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Yang Y, Tan YQ, Wang X, Li JJ, Du BY, Zhu M, Wang P, Wang YF. OPEN STOMATA1 phosphorylates CYCLIC NUCLEOTIDE-GATED CHANNELs to trigger Ca2+ signaling for ABA-induced stomatal closure in Arabidopsis. Plant Cell 2024:koae073. [PMID: 38442317 DOI: 10.1093/plcell/koae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 02/02/2024] [Accepted: 02/09/2024] [Indexed: 03/07/2024]
Abstract
Multiple cyclic nucleotide-gated channels (CNGCs) are abscisic acid (ABA)-activated Ca2+ channels in Arabidopsis (Arabidopsis thaliana) guard cells. In particular, CNGC5, CNGC6, CNGC9, and CNGC12 are essential for ABA-specific cytosolic Ca2+ signaling and stomatal movements. However, the mechanisms underlying ABA-mediated regulation of CNGCs and Ca2+ signaling are still unknown. In this study, we identified the Ca2+-independent protein kinase OPEN STOMATA1 (OST1) as a CNGC activator in Arabidopsis. OST1-targeted phosphorylation sites were identified in CNGC5, CNGC6, CNGC9 and CNGC12. These CNGCs were strongly inhibited by Ser-to-Ala mutations and fully activated by Ser-to-Asp mutations at the OST1-targeted sites. The overexpression of individual inactive CNGCs (iCNGCs) under the UBIQUITIN10 promoter in wild-type Arabidopsis conferred a strong dominant-negative-like ABA-insensitive stomatal closure phenotype. In contrast, expressing active CNGCs (aCNGCs) under their respective native promoters in the cngc5-1 cngc6-2 cngc9-1 cngc12-1 quadruple mutant fully restored ABA-activated cytosolic Ca2+ oscillations and Ca2+ currents in guard cells, and rescued the ABA-insensitive stomatal movement mutant phenotypes. Thus, we uncovered that ABA elicits cytosolic Ca2+ signaling via an OST1-CNGC module, in which OST1 functions as a convergence point of the Ca2+-dependent and -independent pathways in Arabidopsis guard cells.
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Affiliation(s)
- Yang Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Yan-Qiu Tan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xinyong Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Jia-Jun Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Bo-Ya Du
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Meijun Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Pengcheng Wang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yong-Fei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
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Zhan X, Liu Y, Jannu AJ, Huang S, Ye B, Wei W, Pandya PH, Ye X, Pollok KE, Renbarger JL, Huang K, Zhang J. Identify potential driver genes for PAX-FOXO1 fusion-negative rhabdomyosarcoma through frequent gene co-expression network mining. Front Oncol 2023; 13:1080989. [PMID: 36793601 PMCID: PMC9924292 DOI: 10.3389/fonc.2023.1080989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023] Open
Abstract
Background Rhabdomyosarcoma (RMS) is a soft tissue sarcoma usually originated from skeletal muscle. Currently, RMS classification based on PAX-FOXO1 fusion is widely adopted. However, compared to relatively clear understanding of the tumorigenesis in the fusion-positive RMS, little is known for that in fusion-negative RMS (FN-RMS). Methods We explored the molecular mechanisms and the driver genes of FN-RMS through frequent gene co-expression network mining (fGCN), differential copy number (CN) and differential expression analyses on multiple RMS transcriptomic datasets. Results We obtained 50 fGCN modules, among which five are differentially expressed between different fusion status. A closer look showed 23% of Module 2 genes are concentrated on several cytobands of chromosome 8. Upstream regulators such as MYC, YAP1, TWIST1 were identified for the fGCN modules. Using in a separate dataset we confirmed that, comparing to FP-RMS, 59 Module 2 genes show consistent CN amplification and mRNA overexpression, among which 28 are on the identified chr8 cytobands. Such CN amplification and nearby MYC (also resides on one of the above cytobands) and other upstream regulators (YAP1, TWIST1) may work together to drive FN-RMS tumorigenesis and progression. Up to 43.1% downstream targets of Yap1 and 45.8% of the targets of Myc are differentially expressed in FN-RMS vs. normal comparisons, which also confirmed the driving force of these regulators. Discussion We discovered that copy number amplification of specific cytobands on chr8 and the upstream regulators MYC, YAP1 and TWIST1 work together to affect the downstream gene co-expression and promote FN-RMS tumorigenesis and progression. Our findings provide new insights for FN-RMS tumorigenesis and offer promising targets for precision therapy. Experimental investigation about the functions of identified potential drivers in FN-RMS are in progress.
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Affiliation(s)
- Xiaohui Zhan
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yusong Liu
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Asha Jacob Jannu
- Department of Biostatistics and Health Data Science, Indiana University, School of Medicine, Indianapolis, IN, United States
| | | | - Bo Ye
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Wei Wei
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Pankita H Pandya
- Department of Pediatrics, Indiana University, School of Medicine, Indianapolis, IN, United States
| | - Xiufen Ye
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Karen E Pollok
- Department of Pediatrics, Indiana University, School of Medicine, Indianapolis, IN, United States
| | - Jamie L Renbarger
- Department of Pediatrics, Indiana University, School of Medicine, Indianapolis, IN, United States
| | - Kun Huang
- Department of Biostatistics and Health Data Science, Indiana University, School of Medicine, Indianapolis, IN, United States
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, IN, United States
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Liu Y, Jones C, Coward K. An investigation of mechanisms underlying mouse blastocyst hatching: a ribonucleic acid sequencing study. F S Sci 2022; 3:35-48. [PMID: 35559994 DOI: 10.1016/j.xfss.2021.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To investigate the regulatory mechanisms and signaling molecules underlying hatching in mouse embryos. DESIGN Experimental laboratory study using a mouse embryo model. SETTING University-based basic scientific research laboratory. ANIMALS A total of 40 B6C3F1 × B6D2F1 mouse embryos were used in this study. INTERVENTION(S) Frozen/thawed mouse embryos, at the 8-cell stage, were cultured in vitro for 2 days. The resulting hatching and prehatching blastocysts were then used for complementary deoxyribonucleic acid (cDNA) library preparation and ribonucleic acid (RNA) sequencing analysis (n = 8 for each group). Differentially expressed genes were then used for downstream functional analysis. In addition, a list of genes related to developmental progression in humans was used to identify genes that were potentially related to the hatching of human embryos. MAIN OUTCOME MEASURE(S) Differentially expressed genes, enriched Gene Ontology terms and canonical pathways, clustered gene networks, activated upstream regulators, and common genes between a gene list of hatching-related genes in mice and a gene list associated with developmental progression in humans. RESULT(S) A total 275 differentially expressed genes were identified between hatching and prehatching blastocysts: 230 up-regulated and 45 down-regulated genes. Functional enrichment analysis suggested that blastocyst hatching in vitro is an adenosine triphosphate (ATP)-dependent process that involves protein biosynthesis and organization of the cytoskeleton. Furthermore, by regulating cell motility, the RhoA signaling pathway (including Arpc2, Cfl1, Gsn, Pfn1, Tpi1, Grb2, Tmsb10, Enah, and Rnd3 genes) may be a crucial signaling pathway during hatching. We also identified a cluster of genes (Krt8, Krt7, Cldn4, and Aqp3) that exerted functional roles in cell-cell junctions and water homeostasis during hatching. Moreover, some growth factors (angiotensinogen and fibroblast growth factor 2) and endocrine factors (estrogen receptor and prolactin) were predicted to be involved in the regulation of embryo hatching. In addition, we identified 81 potential genes that are potentially involved in the hatching process in human embryos. CONCLUSION(S) Our analysis identified potential genes and molecular regulatory pathways involved in the blastocyst hatching process in mice; we also identified genes that may potentially regulate hatching in human embryos. Our findings enhance our knowledge of embryo development and provide useful information for further exploring the mechanisms underlying embryo hatching.
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Affiliation(s)
- Yaqiong Liu
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Celine Jones
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Kevin Coward
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, Headington, Oxford, United Kingdom.
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Gozutok O, Helmold BR, Ozdinler PH. Mutations and Protein Interaction Landscape Reveal Key Cellular Events Perturbed in Upper Motor Neurons with HSP and PLS. Brain Sci 2021; 11:578. [PMID: 33947096 DOI: 10.3390/brainsci11050578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 01/06/2023] Open
Abstract
Hereditary spastic paraplegia (HSP) and primary lateral sclerosis (PLS) are rare motor neuron diseases, which affect mostly the upper motor neurons (UMNs) in patients. The UMNs display early vulnerability and progressive degeneration, while other cortical neurons mostly remain functional. Identification of numerous mutations either directly linked or associated with HSP and PLS begins to reveal the genetic component of UMN diseases. Since each of these mutations are identified on genes that code for a protein, and because cellular functions mostly depend on protein-protein interactions, we hypothesized that the mutations detected in patients and the alterations in protein interaction domains would hold the key to unravel the underlying causes of their vulnerability. In an effort to bring a mechanistic insight, we utilized computational analyses to identify interaction partners of proteins and developed the protein-protein interaction landscape with respect to HSP and PLS. Protein-protein interaction domains, upstream regulators and canonical pathways begin to highlight key cellular events. Here we report that proteins involved in maintaining lipid homeostasis and cytoarchitectural dynamics and their interactions are of great importance for UMN health and stability. Their perturbation may result in neuronal vulnerability, and thus maintaining their balance could offer therapeutic interventions.
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Padariya M, Sznarkowska A, Kote S, Gómez-Herranz M, Mikac S, Pilch M, Alfaro J, Fahraeus R, Hupp T, Kalathiya U. Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes. Biomolecules 2021; 11:622. [PMID: 33922087 DOI: 10.3390/biom11050622] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Interferon (IFN)-related DNA damage resistant signature (IRDS) genes are a subgroup of interferon-stimulated genes (ISGs) found upregulated in different cancer types, which promotes resistance to DNA damaging chemotherapy and radiotherapy. Along with briefly discussing IFNs and signalling in this review, we highlighted how different IRDS genes are affected by viruses. On the contrary, different strategies adopted to suppress a set of IRDS genes (STAT1, IRF7, OAS family, and BST2) to induce (chemo- and radiotherapy) sensitivity were deliberated. Significant biological pathways that comprise these genes were classified, along with their frequently associated genes (IFIT1/3, IFITM1, IRF7, ISG15, MX1/2 and OAS1/3/L). Major upstream regulators from the IRDS genes were identified, and different IFN types regulating these genes were outlined. Functional interfaces of IRDS proteins with DNA/RNA/ATP/GTP/NADP biomolecules featured a well-defined pharmacophore model for STAT1/IRF7-dsDNA and OAS1/OAS3/IFIH1-dsRNA complexes, as well as for the genes binding to GDP or NADP+. The Lys amino acid was found commonly interacting with the ATP phosphate group from OAS1/EIF2AK2/IFIH1 genes. Considering the premise that targeting IRDS genes mediated resistance offers an efficient strategy to resensitize tumour cells and enhances the outcome of anti-cancer treatment, this review can add some novel insights to the field.
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Mihara Y, Maekawa R, Sato S, Shimizu N, Doi-Tanaka Y, Takagi H, Shirafuta Y, Shinagawa M, Tamura I, Taketani T, Tamura H, Abe T, Asai Y, Sugino N. An Integrated Genomic Approach Identifies HOXC8 as an Upstream Regulator in Ovarian Endometrioma. J Clin Endocrinol Metab 2020; 105:5900720. [PMID: 32877504 DOI: 10.1210/clinem/dgaa618] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
PURPOSE To identify the upstream regulators (URs) involved in the onset and pathogenesis of ovarian endometrioma. METHODS Recently, a method called Significance-based Modules Integrating the Transcriptome and Epigenome (SMITE) that uses transcriptome data in combination with publicly available data for identifying URs of cellular processes has been developed. Here, we used SMITE with transcriptome data from ovarian endometrioma stromal cells (ovESCs) and eutopic endometrium stromal cells (euESCs) in combination with publicly available gene regulatory network data. To confirm the URs identified by SMITE, we developed a Boolean network simulation to see if correcting aberrant expressions of the identified genes could restore the entire gene expression profile of ovESCs to a profile similar to that of euESCs. We then established euESCs overexpressing the identified gene and characterized them by cell function assays and transcriptome analysis. RESULTS SMITE identified 12 potential URs in ovarian endometrioma that were confirmed by the Boolean simulation. One of the URs, HOXC8, was confirmed to be overexpressed in ovESCs. HOXC8 overexpression significantly enhanced cell proliferation, migration, adhesion, and fibrotic activities, and altered expression statuses of the genes involved in transforming growth factor (TGF)-β signaling. HOXC8 overexpression also increased the expression levels of phosphorylated SMAD2/SMAD3. The increased adhesion and fibrosis activities by HOXC8 were significantly inhibited by E-616452, a selective inhibitor of TGF-β receptor type I kinases. MAIN CONCLUSIONS Integrated genomic approaches identified HOXC8 as an UR in ovarian endometrioma. The pathological features of ovarian endometrioma including cell proliferation, adhesion, and fibrosis were induced by HOXC8 and its subsequent activation of TGF-β signaling.
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Affiliation(s)
- Yumiko Mihara
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Natsuko Shimizu
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yumiko Doi-Tanaka
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Haruka Takagi
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yuichiro Shirafuta
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Masahiro Shinagawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Toshiaki Taketani
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Hiroshi Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Takeshi Abe
- Department of Systems Bioinformatics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yoshiyuki Asai
- Department of Systems Bioinformatics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
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Abstract
The NAC transcription factor (TF) is one of the largest families of TFs in plants and plays an important role in plant growth, development, and response to environmental stress. The structural and functional characteristics of NAC TFs have been uncovered in the past years, including sequence binding features of the DNA-binding domain located in the N-terminus and dynamic interplay between the domain located at the C-terminus and other proteins. Studies on NAC TF are increasing in number; these studies distinctly contribute to our understanding of the regulatory networks of NAC-mediated complex signaling and transcriptional reprogramming. Previous studies have indicated that NAC TFs are key regulators of the plant stress response. However, these studies have been for six years so far and mainly focused on drought and salt stress. There are relatively few reports about NAC TFs in plant cold signal pathway and no related reviews have been published. In this review article, we summarize the structural features of NAC TFs, the target genes, upstream regulators and interaction proteins of stress-responsive NAC TFs, and the roles NAC TFs play in plant cold stress signal pathway.
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Affiliation(s)
- Pengfei Diao
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an, Shandong, China
| | - Chong Chen
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an, Shandong, China
- Nana Ma State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, Shandong, 271018, China
| | - Yuzhen Zhang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an, Shandong, China
| | - Qingwei Meng
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an, Shandong, China
| | - Wei Lv
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an, Shandong, China
- CONTACT Wei Lv
| | - Nana Ma
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an, Shandong, China
- Nana Ma State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, Shandong, 271018, China
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Hur YS, Kim J, Kim S, Son O, Kim WY, Kim GT, Ohme-Takagi M, Cheon CI. Identification of TCP13 as an Upstream Regulator of ATHB12 during Leaf Development. Genes (Basel) 2019; 10:E644. [PMID: 31455029 DOI: 10.3390/genes10090644] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 01/24/2023] Open
Abstract
Leaves grow by distinct phases controlled by gene regulatory networks including many transcription factors. Arabidopsis thaliana homeobox 12 (ATHB12) promotes leaf growth especially during the cell expansion phase. In this study, we identify TCP13, a member of the TCP transcription factor family, as an upstream inhibitor of ATHB12. Yeast one-hybrid screening using a 1.2-kb upstream region of ATHB12 resulted in the isolation of TCP13 as well as other transcription factors. Transgenic plants constitutively expressing TCP13 displays a significant reduction in leaf cell size especially during the cell expansion period, while repression of TCP13 and its paralogs (TCP5 and TCP17) result in enlarged leaf cells, indicating that TCP13 and its paralogs inhibit leaf development, mainly at the cell expansion phase. Its expression pattern during leaf expansion phase is opposite to ATHB12 expression. Consistently, the expression of ATHB12 and its downstream genes decreases when TCP13 was overexpressed, and increases when the expression of TCP13 and its paralogs is repressed. In chromatin immunoprecipitation assays using TCP13-GFP plants, a fragment of the ATHB12 upstream region that contains the consensus sequence for TCP binding is strongly enriched. Taken together, these findings indicate that TCP13 and its paralogs inhibit leaf growth by repressing ATHB12 expression.
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