1
|
Martynova NY, Parshina EA, Zaraisky AG. Cytoskeletal protein Zyxin in embryonic development: from controlling cell movements and pluripotency to regulating embryonic patterning. FEBS J 2023; 290:66-72. [PMID: 34854244 DOI: 10.1111/febs.16308] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/29/2021] [Accepted: 11/30/2021] [Indexed: 01/14/2023]
Abstract
The Lim-domain protein Zyxin was initially identified as a minor actin cytoskeleton protein that regulates the assembly and repair of actin filaments. At the same time, additional functions revealed for Zyxin in recent decades indicate that this protein can also play an important role in regulating gene expression and cell differentiation. In this review, we analysed the data in the literature pointing to Zyxin as one of the possible molecular hubs linking morphogenetic cell movements with gene expression, stem cell status regulation and pattern formation during the most complex processes in organism life, embryogenesis.
Collapse
Affiliation(s)
- Natalia Y Martynova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Elena A Parshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
2
|
Protocol for separation of the nuclear and the cytoplasmic fractions of Xenopus laevis embryonic cells for studying protein shuttling. STAR Protoc 2021; 2:100449. [PMID: 33997802 PMCID: PMC8091922 DOI: 10.1016/j.xpro.2021.100449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
This protocol for the separation of nuclear and cytoplasmic fractions of cells of Xenopus laevis embryos was developed to study changes in the intracellular localization of the Zyxin and Ybx1 proteins, which are capable of changing localization in response to certain stimuli. Western blot analysis allows the quantification of changes in the distribution of these proteins between the cytoplasm and nucleus, whereas the posttranslational modifications specific to each compartment can be identified by changes in electrophoretic mobility. For complete details on the use and execution of this protocol, please refer to Parshina et al. (2020). A simple way to obtain tagged proteins in Xenopus embryos Rapid separation of Xenopus embryonic cells into nuclear, cytoplasmic fractions Quantifying the distribution of shuttle proteins between the cytoplasm and nucleus Protein posttranslational modifications specific to the cytoplasm and nucleus can be studied
Collapse
|
3
|
Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins. Int J Mol Sci 2021; 22:ijms22052647. [PMID: 33808029 PMCID: PMC7961639 DOI: 10.3390/ijms22052647] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share similarities with transcriptional regulators and have positively charged electrostatic patches, which may indicate that they have previously unanticipated nucleic acid binding properties. Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3. Furthermore, we analyzed protein expression and mutational frequency in various malignancies, as well as mapped protein-protein interaction networks they are involved in. Overall, our comprehensive bioinformatic analysis suggests that these proteins may play important roles in mediating protein-protein and protein-nucleic acid interactions.
Collapse
|
4
|
Fan Y, He L, Wang Y, Fu S, Han Y, Fan J, Wen Q. CLIP4 Shows Putative Tumor Suppressor Characteristics in Breast Cancer: An Integrated Analysis. Front Mol Biosci 2021; 7:616190. [PMID: 33575272 PMCID: PMC7870488 DOI: 10.3389/fmolb.2020.616190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
Background: CAP-Gly domain containing linker protein family member 4 (CLIP4) plays an important role in cancers. However, its expression, prognostic value, and biological effect in breast cancer remain unclear. Methods: Data on patients diagnosed with breast cancer were retrieved from the TCGA-BRCA and other public omics databases. The expression profile of CLIP4 was analyzed using Oncomine, bc-GenExMiner, and TCGA. The prognostic value of CLIP4 was determined by Kaplan-Meier Plotter and Human Protein Atlas. Identification of genes co-expressed with CLIP4 and potential mechanism analyses were performed using UALCAN, STRING, Metascape, and GSEA. The epigenetic characteristics of CLIP4 were determined by DiseaseMeth and MEXPRESS. Results: CLIP4 was downregulated and its expression was negatively correlated with estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor type 2 (HER2) status, Nottingham prognostic index (NPI), and Scarff-Bloom-Richardson (SBR) grade in breast cancer, whereas it was positively linked to basal-like and triple negative breast cancer status. Ectopic expression of CLIP4 was related with poor prognosis. In the analysis of genes co-expressed with CLIP4, GSEA showed that the Hedgehog (Hh), JAK-STAT, ERBB, Wnt signaling pathway, cell adhesion molecules, and pathways in cancer were dissimilarly enriched in the CLIP4 expression high phenotype. Analysis of the genetics and epigenetics of CLIP4 indicated that its expression was negatively correlated with DNA methylation. Conclusion: Methylated CLIP4 may be a novel prognostic and therapeutic biomarker for breast cancer.
Collapse
Affiliation(s)
- Yu Fan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Lijia He
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Yu Wang
- Health Management Department, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shaozhi Fu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Yunwei Han
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Juan Fan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| |
Collapse
|
5
|
Martynova NY, Parshina EA, Eroshkin FM, Zaraisky AG. The Cytoskeletal Protein Zyxin Modulates the Expression of the Target Genes of the Shh Signaling Cascade in the Cells of the Neural Plate of Embryos of the Spur-Toed Frog Xenopus laevis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
6
|
Sabino F, Madzharova E, Auf dem Keller U. Cell density-dependent proteolysis by HtrA1 induces translocation of zyxin to the nucleus and increased cell survival. Cell Death Dis 2020; 11:674. [PMID: 32826880 PMCID: PMC7442833 DOI: 10.1038/s41419-020-02883-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 01/01/2023]
Abstract
Proteases modulate critical processes in cutaneous tissue repair to orchestrate inflammation, cell proliferation and tissue remodeling. However, the functional consequences and implications in healing impairments of most cleavage events are not understood. Using iTRAQ-based Terminal Amine Isotopic Labeling of Substrates (TAILS) we had characterized proteolytic signatures in a porcine wound healing model and identified two neo-N termini derived from proteolytic cleavage of the focal adhesion protein and mechanotransducer zyxin. Here, we assign these proteolytic events to the activity of either caspase-1 or serine protease HtrA1 and analyze the biological relevance of the resultant zyxin truncations. By cellular expression of full-length and truncated zyxin proteins, we demonstrate nuclear translocation of a C-terminal zyxin fragment that could also be generated in vitro by HtrA1 cleavage and provide evidence for its anti-apoptotic activities, potentially by regulating the expression of modulators of cell proliferation, protein synthesis and genome stability. Targeted degradomics correlated endogenous generation of the same zyxin fragment with increased cell density in human primary dermal fibroblasts. Hence, this newly identified HtrA1-zyxin protease signaling axis might present a novel mechanism to transiently enhance cell survival in environments of increased cell density like in wound granulation tissue.
Collapse
Affiliation(s)
- Fabio Sabino
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Søltofts Plads, 2800, Kongens Lyngby, Denmark
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland
| | - Elizabeta Madzharova
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland
| | - Ulrich Auf dem Keller
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Søltofts Plads, 2800, Kongens Lyngby, Denmark.
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.
| |
Collapse
|
7
|
Belgardt E, Steinberg T, Husari A, Dieterle MP, Hülter-Hassler D, Jung B, Tomakidi P. Force-responsive Zyxin modulation in periodontal ligament cells is regulated by YAP rather than TAZ. Cell Signal 2020; 72:109662. [PMID: 32330602 DOI: 10.1016/j.cellsig.2020.109662] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/03/2023]
Abstract
In the context of mechanically induced force transmission, the modification of the actin cytoskeleton through involvement of zyxin is an established concept. However, in cells of the periodontal ligament (PDL), which is physiologically subjected to intermittent mechanical forces, the force-responsive modulation of zyxin and the molecular key players, which orchestrate its cellular regulation, have not yet been elucidated. By employing indirect immunofluorescence and western blotting with different subcellular fractions, we show here in stretch force-exposed human PDL fibroblasts (hPDLFs) that (i) the zyxin protein is modulated, and (ii) its subcellular localization is altered. More importantly, using a pharmacological intervention approach, to inhibit the nuclear presence of the co-transcriptional activator yes-associated protein (YAP), we evidence for the first time that on the molecular level, the cellular abundance of zyxin, among the Thyrotrophic Embryonic Factor (TEF)-binding proteins, is regulated by YAP rather than TAZ. Our findings provide novel insights into the topic how cells of the periodontium and the periodontal ligament in particular respond and may adapt to mechanical forces, and first time identify YAP as the key player of the intracellular regulation of the mechano-sensor and mechano-transducer zyxin in hPDLFs. Moreover, the findings broaden the current knowledge on YAP, since so far, currently only very few YAP-regulated genes have been identified.
Collapse
Affiliation(s)
- Elisa Belgardt
- Department of Orthodontics, Center for Dental Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany.
| | - Thorsten Steinberg
- Division of Oral Biotechnology, Center for Dental Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany.
| | - Ayman Husari
- Department of Orthodontics, Center for Dental Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; Faculty of Engineering, University of Freiburg, Georges-Köhler-Allee 101, 79110 Freiburg, Germany.
| | - Martin Philipp Dieterle
- Division of Oral Biotechnology, Center for Dental Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany.
| | - Diana Hülter-Hassler
- Department of Orthodontics, Center for Dental Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany.
| | - Britta Jung
- Department of Orthodontics, Center for Dental Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany.
| | - Pascal Tomakidi
- Division of Oral Biotechnology, Center for Dental Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany.
| |
Collapse
|