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Huang X, Su L, Xian B, Yu Q, Zhang M, Fan J, Zhang C, Liu Y, He H, Zhong X, Li M, Chen S, He Y, Li Q. Genome-wide identification and characterization of the sweet orange (Citrus sinensis) basic helix-loop-helix (bHLH) family reveals a role for CsbHLH085 as a regulator of citrus bacterial canker resistance. Int J Biol Macromol 2024; 267:131442. [PMID: 38621573 DOI: 10.1016/j.ijbiomac.2024.131442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024]
Abstract
Citrus bacterial canker (CBC) is a harmful bacterial disease caused by Xanthomonas citri subsp. citri (Xcc), negatively impacting citrus production worldwide. The basic helix-loop-helix (bHLH) transcription factor family plays crucial roles in plant development and stress responses. This study aimed to identify and annotate bHLH proteins encoded in the Citrus sinensis genome and explore their involvement and functional importance in regulating CBC resistance. A total of 135 putative CsbHLHs TFs were identified and categorized into 16 subfamilies. Their chromosomal locations, collinearity, and phylogenetic relationships were comprehensively analyzed. Upon Xcc strain YN1 infection, certain CsbHLHs were differentially regulated in CBC-resistant and CBC-sensitive citrus varieties. Among these, CsbHLH085 was selected for further functional characterization. CsbHLH085 was upregulated in the CBC-resistant citrus variety, was localized in the nucleus, and had a transcriptional activation activity. CsbHLH085 overexpression in Citrus significantly enhanced CBC resistance, accompanied by increased levels of salicylic acid (SA), jasmonic acid (JA), reactive oxygen species (ROS), and decreased levels of abscisic acid (ABA) and antioxidant enzymes. Conversely, CsbHLH085 virus-induced gene silencing resulted in opposite phenotypic and biochemical responses. CsbHLH085 silencing also affected the expression of phytohormone biosynthesis and signaling genes involved in SA, JA, and ABA signaling. These findings highlight the crucial role of CsbHLH085 in regulating CBC resistance, suggesting its potential as a target for biotechnological-assisted breeding citrus varieties with improved resistance against phytopathogens.
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Affiliation(s)
- Xin Huang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Liyan Su
- School of Biological and Environmental Engineering, Xi'an University, Xi'an 710065, China
| | - Baohang Xian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Qiyuan Yu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Miao Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Jie Fan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Chenxi Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Yiqi Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Houzheng He
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Xin Zhong
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Man Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China
| | - Shanchun Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China; National Citrus Engineering Research Center, Chongqing 400712, China
| | - Yongrui He
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China; National Citrus Engineering Research Center, Chongqing 400712, China.
| | - Qiang Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400712, China; National Citrus Engineering Research Center, Chongqing 400712, China.
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Trofimov K, Gratz R, Ivanov R, Stahl Y, Bauer P, Brumbarova T. FER-like iron deficiency-induced transcription factor (FIT) accumulates in nuclear condensates. J Cell Biol 2024; 223:e202311048. [PMID: 38393070 PMCID: PMC10890924 DOI: 10.1083/jcb.202311048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/28/2023] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The functional importance of nuclear protein condensation remains often unclear. The bHLH FER-like iron deficiency-induced transcription factor (FIT) controls iron acquisition and growth in plants. Previously described C-terminal serine residues allow FIT to interact and form active transcription factor complexes with subgroup Ib bHLH factors such as bHLH039. FIT has lower nuclear mobility than mutant FITmSS271AA. Here, we show that FIT undergoes a light-inducible subnuclear partitioning into FIT nuclear bodies (NBs). Using quantitative and qualitative microscopy-based approaches, we characterized FIT NBs as condensates that were reversible and likely formed by liquid-liquid phase separation. FIT accumulated preferentially in NBs versus nucleoplasm when engaged in protein complexes with itself and with bHLH039. FITmSS271AA, instead, localized to NBs with different dynamics. FIT colocalized with splicing and light signaling NB markers. The NB-inducing light conditions were linked with active FIT and elevated FIT target gene expression in roots. FIT condensation may affect nuclear mobility and be relevant for integrating environmental and Fe nutrition signals.
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Affiliation(s)
- Ksenia Trofimov
- Institute of Botany, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Regina Gratz
- Institute of Botany, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tzvetina Brumbarova
- Institute of Botany, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Chandran C, Santra M, Rubin E, Geary ML, Yam GHF. Regenerative Therapy for Corneal Scarring Disorders. Biomedicines 2024; 12:649. [PMID: 38540264 PMCID: PMC10967722 DOI: 10.3390/biomedicines12030649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 05/09/2024] Open
Abstract
The cornea is a transparent and vitally multifaceted component of the eye, playing a pivotal role in vision and ocular health. It has primary refractive and protective functions. Typical corneal dysfunctions include opacities and deformities that result from injuries, infections, or other medical conditions. These can significantly impair vision. The conventional challenges in managing corneal ailments include the limited regenerative capacity (except corneal epithelium), immune response after donor tissue transplantation, a risk of long-term graft rejection, and the global shortage of transplantable donor materials. This review delves into the intricate composition of the cornea, the landscape of corneal regeneration, and the multifaceted repercussions of scar-related pathologies. It will elucidate the etiology and types of dysfunctions, assess current treatments and their limitations, and explore the potential of regenerative therapy that has emerged in both in vivo and clinical trials. This review will shed light on existing gaps in corneal disorder management and discuss the feasibility and challenges of advancing regenerative therapies for corneal stromal scarring.
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Affiliation(s)
- Christine Chandran
- Corneal Regeneration Laboratory, Department of Ophthalmology, Mercy Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; (C.C.); (M.S.); (E.R.); (M.L.G.)
| | - Mithun Santra
- Corneal Regeneration Laboratory, Department of Ophthalmology, Mercy Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; (C.C.); (M.S.); (E.R.); (M.L.G.)
| | - Elizabeth Rubin
- Corneal Regeneration Laboratory, Department of Ophthalmology, Mercy Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; (C.C.); (M.S.); (E.R.); (M.L.G.)
| | - Moira L. Geary
- Corneal Regeneration Laboratory, Department of Ophthalmology, Mercy Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; (C.C.); (M.S.); (E.R.); (M.L.G.)
| | - Gary Hin-Fai Yam
- Corneal Regeneration Laboratory, Department of Ophthalmology, Mercy Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; (C.C.); (M.S.); (E.R.); (M.L.G.)
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
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Schütz S, Bergsdorf C, Hänni-Holzinger S, Lingel A, Renatus M, Gossert AD, Jahnke W. Intrinsically Disordered Regions in the Transcription Factor MYC:MAX Modulate DNA Binding via Intramolecular Interactions. Biochemistry 2024. [PMID: 38264995 DOI: 10.1021/acs.biochem.3c00608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor (TF) MYC is in large part an intrinsically disordered oncoprotein. In complex with its obligate heterodimerization partner MAX, MYC preferentially binds E-Box DNA sequences (CANNTG). At promoters containing these sequence motifs, MYC controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. A vast network of proteins in turn regulates MYC function via intermolecular interactions. In this work, we establish another layer of MYC regulation by intramolecular interactions. We used nuclear magnetic resonance (NMR) spectroscopy to identify and map multiple binding sites for the C-terminal MYC:MAX DNA-binding domain (DBD) on the intrinsically disordered regions (IDRs) in the MYC N-terminus. We find that these binding events in trans are driven by electrostatic attraction, that they have distinct affinities, and that they are competitive with DNA binding. Thereby, we observe the strongest effects for the N-terminal MYC box 0 (Mb0), a conserved motif involved in MYC transactivation and target gene induction. We prepared recombinant full-length MYC:MAX complex and demonstrate that the interactions identified in this work are also relevant in cis, i.e., as intramolecular interactions. These findings are supported by surface plasmon resonance (SPR) experiments, which revealed that intramolecular IDR:DBD interactions in MYC decelerate the association of MYC:MAX complexes to DNA. Our work offers new insights into how bHLH-LZ TFs are regulated by intramolecular interactions, which open up new possibilities for drug discovery.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sandra Hänni-Holzinger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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Osipovich AB, Zhou FY, Chong JJ, Trinh LT, Cottam MA, Shrestha S, Cartailler JP, Magnuson MA. Deletion of Ascl1 in pancreatic β-cells improves insulin secretion, promotes parasympathetic innervation, and attenuates dedifferentiation during metabolic stress. Mol Metab 2023; 78:101811. [PMID: 37769990 PMCID: PMC10570713 DOI: 10.1016/j.molmet.2023.101811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/03/2023] Open
Abstract
OBJECTIVE ASCL1, a pioneer transcription factor, is essential for neural cell differentiation and function. Previous studies have shown that Ascl1 expression is increased in pancreatic β-cells lacking functional KATP channels or after feeding of a high fat diet (HFD) suggesting that it may contribute to the metabolic stress response of β-cells. METHODS We generated β-cell-specific Ascl1 knockout mice (Ascl1βKO) and assessed their glucose homeostasis, islet morphology and gene expression after feeding either a normal diet or HFD for 12 weeks, or in combination with a genetic disruption of Abcc8, an essential KATP channel component. RESULTS Ascl1 expression is increased in response to both a HFD and membrane depolarization and requires CREB-dependent Ca2+ signaling. No differences in glucose homeostasis or islet morphology were observed in Ascl1βKO mice fed a normal diet or in the absence of KATP channels. However, male Ascl1βKO mice fed a HFD exhibited decreased blood glucose levels, improved glucose tolerance, and increased β-cell proliferation. Bulk RNA-seq analysis of islets from Ascl1βKO mice from three studied conditions showed alterations in genes associated with the secretory function. HFD-fed Ascl1βKO mice showed the most extensive changes with increased expression of genes necessary for glucose sensing, insulin secretion and β-cell proliferation, and a decrease in genes associated with β-cell dysfunction, inflammation and dedifferentiation. HFD-fed Ascl1βKO mice also displayed increased expression of parasympathetic neural markers and cholinergic receptors that was accompanied by increased insulin secretion in response to acetylcholine and an increase in islet innervation. CONCLUSIONS Ascl1 expression is induced by stimuli that cause Ca2+-signaling to the nucleus and contributes in a multifactorial manner to the loss of β-cell function by promoting the expression of genes associated with cellular dedifferentiation, attenuating β-cells proliferation, suppressing acetylcholine sensitivity, and repressing parasympathetic innervation of islets. Thus, the removal of Ascl1 from β-cells improves their function in response to metabolic stress.
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Affiliation(s)
- Anna B Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Frank Y Zhou
- College of Arts and Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Judy J Chong
- College of Arts and Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Linh T Trinh
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mathew A Cottam
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Shristi Shrestha
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Mark A Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
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6
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Ge L, Zhao G, Lan C, Song H, Qi D, Huang P, Ke X, Cui H. MESP2 binds competitively to TCF4 to suppress gastric cancer progression by regulating the SKP2/p27 axis. Cell Death Discov 2023; 9:79. [PMID: 36854722 PMCID: PMC9975210 DOI: 10.1038/s41420-023-01367-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Gastric cancer (GC) is a major cause of human deaths worldwide, and is notorious for its high incidence and mortality rates. Mesoderm Posterior Basic Helix-loop-helix (bHLH) transcription factor 2 (MESP2) acts as a transcription factor with a conserved bHLH domain. However, whether MESP2 contributes to tumorigenesis and its potential molecular mechanisms, remain unexplored. Noticeably, MESP2 expression levels are decreased in GC tissues and cell lines compared to those in normal tissue. Further, in vitro and in vivo experiments have confirmed that MESP2 overexpression suppresses GC cell growth, migration, and invasion, whereas MESP2 knockdown results in the exact opposite. Here, we present the first report that MESP2 binds to transcription factor 7-like 2 (TCF7L2/TCF4) to inhibit the activation of the TCF4/beta-catenin transcriptional complex, decrease the occupancy of the complex on the S-phase kinase Associated Protein 2 (SKP2) promoter, and promote p27 accumulation. MESP2 knockdown facilitated tumorigenesis, which was partially suppressed by SKP2 knockdown. Taken together, we conclude that MESP2 binds competitively to TCF4 to suppress GC progression by regulating the SKP2/p27 axis, thus offering a potential therapeutic strategy for future treatment.
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Affiliation(s)
- Lingjun Ge
- grid.263906.80000 0001 0362 4044State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716 China
| | - Gaichao Zhao
- grid.263906.80000 0001 0362 4044State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716 China
| | - Chao Lan
- grid.263906.80000 0001 0362 4044State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716 China
| | - Houji Song
- grid.263906.80000 0001 0362 4044Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716 China
| | - Dan Qi
- grid.263906.80000 0001 0362 4044Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716 China
| | - Pan Huang
- grid.263906.80000 0001 0362 4044State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716 China
| | - Xiaoxue Ke
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China. .,Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China.
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China. .,Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China.
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Bajracharya A, Xi J, Grace KF, Bayer EE, Grant CA, Clutton CH, Baerson SR, Agarwal AK, Qiu Y. PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosensory growth requires the Mediator subunit MED14. PLANT PHYSIOLOGY 2022; 190:2706-2721. [PMID: 36063057 PMCID: PMC9706435 DOI: 10.1093/plphys/kiac412] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/12/2022] [Indexed: 05/19/2023]
Abstract
While moderately elevated ambient temperatures do not trigger stress responses in plants, they do substantially stimulate the growth of specific organs through a process known as thermomorphogenesis. The basic helix-loop-helix transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) plays a central role in regulating thermomorphogenetic hypocotyl elongation in various plant species, including Arabidopsis (Arabidopsis thaliana). Although it is well known that PIF4 and its co-activator HEMERA (HMR) promote plant thermosensory growth by activating genes involved in the biosynthesis and signaling of the phytohormone auxin, the detailed molecular mechanism of such transcriptional activation is not clear. In this report, we investigated the role of the Mediator complex in the PIF4/HMR-mediated thermoresponsive gene expression. Through the characterization of various mutants of the Mediator complex, a tail subunit named MED14 was identified as an essential factor for thermomorphogenetic hypocotyl growth. MED14 was required for the thermal induction of PIF4 target genes but had a marginal effect on the levels of PIF4 and HMR. Further transcriptomic analyses confirmed that the expression of numerous PIF4/HMR-dependent, auxin-related genes required MED14 at warm temperatures. Moreover, PIF4 and HMR physically interacted with MED14 and both were indispensable for the association of MED14 with the promoters of these thermoresponsive genes. While PIF4 did not regulate MED14 levels, HMR was required for the transcript abundance of MED14. Taken together, these results unveil an important thermomorphogenetic mechanism, in which PIF4 and HMR recruit the Mediator complex to activate auxin-related growth-promoting genes when plants sense moderate increases in ambient temperature.
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Affiliation(s)
| | - Jing Xi
- Natural Products Utilization Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Oxford, Mississippi, USA
| | - Karlie F Grace
- Department of Biology, University of Mississippi, Oxford, Mississippi 38677, USA
| | - Eden E Bayer
- Department of Biology, University of Mississippi, Oxford, Mississippi 38677, USA
| | - Chloe A Grant
- Department of Biology, University of Mississippi, Oxford, Mississippi 38677, USA
| | - Caroline H Clutton
- Department of Biology, University of Mississippi, Oxford, Mississippi 38677, USA
| | - Scott R Baerson
- Natural Products Utilization Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Oxford, Mississippi, USA
| | - Ameeta K Agarwal
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, Oxford, Mississippi, USA
- Division of Pharmacology, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, Mississippi, USA
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Zhou H, Hwarari D, Ma H, Xu H, Yang L, Luo Y. Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology. Front Genet 2022; 13:1060546. [PMID: 36437962 PMCID: PMC9682074 DOI: 10.3389/fgene.2022.1060546] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/27/2022] [Indexed: 09/29/2023] Open
Abstract
The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown their presence in early land plants. In this paper, we performed a comparative discussion on the current knowledge of the TCP Transcription Factors in lower and higher plants: their evolutionary history based on the phylogenetics of 849 TCP proteins from 37 plant species, duplication events, and biochemical roles in some of the plants species. Phylogenetics investigations confirmed the classification of TCP TFs into Class I (the PCF1/2), and Class II (the C- clade) factors; the Class II factors were further divided into the CIN- and CYC/TB1- subclade. A trace in the evolution of the TCP Factors revealed an absence of the CYC/TB1subclade in lower plants, and an independent evolution of the CYC/TB1subclade in both eudicot and monocot species. 54% of the total duplication events analyzed were biased towards the dispersed duplication, and we concluded that dispersed duplication events contributed to the expansion of the TCP gene family. Analysis in the TCP factors functional roles confirmed their involvement in various biochemical processes which mainly included promoting cell proliferation in leaves in Class I TCPs, and cell division during plant development in Class II TCP Factors. Apart from growth and development, the TCP Factors were also shown to regulate hormonal and stress response pathways. Although this paper does not exhaust the present knowledge of the TCP Transcription Factors, it provides a base for further exploration of the gene family.
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Affiliation(s)
- Haiying Zhou
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative In-novation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Delight Hwarari
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hongyu Ma
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Haibin Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative In-novation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
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9
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Gupta S, Fink MK, Kempuraj D, Sinha NR, Martin LM, Keele LM, Sinha PR, Giuliano EA, Hesemann NP, Raikwar SP, Chaurasia SS, Mohan RR. Corneal fibrosis abrogation by a localized AAV-mediated inhibitor of differentiation 3 (Id3) gene therapy in rabbit eyes in vivo. Mol Ther 2022; 30:3257-3269. [PMID: 35780298 PMCID: PMC9552811 DOI: 10.1016/j.ymthe.2022.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/18/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022] Open
Abstract
Previously we found that inhibitor of differentiation 3 (Id3) gene, a transcriptional repressor, efficiently inhibits corneal keratocyte differentiation to myofibroblasts in vitro. This study evaluated the potential of adeno-associated virus 5 (AAV5)-mediated Id3 gene therapy to treat corneal scarring using an established rabbit in vivo disease model. Corneal scarring/fibrosis in rabbit eyes was induced by alkali trauma, and 24 h thereafter corneas were administered with either balanced salt solution AAV5-naked vector, or AAV5-Id3 vector (n = 6/group) via an optimized reported method. Therapeutic effects of AAV5-Id3 gene therapy on corneal pathology and ocular health were evaluated with clinical, histological, and molecular techniques. Localized AAV5-Id3 gene therapy significantly inhibited corneal fibrosis/haze clinically from 2.7 to 0.7 on the Fantes scale in live animals (AAV5-naked versus AAV5-Id3; p < 0.001). Furthermore, AAV5-Id3 treatment significantly reduced profibrotic gene mRNA levels: α-smooth muscle actin (α-SMA) (2.8-fold; p < 0.001), fibronectin (3.2-fold; p < 0.001), collagen I (0.8-fold; p < 0.001), and collagen III (1.4-fold; p < 0.001), as well as protein levels of α-SMA (23.8%; p < 0.001) and collagens (1.8-fold; p < 0.001). The anti-fibrotic activity of AAV5-Id3 is attributed to reduced myofibroblast formation by disrupting the binding of E-box proteins to the promoter of α-SMA, a transforming growth factor-β signaling downstream target gene. In conclusion, these results indicate that localized AAV5-Id3 delivery in stroma caused no clinically relevant ocular symptoms or corneal cellular toxicity in the rabbit eyes.
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Affiliation(s)
- Suneel Gupta
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Michael K Fink
- Department of Pathology, School of Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Duraisamy Kempuraj
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Nishant R Sinha
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Lynn M Martin
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Landon M Keele
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Prashant R Sinha
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Elizabeth A Giuliano
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Nathan P Hesemann
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Department of Pathology, School of Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sudhanshu P Raikwar
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Shyam S Chaurasia
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA; Department of Ophthalmology & Visual Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rajiv R Mohan
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA; Mason Eye Institute, School of Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65212, USA.
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10
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Piersimoni L, Abd El Malek M, Bhatia T, Bender J, Brankatschk C, Calvo Sánchez J, Dayhoff GW, Di Ianni A, Figueroa Parra JO, Garcia-Martinez D, Hesselbarth J, Köppen J, Lauth LM, Lippik L, Machner L, Sachan S, Schmidt L, Selle R, Skalidis I, Sorokin O, Ubbiali D, Voigt B, Wedler A, Wei AAJ, Zorn P, Dunker AK, Köhn M, Sinz A, Uversky VN. Lighting up Nobel Prize-winning studies with protein intrinsic disorder. Cell Mol Life Sci 2022; 79:449. [PMID: 35882686 PMCID: PMC11072364 DOI: 10.1007/s00018-022-04468-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.
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Affiliation(s)
- Lolita Piersimoni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Marina Abd El Malek
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Twinkle Bhatia
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julian Bender
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Christin Brankatschk
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jaime Calvo Sánchez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Alessio Di Ianni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Dailen Garcia-Martinez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julia Hesselbarth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Janett Köppen
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Luca M Lauth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Laurin Lippik
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Machner
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Shubhra Sachan
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Schmidt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Robin Selle
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ioannis Skalidis
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Oleksandr Sorokin
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Daniele Ubbiali
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Bruno Voigt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alice Wedler
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan An Jung Wei
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Peter Zorn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Marcel Köhn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Andrea Sinz
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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11
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Bondos SE, Dunker AK, Uversky VN. Intrinsically disordered proteins play diverse roles in cell signaling. Cell Commun Signal 2022; 20:20. [PMID: 35177069 PMCID: PMC8851865 DOI: 10.1186/s12964-022-00821-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered.
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Affiliation(s)
- Sarah E. Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843 USA
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Moscow Region, Russia 142290
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12
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Alves CC, Donadi EA, Giuliatti S. Structural Characterization of the Interaction of Hypoxia Inducible Factor-1 with Its Hypoxia Responsive Element at the -964G > A Variation Site of the HLA-G Promoter Region. Int J Mol Sci 2021; 22:ijms222313046. [PMID: 34884849 PMCID: PMC8657931 DOI: 10.3390/ijms222313046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
Human Antigen Leukocyte-G (HLA-G) gene encodes an immune checkpoint molecule that has restricted tissue expression in physiological conditions; however, the gene may be induced in hypoxic conditions by the interaction with the hypoxia inducible factor-1 (HIF1). Hypoxia regulatory elements (HRE) located at the HLA-G promoter region and at exon 2 are the major HIF1 target sites. Since the G allele of the −964G > A transversion induces higher HLA-G expression when compared to the A allele in hypoxic conditions, here we analyzed HIF1-HRE complex interaction at the pair-atom level considering both −964G > A polymorphism alleles. Mouse HIF2 dimer crystal (Protein Data Bank ID: 4ZPK) was used as template to perform homology modelling of human HIF1 quaternary structure using MODELLER v9.14. Two 3D DNA structures were built from 5′GCRTG’3 HRE sequence containing the −964G/A alleles using x3DNA. Protein-DNA docking was performed using the HADDOCK v2.4 server, and non-covalent bonds were computed by DNAproDB server. Molecular dynamic simulation was carried out per 200 ns, using Gromacs v.2019. HIF1 binding in the HRE containing −964G allele results in more hydrogen bonds and van der Waals contact formation than HRE with −964A allele. Protein-DNA complex trajectory analysis revealed that HIF1-HRE-964G complex is more stable. In conclusion, HIF1 binds in a more stable and specific manner at the HRE with G allele.
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Affiliation(s)
- Cinthia C. Alves
- Department of Genetic, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Eduardo A. Donadi
- Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Silvana Giuliatti
- Department of Genetic, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
- Correspondence:
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13
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Mnt Represses Epithelial Identity To Promote Epithelial-to-Mesenchymal Transition. Mol Cell Biol 2021; 41:e0018321. [PMID: 34460331 DOI: 10.1128/mcb.00183-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The multistep process of epithelial-to-mesenchymal transition (EMT), whereby static epithelial cells become migratory mesenchymal cells, plays a critical role during various developmental contexts, wound healing, and pathological conditions such as cancer metastasis. Despite the established function of basic helix-loop-helix (bHLH) transcription factors (TFs) in cell fate determination, only a few have been examined for their role in EMT. Here, using transcriptome analysis of distinct stages during stepwise progression of transforming growth factor beta (TGFβ)-induced EMT in mammary epithelial cells, we revealed distinct categories of bHLH TFs that show differential expression kinetics during EMT. Using a short interfering RNA-mediated functional screen for bHLH TFs during EMT, we found Max network transcription repressor (MNT) to be essential for EMT in mammary epithelial cells. We show that the depletion of MNT blocks TGFβ-induced morphological changes during EMT, and this is accompanied by derepression of a large number of epithelial genes. We show that MNT mediates the repression of epithelial identity genes during EMT by recruiting HDAC1 and mediating the loss of H3K27ac and chromatin accessibility. Lastly, we show that MNT is expressed at higher levels in EMT-High breast cancer cells and is required for their migration. Taken together, these findings establish MNT as a critical regulator of cell fate changes during mammary EMT. IMPORTANCE The bHLH TF Mnt promotes epithelial to mesenchymal transition through epigenetic repression of the epithelial gene expression program.
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14
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Nesterov SV, Ilyinsky NS, Uversky VN. Liquid-liquid phase separation as a common organizing principle of intracellular space and biomembranes providing dynamic adaptive responses. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119102. [PMID: 34293345 DOI: 10.1016/j.bbamcr.2021.119102] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 02/07/2023]
Abstract
This work is devoted to the phenomenon of liquid-liquid phase separation (LLPS), which has come to be recognized as fundamental organizing principle of living cells. We distinguish separation processes with different dimensions. Well-known 3D-condensation occurs in aqueous solution and leads to membraneless organelle (MLOs) formation. 2D-films may be formed near membrane surfaces and lateral phase separation (membrane rafts) occurs within the membranes themselves. LLPS may also occur on 1D structures like DNA and the cyto- and nucleoskeleton. Phase separation provides efficient transport and sorting of proteins and metabolites, accelerates the assembly of metabolic and signaling complexes, and mediates stress responses. In this work, we propose a model in which the processes of polymerization (1D structures), phase separation in membranes (2D structures), and LLPS in the volume (3D structures) influence each other. Disordered proteins and whole condensates may provide membrane raft separation or polymerization of specific proteins. On the other hand, 1D and 2D structures with special composition or embedded IDRs can nucleate condensates. We hypothesized that environmental change may trigger a LLPS which can propagate within the cell interior moving along the cytoskeleton or as an autowave. New phase propagation quickly and using a low amount of energy adjusts cell signaling and metabolic systems to new demands. Cumulatively, the interconnected phase separation phenomena in different dimensions represent a previously unexplored system of intracellular communication and regulation which cannot be ignored when considering both physiological and pathological cell processes.
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Affiliation(s)
- Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia; Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow 123182, Russia.
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA.
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15
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Sołtys K, Wycisk K, Ożyhar A. Liquid-liquid phase separation of the intrinsically disordered AB region of hRXRγ is driven by hydrophobic interactions. Int J Biol Macromol 2021; 183:936-949. [PMID: 33971237 DOI: 10.1016/j.ijbiomac.2021.05.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022]
Abstract
Nuclear receptors (NRs) are a family of transcription factors that are regulated endogenously by small lipophilic ligands. Recently, liquid-liquid phase separation (LLPS) has appeared as a new aspect of NR function. In the human retinoid X receptor γ (hRXRγ), the inherently disordered AB region undergoes LLPS via homotypic multivalent interactions. To better understand the functions of liquid condensates, a clear view of the molecular interactions underlying the LLPS are required. The phase separation propensity of the AB region of hRXRγ (AB_hRXG) at a high NaCl concentration, a lower critical solution temperature behavior, and also sensitivity to kosmotropic salts and 1,6-hexanediol, which all indicate the importance of hydrophobic interactions in the formation of AB_hRXG liquid condensates, is presented in the paper. Additionally, molecular crowding agents and TMAO shift the equilibrium, in turn enabling phase transition at lower AB_hRXG concentrations. Although the LLPS of the proteins can lead to aggregation, AB_hRXG liquid condensates are not aggregation prone. Interestingly, the formation of AB_hRXG liquid condensates has an impact on the rest of the receptor, as AB_hRXG liquid condensates recruit the remaining fragment of hRXRγ into the droplets. The ability of AB_hRXG to undergo LLPS might be important for gene expression regulation.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Krzysztof Wycisk
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
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16
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Nishide G, Lim K, Mohamed MS, Kobayashi A, Hazawa M, Watanabe-Nakayama T, Kodera N, Ando T, Wong RW. High-Speed Atomic Force Microscopy Reveals Spatiotemporal Dynamics of Histone Protein H2A Involution by DNA Inchworming. J Phys Chem Lett 2021; 12:3837-3846. [PMID: 33852305 DOI: 10.1021/acs.jpclett.1c00697] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA-histone interaction is always perturbed by epigenetic regulators to regulate gene expression. Direct visualization of this interaction is yet to be achieved. By using high-speed atomic force microscopy (HS-AFM), we have observed the dynamic DNA-histone H2A interaction. HS-AFM movies demonstrate the globular core and disordered tail of H2A. DNA-H2A formed the classic "beads-on-string" conformation on poly-l-lysine (PLL) and lipid substrates. Notably, a short-linearized double-stranded DNA (dsDNA), resembling an inchworm, wrapped around a single H2A protein only observed on the lipid substrate. Such a phenomenon does not occur for plasmid DNA or linearized long dsDNA on the same substrate. Strong adsorption of PLL substrate resulted in poor dynamic DNA-H2A interaction. Nonetheless, short-linearized dsDNA-H2A formed stable wrapping with a "diamond ring" topology on the PLL substrate. Reversible liquid-liquid phase separation (LLPS) of the DNA-H2A aggregate was visualized by manipulating salt concentrations. Collectively, our study suggest that HS-AFM is feasible for investigating epigenetically modified DNA-histone interactions.
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Affiliation(s)
- Goro Nishide
- Division of Nano Life Science in the Graduate School of Frontier Science Initiative, WISE Program for Nano-Precision Medicine, Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Keesiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Mahmoud Shaaban Mohamed
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Akiko Kobayashi
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaharu Hazawa
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | | | - Noriyuki Kodera
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Toshio Ando
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Richard W Wong
- Division of Nano Life Science in the Graduate School of Frontier Science Initiative, WISE Program for Nano-Precision Medicine, Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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17
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The Participation of the Intrinsically Disordered Regions of the bHLH-PAS Transcription Factors in Disease Development. Int J Mol Sci 2021; 22:ijms22062868. [PMID: 33799876 PMCID: PMC8001110 DOI: 10.3390/ijms22062868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 12/14/2022] Open
Abstract
The basic helix–loop–helix/Per-ARNT-SIM (bHLH-PAS) proteins are a family of transcription factors regulating expression of a wide range of genes involved in different functions, ranging from differentiation and development control by oxygen and toxins sensing to circadian clock setting. In addition to the well-preserved DNA-binding bHLH and PAS domains, bHLH-PAS proteins contain long intrinsically disordered C-terminal regions, responsible for regulation of their activity. Our aim was to analyze the potential connection between disordered regions of the bHLH-PAS transcription factors, post-transcriptional modifications and liquid-liquid phase separation, in the context of disease-associated missense mutations. Highly flexible disordered regions, enriched in short motives which are more ordered, are responsible for a wide spectrum of interactions with transcriptional co-regulators. Based on our in silico analysis and taking into account the fact that the functions of transcription factors can be modulated by posttranslational modifications and spontaneous phase separation, we assume that the locations of missense mutations inducing disease states are clearly related to sequences directly undergoing these processes or to sequences responsible for their regulation.
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18
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Więch A, Tarczewska A, Ożyhar A, Orłowski M. Metal Ions Induce Liquid Condensate Formation by the F Domain of Aedes aegypti Ecdysteroid Receptor. New Perspectives of Nuclear Receptor Studies. Cells 2021; 10:cells10030571. [PMID: 33807814 PMCID: PMC7999165 DOI: 10.3390/cells10030571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
The superfamily of nuclear receptors (NRs), composed of ligand-activated transcription factors, is responsible for gene expression as a reaction to physiological and environmental changes. Transcriptional machinery may require phase separation to fulfil its role. Although NRs have a similar canonical structure, their C-terminal domains (F domains) are considered the least conserved and known regions. This article focuses on the peculiar molecular properties of the intrinsically disordered F domain of the ecdysteroid receptor from the Aedes aegypti mosquito (AaFEcR), the vector of the world's most devastating human diseases such as dengue and Zika. The His-Pro-rich segment of AaFEcR was recently shown to form the unique poly-proline helix II (PPII) in the presence of Cu2+. Here, using widefield microscopy of fluorescently labeled AaFEcR, Zn2+- and Cu2+-induced liquid-liquid phase separation (LLPS) was observed for the first time for the members of NRs. The perspectives of this finding on future research on the F domain are discussed, especially in relation to other NR members.
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19
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Park SK, Park S, Pentek C, Liebman SW. Tumor suppressor protein p53 expressed in yeast can remain diffuse, form a prion, or form unstable liquid-like droplets. iScience 2020; 24:102000. [PMID: 33490908 PMCID: PMC7811139 DOI: 10.1016/j.isci.2020.102000] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/20/2020] [Accepted: 12/23/2020] [Indexed: 01/08/2023] Open
Abstract
Mutations in the p53 tumor suppressor are frequent causes of cancer. Because p53 aggregates appear in some tumor cells, it has been suggested that p53 could also cause cancer by forming self-replicating protein aggregates (prions). Here, using yeast, we show that transient p53 overexpression induced the formation of p53 prion aggregates that were transmitted for >100 generations, found in lysate pellets, stained with Thioflavin T, and transmitted by cytoplasmic transfer, or transfection with lysates of cells carrying the prion or with p53 amyloid peptide. As predicted for a prion, transient interruption of p53 expression caused permanent p53 prion loss. Importantly, p53 transcription factor activity was reduced by prion formation suggesting that prion aggregation could cause cancer. p53 has also been found in liquid-like nuclear droplets in animal cell culture. In yeast, we found that liquid-like p53 foci appear in response to stress and disappear with stress removal. A published yeast model of functional nuclear human p53 tumor suppressor was used Upon transient overexpression p53 loses its transcription function and aggregates These p53 aggregates are cytoplasmic and behave like stable heritable prions Stress induces p53 to form liquid-like droplets that are unstable and not prion-like
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Affiliation(s)
- Sei-Kyoung Park
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Sangeun Park
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Christine Pentek
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Susan W Liebman
- Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
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20
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Binding and folding in transcriptional complexes. Curr Opin Struct Biol 2020; 66:156-162. [PMID: 33248428 DOI: 10.1016/j.sbi.2020.10.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/16/2020] [Accepted: 10/27/2020] [Indexed: 01/13/2023]
Abstract
Transcription factors are among the classes of proteins with the highest levels of disorder. Investigation of these regulatory proteins is uncovering not just the mechanisms that underlie gene regulation, but relationships that apply to all intrinsically disordered proteins. Recent studies confirm that binding does not necessarily induce folding but that when it does, it tends to follow induced fit mechanisms. Other work emphasises the importance of electrostatics to interactions involving intrinsically disordered proteins, and roles of intrinsic disorder in phase transitions. All these features help direct transcription factors to target sites in the genome to upregulate or downregulate transcription.
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Gupta S, Martin LM, Sinha NR, Smith KE, Sinha PR, Dailey EM, Hesemann NP, Mohan RR. Role of inhibitor of differentiation 3 gene in cellular differentiation of human corneal stromal fibroblasts. Mol Vis 2020; 26:742-756. [PMID: 33273801 PMCID: PMC7700910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 11/23/2020] [Indexed: 11/07/2022] Open
Abstract
Purpose Inhibitor of differentiation (Id) proteins are helix-loop-helix (HLH) transcriptional repressors that modulate a range of developmental and cellular processes, including cell differentiation and cell cycle mobilization. The inhibitor of differentiation 3 (Id3) gene, a member of the Id gene family, governs the expression and progression of transforming growth factor beta (TGFβ)-mediated cell differentiation. In the face of mechanical, chemical, or surgical corneal insults, corneal keratocytes differentiate into myofibroblasts for wound repair. Excessive development or persistence or both of myofibroblasts after wound repair results in corneal haze that compromises corneal clarity and visual function. The objective of this study was to investigate whether Id3 overexpression in human corneal stromal fibroblasts governs TGFβ-driven cellular differentiation and inhibits keratocyte to myofibroblast transformation. Methods Primary human corneal stromal fibroblast (h-CSF) cultures were generated from donor human corneas. Human corneal myofibroblasts (h-CMFs) were produced by growing h-CSF in the presence of TGFβ1 under serum-free conditions. The Id3 gene was cloned into a mammalian expression vector (pcDNA3 mCherry LIC cloning vector), and the nucleotide sequence of the vector constructs was confirmed with sequencing as well as through restriction enzyme analysis. The Id3 mammalian overexpression vector was introduced into h-CSFs using a lipofectamine transfection kit. The expression of Id3 in selected clones was characterized with quantitative real-time PCR (qRT-PCR), immunocytochemistry, and western blotting. Phase contrast microscopy and trypan blue exclusion assays were used to evaluate the effects of the transfer of the Id3 gene on the hCSF phenotype and viability, respectively. To analyze the inhibitory effects of the Id3 gene transfer on TGFβ-induced formation of h-CMFs, expression of the mRNA and protein of the myofibroblast marker alpha smooth muscle actin (α-SMA) was examined with qRT-PCR, western blotting, and immunocytochemistry. Student t test, analysis of variance (ANOVA), and Bonferroni adjustment for repeated measures were used for statistical analysis. Results The results indicate that Id3 overexpression does not alter the cellular phenotype or viability of h-CSFs. Overexpression of the Id3 gene in h-CSF cells grown in the presence of TGFβ1 under serum-free conditions showed a statistically significant decrease (76.3±4.3%) in α-SMA expression (p<0.01) compared to the naked-vector transfected or non-transfected h-CSF cells. Id3-transfected, naked-vector transfected, and non-transfected h-CSF cells grown in the absence of TGFβ1 showed the expected low expression of α-SMA (0-5%). Furthermore, Id3 overexpression statistically significantly decreased TGFβ-induced mRNA levels of profibrogenic genes such as fibronectin, collagen type I, and collagen type IV (1.80±0.26-, 1.70±0.35- and 1.70±0.36-fold, respectively; p<0.05) that a play role in stromal matrix modulation and corneal wound healing. Results of the protein analysis with western blotting indicated that Id3 overexpression in h-CSF cells effectively slows TGFβ-driven differentiation and formation of h-CMFs. Results for subsequent overexpression studies showed that this process occurs through the regulation of E2A, a TATA box protein. Conclusions Id3 regulates TGFβ-driven differentiation of h-CSFs and formation of h-CMFs in vitro. Targeted Id3 gene delivery has potential to treat corneal fibrosis and reestablish corneal clarity in vivo.
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Affiliation(s)
- Suneel Gupta
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- One-Health Vision Research Program, Department of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - Lynn M. Martin
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- One-Health Vision Research Program, Department of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - Nishant R. Sinha
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- One-Health Vision Research Program, Department of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - Kaitlin E. Smith
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO
| | - Prashant R. Sinha
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- One-Health Vision Research Program, Department of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - Emilee M. Dailey
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO
| | - Nathan P. Hesemann
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO
| | - Rajiv R. Mohan
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- One-Health Vision Research Program, Department of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO
- Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO
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Razin SV, Ulianov SV. Divide and Rule: Phase Separation in Eukaryotic Genome Functioning. Cells 2020; 9:cells9112480. [PMID: 33203115 PMCID: PMC7696541 DOI: 10.3390/cells9112480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
The functioning of a cell at various organizational levels is determined by the interactions between macromolecules that promote cellular organelle formation and orchestrate metabolic pathways via the control of enzymatic activities. Although highly specific and relatively stable protein-protein, protein-DNA, and protein-RNA interactions are traditionally suggested as the drivers for cellular function realization, recent advances in the discovery of weak multivalent interactions have uncovered the role of so-called macromolecule condensates. These structures, which are highly divergent in size, composition, function, and cellular localization are predominantly formed by liquid-liquid phase separation (LLPS): a physical-chemical process where an initially homogenous solution turns into two distinct phases, one of which contains the major portion of the dissolved macromolecules and the other one containing the solvent. In a living cell, LLPS drives the formation of membrane-less organelles such as the nucleolus, nuclear bodies, and viral replication factories and facilitates the assembly of complex macromolecule aggregates possessing regulatory, structural, and enzymatic functions. Here, we discuss the role of LLPS in the spatial organization of eukaryotic chromatin and regulation of gene expression in normal and pathological conditions.
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Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119017 Moscow, Russia;
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119017 Moscow, Russia
| | - Sergey V. Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119017 Moscow, Russia;
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119017 Moscow, Russia
- Correspondence: ; Tel.: +7-499-135-9787
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Tarczewska A, Wycisk K, Orłowski M, Waligórska A, Dobrucki J, Drewniak-Świtalska M, Berlicki Ł, Ożyhar A. Nuclear immunophilin FKBP39 from Drosophila melanogaster drives spontaneous liquid-liquid phase separation. Int J Biol Macromol 2020; 163:108-119. [PMID: 32615218 DOI: 10.1016/j.ijbiomac.2020.06.255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 11/27/2022]
Abstract
The FKBP39 from Drosophila melanogaster is a multifunctional regulatory immunophilin. It contains two globular domains linked by a highly charged disordered region. The N-terminal domain shows homology to the nucleoplasmin core domain, and the C-terminal domain is characteristic for the family of the FKBP immunophilin ligand binding domain. The specific partially disordered structure of the protein inspired us to investigate whether FKBP39 can drive spontaneous liquid-liquid phase separation (LLPS). Preliminary analyses using CatGranule and Pi-Pi contact predictors suggested a propensity for LLPS. Microscopy observations revealed that FKBP39 can self-concentrate to form liquid condensates. We also found that FKBP39 can lead to LLPS in the presence of RNA and peptides containing Arg-rich linear motifs derived from selected nuclear and nucleolar proteins. These heterotypic interactions have a stronger propensity for driving LLPS when compared to the interactions mediated by self-associating FKBP39 molecules. To investigate whether FKBP39 can drive LLPS in the cellular environment, we analysed it in fusion with YFP in COS-7 cells. The specific distribution and diffusion kinetics of FKBP39 examined by FRAP experiments provided evidence that immunophilin is an important driver of phase separation. The ability of FKBP39 to go into heterotypic interaction may be fundamental for ribosome subunits assembly.
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Affiliation(s)
- Aneta Tarczewska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Krzysztof Wycisk
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Marek Orłowski
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Agnieszka Waligórska
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jurek Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Magda Drewniak-Świtalska
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
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Kantidze OL, Razin SV. Weak interactions in higher-order chromatin organization. Nucleic Acids Res 2020; 48:4614-4626. [PMID: 32313950 PMCID: PMC7229822 DOI: 10.1093/nar/gkaa261] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are involved in their establishment and maintenance have been characterized. Generally, protein-protein and protein-DNA interactions underlie the spatial genome organization in eukaryotes. However, it is becoming increasingly evident that weak interactions, which exist in biological systems, also contribute to the 3D genome. Here, we provide a snapshot of our current understanding of the role of the weak interactions in the establishment and maintenance of the 3D genome organization. We discuss how weak biological forces, such as entropic forces operating in crowded solutions, electrostatic interactions of the biomolecules, liquid-liquid phase separation, DNA supercoiling, and RNA environment participate in chromosome segregation into structural and functional units and drive intranuclear functional compartmentalization.
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Affiliation(s)
- Omar L Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
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Razin SV, Gavrilov AA. The Role of Liquid–Liquid Phase Separation in the Compartmentalization of Cell Nucleus and Spatial Genome Organization. BIOCHEMISTRY (MOSCOW) 2020; 85:643-650. [DOI: 10.1134/s0006297920060012] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Simon I. Macromolecular Interactions of Disordered Proteins. Int J Mol Sci 2020; 21:ijms21020504. [PMID: 31941113 PMCID: PMC7014052 DOI: 10.3390/ijms21020504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 02/03/2023] Open
Affiliation(s)
- István Simon
- Institute of Enzymology, RCNS, Lorand Eotvos Research Network, Center of Excellence of the Hungarian Academy of Sciences, Magyar Tudósok krt. 2., H-1117 Budapest, Hungary
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