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Ermakova GV, Kucheryavyy AV, Zaraisky AG, Bayramov AV. The Molecular Mechanism of Body Axis Induction in Lampreys May Differ from That in Amphibians. Int J Mol Sci 2024; 25:2412. [PMID: 38397089 PMCID: PMC10889193 DOI: 10.3390/ijms25042412] [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: 01/15/2024] [Revised: 02/12/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Lamprey homologues of the classic embryonic inducer Noggin are similar in expression pattern and functional properties to Noggin homologues of jawed vertebrates. All noggin genes of vertebrates apparently originated from a single ancestral gene as a result of genome duplications. nogginA, nogginB and nogginC of lampreys, like noggin1 and noggin2 of gnathostomes, demonstrate the ability to induce complete secondary axes with forebrain and eye structures when overexpressed in Xenopus laevis embryos. According to current views, this finding indicates the ability of lamprey Noggin proteins to suppress the activity of the BMP, Nodal/Activin and Wnt/beta-catenin signaling pathways, as shown for Noggin proteins of gnathostomes. In this work, by analogy with experiments in Xenopus embryos, we attempted to induce secondary axes in the European river lamprey Lampetra fluviatilis by injecting noggin mRNAs into lamprey eggs in vivo. Surprisingly, unlike what occurs in amphibians, secondary axis induction in the lampreys either by noggin mRNAs or by chordin and cerberus mRNAs, the inductive properties of which have been described, was not observed. Only wnt8a mRNA demonstrated the ability to induce secondary axes in the lampreys. Such results may indicate that the mechanism of axial specification in lampreys, which represent jawless vertebrates, may differ in detail from that in the jawed clade.
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Affiliation(s)
- Galina V. Ermakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
| | - Aleksandr V. Kucheryavyy
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia;
| | - Andrey G. Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
- Department of Regenerative Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Andrey V. Bayramov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
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Ermakova GV, Meyntser IV, Zaraisky AG, Bayramov AV. Loss of noggin1, a classic embryonic inducer gene, in elasmobranchs. Sci Rep 2024; 14:3805. [PMID: 38360907 PMCID: PMC10869764 DOI: 10.1038/s41598-024-54435-9] [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: 10/11/2023] [Accepted: 02/13/2024] [Indexed: 02/17/2024] Open
Abstract
Secreted proteins of the Noggin family serve as pivotal regulators of early development and cell differentiation in all multicellular animals, including vertebrates. Noggin1 was identified first among all Noggins. Moreover, it was described as the first known embryonic inducer specifically secreted by the Spemann organizer and capable of inducing a secondary body axis when expressed ectopically. In the classical default model of neural induction, Noggin1 is presented as an antagonist of BMP signalling, playing a role as a neural inducer. Additionally, Noggin1 is involved in the dorsalization of embryonic mesoderm and later controls the differentiation of various tissues, including muscles, bones, and neural crest derivatives. Hitherto, noggin1 was found in all studied vertebrates. Here, we report the loss of noggin1 in elasmobranchs (sharks, rays and skates), which is a unique case among vertebrates. noggin2 and noggin4 retained in this group and studied in the embryos of the grey bamboo shark Chiloscyllium griseum revealed similarities in expression patterns and functional properties with their orthologues described in other vertebrates. The loss of noggin1 in elasmobranchs may be associated with histological features of the formation of their unique internal cartilaginous skeleton, although additional research is required to establish functional connections between these events.
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Affiliation(s)
- Galina V Ermakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Irina V Meyntser
- Moskvarium Center for Oceanography and Marine Biology, Moscow, 129223, Russia
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia.
| | - Andrey V Bayramov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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Eroshkin FM, Fefelova EA, Bredov DV, Orlov EE, Kolyupanova NM, Mazur AM, Sokolov AS, Zhigalova NA, Prokhortchouk EB, Nesterenko AM, Zaraisky AG. Mechanical Tensions Regulate Gene Expression in the Xenopus laevis Axial Tissues. Int J Mol Sci 2024; 25:870. [PMID: 38255964 PMCID: PMC10815341 DOI: 10.3390/ijms25020870] [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: 11/09/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
During gastrulation and neurulation, the chordamesoderm and overlying neuroectoderm of vertebrate embryos converge under the control of a specific genetic programme to the dorsal midline, simultaneously extending along it. However, whether mechanical tensions resulting from these morphogenetic movements play a role in long-range feedback signaling that in turn regulates gene expression in the chordamesoderm and neuroectoderm is unclear. In the present work, by using a model of artificially stretched explants of Xenopus midgastrula embryos and full-transcriptome sequencing, we identified genes with altered expression in response to external mechanical stretching. Importantly, mechanically activated genes appeared to be expressed during normal development in the trunk, i.e., in the stretched region only. By contrast, genes inhibited by mechanical stretching were normally expressed in the anterior neuroectoderm, where mechanical stress is low. These results indicate that mechanical tensions may play the role of a long-range signaling factor that regulates patterning of the embryo, serving as a link coupling morphogenesis and cell differentiation.
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Affiliation(s)
- Fedor M. Eroshkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Elena A. Fefelova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Denis V. Bredov
- Laboratory of Development Biophysics, Department of Embryology, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugeny E. Orlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Nataliya M. Kolyupanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Alexander M. Mazur
- Federal State Institution “Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences”, Leninsky Prospect, 33 Build. 2, 119071 Moscow, Russia
| | - Alexey S. Sokolov
- Federal State Institution “Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences”, Leninsky Prospect, 33 Build. 2, 119071 Moscow, Russia
| | - Nadezhda A. Zhigalova
- Federal State Institution “Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences”, Leninsky Prospect, 33 Build. 2, 119071 Moscow, Russia
| | - Egor B. Prokhortchouk
- Federal State Institution “Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences”, Leninsky Prospect, 33 Build. 2, 119071 Moscow, Russia
| | - Alexey M. Nesterenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya Str., 117997 Moscow, Russia
- Federal Center of Brain Research and Biotechnologies of Federal Medical-Biological Agency, 1 Build 10 Ostrovityanova Str., 117513 Moscow, Russia
| | - Andrey G. Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS), 16/10 Miklukho-Maklaya Str., 117997 Moscow, Russia
- Department of Regenerative Medicine, Pirogov Russian National Research Medical University, 1 Build 70 Ostrovityanova Str., 117513 Moscow, Russia
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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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Salomão R, Assis V, de Sousa Neto IV, Petriz B, Babault N, Durigan JLQ, de Cássia Marqueti R. Involvement of Matrix Metalloproteinases in COVID-19: Molecular Targets, Mechanisms, and Insights for Therapeutic Interventions. BIOLOGY 2023; 12:843. [PMID: 37372128 PMCID: PMC10295079 DOI: 10.3390/biology12060843] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023]
Abstract
MMPs are enzymes involved in SARS-CoV-2 pathogenesis. Notably, the proteolytic activation of MMPs can occur through angiotensin II, immune cells, cytokines, and pro-oxidant agents. However, comprehensive information regarding the impact of MMPs in the different physiological systems with disease progression is not fully understood. In the current study, we review the recent biological advances in understanding the function of MMPs and examine time-course changes in MMPs during COVID-19. In addition, we explore the interplay between pre-existing comorbidities, disease severity, and MMPs. The reviewed studies showed increases in different MMP classes in the cerebrospinal fluid, lung, myocardium, peripheral blood cells, serum, and plasma in patients with COVID-19 compared to non-infected individuals. Individuals with arthritis, obesity, diabetes, hypertension, autoimmune diseases, and cancer had higher MMP levels when infected. Furthermore, this up-regulation may be associated with disease severity and the hospitalization period. Clarifying the molecular pathways and specific mechanisms that mediate MMP activity is important in developing optimized interventions to improve health and clinical outcomes during COVID-19. Furthermore, better knowledge of MMPs will likely provide possible pharmacological and non-pharmacological interventions. This relevant topic might add new concepts and implications for public health in the near future.
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Affiliation(s)
- Rebecca Salomão
- Laboratory of Molecular Analysis, Postgraduate Program in Health and Sciences and Technology, Faculty of Ceilândia, University of Brasilia, Brasilia 72220-275, DF, Brazil
| | - Victoria Assis
- Laboratory of Molecular Analysis, Postgraduate Program in Rehabilitation Sciences, Faculty of Ceilândia, University of Brasilia, Brasilia 72220-275, DF, Brazil; (V.A.); (J.L.Q.D.)
| | - Ivo Vieira de Sousa Neto
- School of Physical Education and Sport of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-907, SP, Brazil;
| | - Bernardo Petriz
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasilia, Brasilia 71966-700, DF, Brazil;
- Laboratory of Exercise Molecular Physiology, University Center UDF, Brasília 71966-900, DF, Brazil
| | - Nicolas Babault
- INSERM UMR1093-CAPS, UFR des Sciences du Sport, Université de Bourgogne, F-21000 Dijon, France;
- Centre d’Expertise de la Performance, UFR des Sciences du Sport, Université de Bourgogne, F-21000 Dijon, France
| | - João Luiz Quaglioti Durigan
- Laboratory of Molecular Analysis, Postgraduate Program in Rehabilitation Sciences, Faculty of Ceilândia, University of Brasilia, Brasilia 72220-275, DF, Brazil; (V.A.); (J.L.Q.D.)
| | - Rita de Cássia Marqueti
- Laboratory of Molecular Analysis, Postgraduate Program in Health and Sciences and Technology, Faculty of Ceilândia, University of Brasilia, Brasilia 72220-275, DF, Brazil
- Laboratory of Molecular Analysis, Postgraduate Program in Rehabilitation Sciences, Faculty of Ceilândia, University of Brasilia, Brasilia 72220-275, DF, Brazil; (V.A.); (J.L.Q.D.)
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Insulin Receptor-Related Receptor Regulates the Rate of Early Development in Xenopus laevis. Int J Mol Sci 2022; 23:ijms23169250. [PMID: 36012515 PMCID: PMC9409083 DOI: 10.3390/ijms23169250] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
The orphan insulin receptor-related receptor (IRR) encoded by insrr gene is the third member of the insulin receptor family, also including the insulin receptor (IR) and the insulin-like growth factor receptor (IGF-1R). IRR is the extracellular alkaline medium sensor. In mice, insrr is expressed only in small populations of cells in specific tissues, which contain extracorporeal liquids of extreme pH. In particular, IRR regulates the metabolic bicarbonate excess in the kidney. In contrast, the role of IRR during Xenopus laevis embryogenesis is unknown, although insrr is highly expressed in frog embryos. Here, we examined the insrr function during the Xenopus laevis early development by the morpholino-induced knockdown. We demonstrated that insrr downregulation leads to development retardation, which can be restored by the incubation of embryos in an alkaline medium. Using bulk RNA-seq of embryos at the middle neurula stage, we showed that insrr downregulation elicited a general shift of expression towards genes specifically expressed before and at the onset of gastrulation. At the same time, alkali treatment partially restored the expression of the neurula-specific genes. Thus, our results demonstrate the critical role of insrr in the regulation of the early development rate in Xenopus laevis.
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