095 DOI: 10.1134/s1068162015050076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
ATP-Dependent protease LonA from E. coli (Ec-Lon), belonging to the superfamily of AAA+ proteins, is a key member of the protein quality control system in bacterial cells. Ec-Lon functions as homohexamer and degrades abnormal and defective polypeptides as well as a number of regulatory proteins by the processive mechanism. Ec-Lon subunit includes--the both ATPase and proteolytic components (AAA+ module and P domain) in addition to the unique non-catalytic region formed by the N-terminal (N) and the inserted c-helical (HI(CC)) domains. The mutant forms Lon-R164A, Lon-R192A and Lon-Y294A have been obtained and characterized in order to reveal the role of the HI (CC) domain for the enzyme functioning. C-Terminal part of the HI (CC) domain is shown to display an allosteric effect on the efficiency of the enzyme ATPase and proteolytic sites while its coiled-coil (CC) region is involved in the interaction with the protein substrate.
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Serova OV, Radionov NV, Shayahmetova DM, Deyev IE, Petrenko AG. Structural and functional analyses of the sixth site of neurexin alternative splicing. DOKL BIOCHEM BIOPHYS 2015; 463:239-42. [PMID: 26335821 DOI: 10.1134/s1607672915040110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Indexed: 11/23/2022]
Abstract
In this study, we found the sixth site of alternative splicing (SS6) of neurexin 1a from the rat brain. This site is located between the fifth LNS and the third EGF-like domains. The insertion in the SS6 site corresponds to the 9-residue peptide VALMKADLQ, which is conserved among animals. We demonstrated that the SS6 insertion regulates tissue-specific expression of neurexin 1α.
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Affiliation(s)
- O V Serova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia,
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Andrianova AG, Kudzhaev AM, Serova OV, Dergousova NI, Rotanova TV. [Role of the α-helical domains in the functioning of ATP-dependent Lon protease of Escherichia coli]. Bioorg Khim 2015; 40:673-81. [PMID: 25895363 DOI: 10.1134/s106816201406003x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Homooligomeric ATP-dependent LonA proteases are bifunctional enzymes belonging to the superfamily of AAA+ proteins. Their subunits are formed by five successively connected domains: N-terminal (N), α-helical (HI(CC)), nucleotide binding (NB), the second α-helical (H) and proteolytic (P). The presence of the inserted HI(CC) domain defines the uniqueness of LonA proteases among AAA+ proteins. The role of α-helical domains in the LonA protease functioning is investigated on the example of E. coli Lon protease (Ec-Lon). A comparative study of properties of the intact Ec-Lon and its mutants of Lon-R164A and Lon-R542A with the substitutions of arginine residues located in similar positions in the HI(CC) and H domains is carried out. The H domain is shown to play a crucial role for the ATP hydrolysis and enzyme binding to the target protein. HI(CC) domain does not have a fundamental significance for the catalytic properties of the enzyme. However, it affects the functioning of Lon ATPase and peptidase sites and is involved in maintaining the enzyme stability. The participation of HI(CC) domain in formation of the spatial structures of LonA proteases and/or formation of their complexes with DNA is suggested.
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Deyev IE, Rzhevsky DI, Berchatova AA, Serova OV, Popova NV, Murashev AN, Petrenko AG. Deficient Response to Experimentally Induced Alkalosis in Mice with the Inactivated insrr Gene. Acta Naturae 2011. [DOI: 10.32607/20758251-2011-3-4-114-117] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Serova OV, Deyev IE, Petrenko AG. Novel GPS-containing G protein-coupled receptor from Monosiga brevicollis. DOKL BIOCHEM BIOPHYS 2009; 427:191-4. [PMID: 19817134 DOI: 10.1134/s1607672909040061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- O V Serova
- Shemyakin-Ovchinnikov Institute ofBioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
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Abstract
A thorough analysis of proteins capable of interacting with presynaptic receptors of alpha-latrotoxin was carried out. The protein components of receptor complexes were isolated from rat brain membranes by affinity chromatography on immobilized alpha-latrotoxin and antibodies to the cytoplasmic moiety of the calcium-independent receptor of alpha-latrotoxin (CIRL) followed by analysis by mass spectrometry. Several proteins were identified, with structural proteins, intracellular signal proteins, and proteins involved in the endocytosis and transport of synaptic vesicles being among them.
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Affiliation(s)
- O V Serova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997 Russia
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Deev IE, Vasilenko KP, Kurmangaliev EZ, Serova OV, Popova NV, Galagan YS, Burova EB, Zozulya SA, Nikol'skii NN, Petrenko AG. Effect of changes in ambient pH on phosphorylation of cellular proteins. DOKL BIOCHEM BIOPHYS 2006; 408:184-7. [PMID: 16913425 DOI: 10.1134/s1607672906030203] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- I E Deev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
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