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Gantsova E, Serova O, Vishnyakova P, Deyev I, Elchaninov A, Fatkhudinov T. Mechanisms and physiological relevance of acid-base exchange in functional units of the kidney. PeerJ 2024; 12:e17316. [PMID: 38699185 PMCID: PMC11064853 DOI: 10.7717/peerj.17316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/09/2024] [Indexed: 05/05/2024] Open
Abstract
This review discusses the importance of homeostasis with a particular emphasis on the acid-base (AB) balance, a crucial aspect of pH regulation in living systems. Two primary organ systems correct deviations from the standard pH balance: the respiratory system via gas exchange and the kidneys via proton/bicarbonate secretion and reabsorption. Focusing on kidney functions, we describe the complexity of renal architecture and its challenges for experimental research. We address specific roles of different nephron segments (the proximal convoluted tubule, the loop of Henle and the distal convoluted tubule) in pH homeostasis, while explaining the physiological significance of ion exchange processes maintained by the kidneys, particularly the role of bicarbonate ions (HCO3-) as an essential buffer system of the body. The review will be of interest to researchers in the fields of physiology, biochemistry and molecular biology, which builds a strong foundation and critically evaluates existing studies. Our review helps identify the gaps of knowledge by thoroughly understanding the existing literature related to kidney acid-base homeostasis.
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Affiliation(s)
- Elena Gantsova
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution “Petrovsky National Research Centre of Surgery”, Moscow, Russia
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
| | - Oxana Serova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Polina Vishnyakova
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russian Federation
| | - Igor Deyev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Andrey Elchaninov
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution “Petrovsky National Research Centre of Surgery”, Moscow, Russia
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
| | - Timur Fatkhudinov
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution “Petrovsky National Research Centre of Surgery”, Moscow, Russia
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
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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] [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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Lyubetsky VA, Rubanov LI, Tereshina MB, Ivanova AS, Araslanova KR, Uroshlev LA, Goremykina GI, Yang JR, Kanovei VG, Zverkov OA, Shitikov AD, Korotkova DD, Zaraisky AG. Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations. Biol Direct 2023; 18:45. [PMID: 37568147 PMCID: PMC10416458 DOI: 10.1186/s13062-023-00405-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND It is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid contents of proteins. Recently, evidence has accumulated that significant evolutionary transformations could also be associated with the loss/emergence of whole genes. The targeted identification of such genes is a challenging problem for both bioinformatics and evo-devo research. RESULTS To solve this problem we propose the WINEGRET method, named after the first letters of the title. Its main idea is to search for genes that satisfy two requirements: first, the desired genes were lost/emerged at the same evolutionary stage at which the phenotypic trait of interest was lost/emerged, and second, the expression of these genes changes significantly during the development of the trait of interest in the model organism. To verify the first requirement, we do not use existing databases of orthologs, but rely purely on gene homology and local synteny by using some novel quickly computable conditions. Genes satisfying the second requirement are found by deep RNA sequencing. As a proof of principle, we used our method to find genes absent in extant amniotes (reptiles, birds, mammals) but present in anamniotes (fish and amphibians), in which these genes are involved in the regeneration of large body appendages. As a result, 57 genes were identified. For three of them, c-c motif chemokine 4, eotaxin-like, and a previously unknown gene called here sod4, essential roles for tail regeneration were demonstrated. Noteworthy, we established that the latter gene belongs to a novel family of Cu/Zn-superoxide dismutases lost by amniotes, SOD4. CONCLUSIONS We present a method for targeted identification of genes whose loss/emergence in evolution could be associated with the loss/emergence of a phenotypic trait of interest. In a proof-of-principle study, we identified genes absent in amniotes that participate in body appendage regeneration in anamniotes. Our method provides a wide range of opportunities for studying the relationship between the loss/emergence of phenotypic traits and the loss/emergence of specific genes in evolution.
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Affiliation(s)
- Vassily A Lyubetsky
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
- Department of Mechanics and Mathematics, Lomonosov Moscow State University, Kolmogorova Str., 1, Moscow, Russia, 119234
| | - Lev I Rubanov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
| | - Maria B Tereshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anastasiya S Ivanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, USA
| | - Karina R Araslanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
| | - Leonid A Uroshlev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32, Vavilova Str., Moscow, Russia, 119991
| | - Galina I Goremykina
- Plekhanov Russian University of Economics, Stremyanny Lane 36, Moscow, Russia
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Vladimir G Kanovei
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
| | - Oleg A Zverkov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
| | - Alexander D Shitikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
| | - Daria D Korotkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997.
- Pirogov Russian National Research Medical University, Moscow, Russia.
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