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Fagre C, Gilbert W. Beyond reader proteins: RNA binding proteins and RNA modifications in conversation to regulate gene expression. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1834. [PMID: 38444048 DOI: 10.1002/wrna.1834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/07/2024]
Abstract
Post-transcriptional mRNA modifications play diverse roles in gene expression and RNA function. In many cases, RNA modifications function by altering how cellular machinery such as RNA binding proteins (RBPs) interact with RNA substrates. For instance, N6-methyladenosine (m6A) is recognized by the well-characterized YTH domain-containing family of "reader" proteins. For other mRNA modifications, similar global readers of modification status have not been clearly defined. Rather, most interactions between RBPs and RNA modifications have a more complicated dependence on sequence context and binding modality. The current handful of studies that demonstrate modifications impacting protein binding likely represent only a fraction of the full landscape. In this review, we dissect the known instances of RNA modifications altering RBP binding, specifically m6A, N1-methyladenosine (m1A), 5-methylcytosine (m5C), pseudouridine (Ψ), and internal N7-methylguanosine. We then review the biochemical properties of these and other identified mRNA modifications including dihydrouridine (D), N4-acetylcytosine (ac4C), and 2'-O-Methylation (Nme). We focus on how these properties would be likely to impact RNA:RBP interactions, including by changes to hydrogen bond potential, base-stacking efficiency, and RNA conformational preferences. The effects of RNA modifications on secondary structure have been well-studied, and we briefly discuss how structural effects imparted by modifications can lead to protein binding changes. Finally, we discuss strategies for uncovering as-yet-to-be identified modification-sensitive RBP:RNA Interactions. Coordinating future efforts to intersect the epitranscriptome and the RNA-protein interactome will illuminate the rules governing RNA modification recognition and the mechanisms responsible for the biological consequences of mRNA modification. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Christian Fagre
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Wendy Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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Wu W, Xu J, Gao D, Xie Z, Chen W, Li W, Yuan Q, Duan L, Zhang Y, Yang X, Chen Y, Dong Z, Liu K, Jiang Y. TOPK promotes the growth of esophageal cancer in vitro and in vivo by enhancing YB1/eEF1A1 signal pathway. Cell Death Dis 2023; 14:364. [PMID: 37328464 PMCID: PMC10276051 DOI: 10.1038/s41419-023-05883-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/30/2023] [Accepted: 06/08/2023] [Indexed: 06/18/2023]
Abstract
T-LAK-originated protein kinase (TOPK), a dual specificity serine/threonine kinase, is up-regulated and related to poor prognosis in many types of cancers. Y-box binding protein 1 (YB1) is a DNA/RNA binding protein and serves important roles in multiple cellular processes. Here, we reported that TOPK and YB1 were both highly expressed in esophageal cancer (EC) and correlated with poor prognosis. TOPK knockout effectively suppressed EC cell proliferation and these effects were reversible by rescuing YB1 expression. Notably, TOPK phosphorylated YB1 at Thr 89 (T89) and Ser 209 (S209) amino acid residues, then the phosphorylated YB1 bound with the promoter of the eukaryotic translation elongation factor 1 alpha 1 (eEF1A1) to activate its transcription. Consequently, the AKT/mTOR signal pathway was activated by up-regulated eEF1A1 protein. Importantly, TOPK inhibitor HI-TOPK-032 suppressed the EC cell proliferation and tumor growth by TOPK/YB1/eEF1A1 signal pathway in vitro and in vivo. Taken together, our study reveals that TOPK and YB1 are essential for the growth of EC, and TOPK inhibitors may be applied to retard cell proliferation in EC. This study highlights the promising therapeutic potential of TOPK as a target for treatment of EC.
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Affiliation(s)
- Wenjie Wu
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Jialuo Xu
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Dan Gao
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhenliang Xie
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Wenjing Chen
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Wenjing Li
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Qiang Yuan
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Lina Duan
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Yuhan Zhang
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Xiaoxiao Yang
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Yingying Chen
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Ziming Dong
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Kangdong Liu
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- Research Center of Basic Medical Science, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, Henan, 450052, China.
- Cancer Chemoprevention International Collaboration Laboratory, Zhengzhou, Henan, 450000, China.
| | - Yanan Jiang
- Pathophysiology Department, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Research Center of Basic Medical Science, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, Henan, 450052, China.
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Cellular RNA Targets of Cold Shock Proteins CspC and CspE and Their Importance for Serum Resistance in Septicemic Escherichia coli. mSystems 2022; 7:e0008622. [PMID: 35695420 PMCID: PMC9426608 DOI: 10.1128/msystems.00086-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The RNA chaperones, cold shock proteins CspC and CspE, are important in stress response and adaptation. We studied their role in the pathogenesis of a virulent Escherichia coli, representative of extraintestinal pathogenic E. coli (ExPEC) which are serum resistant and septicemic. We performed a global analysis to identify transcripts that interact with these cold shock proteins (CSPs), focusing on virulence-related genes. We used CLIP-seq, which combines UV cross-linking, immunoprecipitation and RNA sequencing. A large number of transcripts bound to the CSPs were identified, and many bind both CspC and CspE. Many transcripts were of genes involved in protein synthesis, transcription and energy metabolism. In addition, there were virulence-related genes, (i.e., fur and ryhB), essential for iron homeostasis. The CLIP-seq results were validated on two transcripts, clpX and tdcA, reported as virulence-associated. Deletion of either CspC or CspE significantly decreased their transcript levels and in a double deletion mutant cspC/cspE, the transcript stability of tdcA and clpX was reduced by 32-fold and 10-fold, respectively. We showed that these two genes are important for virulence, as deleting either of them resulted in loss of serum resistance, a requirement for sepsis. As several virulence-related transcripts interact with CspC or CspE, we determined the importance of these proteins for growth in serum and showed that deletion of either gene significantly reduced serum survival. This phenotype could be partially complemented by cspE and fully complemented by cspC. These results indicate that the two RNA chaperones are essential for virulence, and that CspC particularly critical. IMPORTANCE Virulent Escherichia coli strains that cause infections outside the intestinal tract—extraintestinal pathogenic E. coli (ExPEC)—constitute a major clinical problem worldwide. They are involved in several distinct conditions, including urinary tract infections, newborn meningitis, and sepsis. Due to increasing antibiotic resistance, these strains are a main factor in hospital and community-acquired infections. Because many strains, which do not cross-react immunologically are involved, developing a simple vaccine is not possible. Therefore, it is essential to understand the pathogenesis of these bacteria to identify potential targets for developing drugs or vaccines. One of the least investigated systems involves RNA binding proteins, important for stability of transcripts and global gene regulation. Two such proteins are CspC and CspE (“cold shock proteins”), RNA chaperones involved in stress adaptation. Here we performed a global analysis to identify the transcripts which are affected by these two chaperones, with focus on virulence-associated transcripts.
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Kretov DA. Role of Y-Box Binding Proteins in Ontogenesis. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S71-S74. [PMID: 35501987 DOI: 10.1134/s0006297922140061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding proteins (YB proteins) are multifunctional DNA/RNA-binding proteins capable of regulating gene expression at multiple levels. At present, the most studied function of these proteins is the regulation of protein synthesis. Special attention in this review has been paid to the role of YB proteins in the control of mRNA translation and stability at the earliest stages of organism formation, from fertilization to gastrulation. Furthermore, the functions of YB proteins in the formation of germ cells, in which they accumulate in large amounts, are summarized. The review then discusses the contribution of YB proteins to the regulation of gene expression during the differentiation of various types of somatic cells. Finally, future directions in the study of YB proteins and their role in ontogenesis are considered.
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Affiliation(s)
- Dmitry A Kretov
- Department of Biochemistry, School of Medicine, Boston University, Boston, USA, 02218.
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McCauley C, Anang V, Cole B, Simmons GE. Potential Links between YB-1 and Fatty Acid Synthesis in Clear Cell Renal Carcinoma. ACTA ACUST UNITED AC 2020; 8. [PMID: 33778158 DOI: 10.18103/mra.v8i10.2273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
According to the National Institutes of Health, clear cell renal cell carcinoma (ccRCC) is the most common type of Renal Cell Carcinoma (RCC), making up approximately 75% of total renal carcinoma cases. Clear cell Renal Cell Carcinoma is characterized by a significant accumulation of lipids in the cytoplasm, which allows light from microscopes to pass through giving them a "clear" phenotype. Many of these lipids are in the form of fatty acids, both free and incorporated into lipid droplets. RCC is typically associated with a poor prognosis due to the lack of specific symptoms. Some symptoms include blood in urine, fever, lump on the side, weight loss, fatigue, to name a few; all of which can be associated with non-specific, non-cancerous, health conditions that contribute to difficult diagnosis. Treatment of RCC has typically been centered around radical nephrectomy as the standard of care, but due to the potentially small size of lesions and the possibility of causing surgically induced chronic kidney disease, treatments have shifted to more cautious, less invasive approaches. These approaches include active surveillance, nephron-sparing surgery, and other minimally invasive techniques like cryotherapy and renal ablation. Although these techniques have had the desired effect of reducing the number of surgeries, there is still considerable potential for renal impairment and the chance that tumors can grow out of control without surgery. With the difficulty that surrounds the treatment of ccRCC and its considerably high mortality rate amongst urological cancers, it is important to look for novel approaches to improve patient outcomes. This review looks at available literature and our data that suggests the lipogenic enzyme stearoyl-CoA desaturase may be more beneficial to patient survival than once thought. As our understanding of the importance of lipids in cell metabolism and longevity matures, it is important to present new perspectives that present a new understanding of ccRCC and the role of lipids in survival mechanisms engaged by transformed cells during cancer progression. In this review, we provide evidence that pharmacological inhibition of lipid desaturation in renal cancer patients is not without risk, and that the presence of unsaturated fatty acids may be a beneficial factor in patient outcomes. Although more direct experimental evidence is needed to make definitive conclusions, it is clear that the work reviewed herein should challenge our current understanding of cancer biology and may inform novel approaches to the diagnosis and treatment of ccRCC.
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Affiliation(s)
- Carter McCauley
- University of Minnesota Medical School, Duluth, MN, MN 55812, USA
| | - Vasthy Anang
- Clinical and Translational Science Institute PREP Program, University of Minnesota Medical School, Minneapolis, MN, MN 55812, USA
| | - Breanna Cole
- Department of Biology, The College of St. Scholastica, Duluth, MN, 55811, USA
| | - Glenn E Simmons
- University of Minnesota Medical School, Duluth, MN, MN 55812, USA.,Clinical and Translational Science Institute PREP Program, University of Minnesota Medical School, Minneapolis, MN, MN 55812, USA.,Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, MN 55812, USA.,Carcinogenesis and Chemoprevention program, Masonic Cancer Center, Minneapolis, MN 55455, USA
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Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Mooijman D, Benes V, Savitski MM, Gebauer F, Hennig J. Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras. Cell Rep 2020; 32:107930. [PMID: 32697992 PMCID: PMC7383231 DOI: 10.1016/j.celrep.2020.107930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) commonly feature multiple RNA-binding domains (RBDs), which provide these proteins with a modular architecture. Accumulating evidence supports that RBP architectural modularity and adaptability define the specificity of their interactions with RNA. However, how multiple RBDs recognize their cognate single-stranded RNA (ssRNA) sequences in concert remains poorly understood. Here, we use Upstream of N-Ras (Unr) as a model system to address this question. Although reported to contain five ssRNA-binding cold-shock domains (CSDs), we demonstrate that Unr includes an additional four CSDs that do not bind RNA (pseudo-RBDs) but are involved in mediating RNA tertiary structure specificity by reducing the conformational heterogeneity of Unr. Disrupting the interactions between canonical and non-canonical CSDs impacts RNA binding, Unr-mediated translation regulation, and the Unr-dependent RNA interactome. Taken together, our studies reveal a new paradigm in protein-RNA recognition, where interactions between RBDs and pseudo-RBDs select RNA tertiary structures, influence RNP assembly, and define target specificity.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | | | - Pawel Masiewicz
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jan Provaznik
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lara Jayne Sweetapple
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Laura Villacorta
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Dylan Mooijman
- Developmental Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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Y-Box Binding Proteins in mRNP Assembly, Translation, and Stability Control. Biomolecules 2020; 10:biom10040591. [PMID: 32290447 PMCID: PMC7226217 DOI: 10.3390/biom10040591] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
Y-box binding proteins (YB proteins) are DNA/RNA-binding proteins belonging to a large family of proteins with the cold shock domain. Functionally, these proteins are known to be the most diverse, although the literature hardly offers any molecular mechanisms governing their activities in the cell, tissue, or the whole organism. This review describes the involvement of YB proteins in RNA-dependent processes, such as mRNA packaging into mRNPs, mRNA translation, and mRNA stabilization. In addition, recent data on the structural peculiarities of YB proteins underlying their interactions with nucleic acids are discussed.
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Corley M, Burns MC, Yeo GW. How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms. Mol Cell 2020; 78:9-29. [PMID: 32243832 PMCID: PMC7202378 DOI: 10.1016/j.molcel.2020.03.011] [Citation(s) in RCA: 354] [Impact Index Per Article: 88.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/13/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
RNA-binding proteins (RBPs) comprise a large class of over 2,000 proteins that interact with transcripts in all manner of RNA-driven processes. The structures and mechanisms that RBPs use to bind and regulate RNA are incredibly diverse. In this review, we take a look at the components of protein-RNA interaction, from the molecular level to multi-component interaction. We first summarize what is known about protein-RNA molecular interactions based on analyses of solved structures. We additionally describe software currently available for predicting protein-RNA interaction and other resources useful for the study of RBPs. We then review the structure and function of seventeen known RNA-binding domains and analyze the hydrogen bonds adopted by protein-RNA structures on a domain-by-domain basis. We conclude with a summary of the higher-level mechanisms that regulate protein-RNA interactions.
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Affiliation(s)
- Meredith Corley
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Margaret C Burns
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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Budkina KS, Zlobin NE, Kononova SV, Ovchinnikov LP, Babakov AV. Cold Shock Domain Proteins: Structure and Interaction with Nucleic Acids. BIOCHEMISTRY (MOSCOW) 2020; 85:S1-S19. [DOI: 10.1134/s0006297920140011] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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10
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Wang S, He F, Li Z, Hu Y, Huangfu N, Chen X. YB1 protects cardiac myocytes against H2O2‑induced injury via suppression of PIAS3 mRNA and phosphorylation of STAT3. Mol Med Rep 2019; 19:4579-4588. [PMID: 30942400 PMCID: PMC6522804 DOI: 10.3892/mmr.2019.10119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/06/2019] [Indexed: 12/11/2022] Open
Abstract
Oxidative stress serves important roles in cardiac injury during the process of ischemia/reperfusion (I/R). Y-box protein 1 (YB1), a member of the highly conserved Y-box protein family, is closely associated with inflammation and stress responses by regulating gene transcription, RNA splicing and mRNA translation. However, the roles of YB1 in oxidative stress-induced myocardial-I/R (M-I/R) injury are unknown. The aim of the present study was to examine the effects of YB1 on H2O2-induced cardiomyocyte injury and its underlying mechanism. The results demonstrated that YB1 expression was upregulated during H2O2-induced myocardial injury. YB1 knockdown through transfection of small interfering RNA significantly aggravated cardiac cell apoptosis. Furthermore, YB1 knockdown significantly reversed the H2O2-mediated increase in phosphorylated signal transducer and activator of transcription (STAT)3, but did not affect the phosphorylation of P38, extracellular signal-regulated kinases 1/2, c-Jun N-terminal kinases, P65, Janus kinase 1 and 2 or STAT1. Moreover, protein co-immunoprecipitation and RNA-binding protein immunoprecipitation assays revealed that YB1 interacted with protein inhibitor of activated STAT 3 (PIAS3) mRNA but not its translated protein. YB1 overexpression may have promoted PIAS3 mRNA decay, decreasing PIAS3 protein levels, and therefore increased the levels of phosphorylated STAT3. Finally, YB1 knockdown, mediated by a lentivirus carrying YB1 targeted short hairpin RNA, significantly decreased left ventricle percentage fractional shortening and ejection fraction values, while increasing the infarct sizes in a rat model of M-I/R injury. These results demonstrated for the first time (to the best of our knowledge) that YB1 may protect cardiac myocytes against H2O2 or M-I/R-induced injury by binding to PIAS3 mRNA and resulting in the phosphorylation of STAT3.
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Affiliation(s)
- Shiqi Wang
- Department of Cardiology, The Affiliated Hospital Ningbo No. 1 Hospital, Zhejiang University, Ningbo, Zhejiang 315000, P.R. China
| | - Fuwei He
- Department of Cardiology, The Affiliated Hospital Ningbo No. 1 Hospital, Zhejiang University, Ningbo, Zhejiang 315000, P.R. China
| | - Zhenwei Li
- Department of Cardiology, The Affiliated Hospital Ningbo No. 1 Hospital, Zhejiang University, Ningbo, Zhejiang 315000, P.R. China
| | - Yewen Hu
- Department of Cardiology, The Affiliated Hospital Ningbo No. 1 Hospital, Zhejiang University, Ningbo, Zhejiang 315000, P.R. China
| | - Ning Huangfu
- Department of Cardiology, The Affiliated Hospital Ningbo No. 1 Hospital, Zhejiang University, Ningbo, Zhejiang 315000, P.R. China
| | - Xiaomin Chen
- Department of Cardiology, The Affiliated Hospital Ningbo No. 1 Hospital, Zhejiang University, Ningbo, Zhejiang 315000, P.R. China
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Rambout X, Dequiedt F, Maquat LE. Beyond Transcription: Roles of Transcription Factors in Pre-mRNA Splicing. Chem Rev 2017; 118:4339-4364. [PMID: 29251915 DOI: 10.1021/acs.chemrev.7b00470] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Whereas individual steps of protein-coding gene expression in eukaryotes can be studied in isolation in vitro, it has become clear that these steps are intimately connected within cells. Connections not only ensure quality control but also fine-tune the gene expression process, which must adapt to environmental changes while remaining robust. In this review, we systematically present proven and potential mechanisms by which sequence-specific DNA-binding transcription factors can alter gene expression beyond transcription initiation and regulate pre-mRNA splicing, and thereby mRNA isoform production, by (i) influencing transcription elongation rates, (ii) binding to pre-mRNA to recruit splicing factors, and/or (iii) blocking the association of splicing factors with pre-mRNA. We propose various mechanistic models throughout the review, in some cases without explicit supportive evidence, in hopes of providing fertile ground for future studies.
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12
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Di Liegro CM, Schiera G, Di Liegro I. Extracellular Vesicle-Associated RNA as a Carrier of Epigenetic Information. Genes (Basel) 2017; 8:genes8100240. [PMID: 28937658 PMCID: PMC5664090 DOI: 10.3390/genes8100240] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/08/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022] Open
Abstract
Post-transcriptional regulation of messenger RNA (mRNA) metabolism and subcellular localization is of the utmost importance both during development and in cell differentiation. Besides carrying genetic information, mRNAs contain cis-acting signals (zip codes), usually present in their 5'- and 3'-untranslated regions (UTRs). By binding to these signals, trans-acting factors, such as RNA-binding proteins (RBPs), and/or non-coding RNAs (ncRNAs), control mRNA localization, translation and stability. RBPs can also form complexes with non-coding RNAs of different sizes. The release of extracellular vesicles (EVs) is a conserved process that allows both normal and cancer cells to horizontally transfer molecules, and hence properties, to neighboring cells. By interacting with proteins that are specifically sorted to EVs, mRNAs as well as ncRNAs can be transferred from cell to cell. In this review, we discuss the mechanisms underlying the sorting to EVs of different classes of molecules, as well as the role of extracellular RNAs and the associated proteins in altering gene expression in the recipient cells. Importantly, if, on the one hand, RBPs play a critical role in transferring RNAs through EVs, RNA itself could, on the other hand, function as a carrier to transfer proteins (i.e., chromatin modifiers, and transcription factors) that, once transferred, can alter the cell's epigenome.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo (UNIPA), I-90128 Palermo, Italy.
| | - Gabriella Schiera
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo (UNIPA), I-90128 Palermo, Italy.
| | - Italia Di Liegro
- Department of Experimental Biomedicine and Clinical Neurosciences (BIONEC), University of Palermo,I-90127 Palermo,Italy.
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Zlobin N, Evlakov K, Alekseev Y, Blagodatskikh K, Babakov A, Taranov V. High DNA melting activity of extremophyte Eutrema salsugineum cold shock domain proteins EsCSDP1 and EsCSDP3. Biochem Biophys Rep 2016; 5:502-508. [PMID: 28955858 PMCID: PMC5600361 DOI: 10.1016/j.bbrep.2016.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/31/2015] [Accepted: 02/04/2016] [Indexed: 10/27/2022] Open
Abstract
Plant cold shock domain proteins (CSDP) participate in maintenance of plant stress tolerance and in regulating their development. In the present paper we show that two out of three extremophyte plant Eutrema salsugineum proteins EsCSDP1-3, namely EsCSDP1 and EsCSDP3, possess high DNA-melting activity. DNA-melting activity of proteins was evaluated using molecular beacon assay in two ways: by measuring Tm parameter (the temperature at which half of the DNA beacon molecules is fully melted) and the beacon fluorescence at 4 °C. As the ratio protein/beacon was increased, a decrease in Tm was observed. Besides DNA-melting activity of full proteins, activity was measured for three isolated cold shock domains EsCSD1-3, C-terminal domain of EsCSDP1 (EsZnF1), as well as a mixture of EsCSD1 and EsZnF1. The Tm reduction efficiency of proteins formed the following sequence: EsCSDP3≈EsCSDP1>(EsCSD1+EsZnF1)>EsZnF1>EsCSDP2. Only full proteins EsCSDP3 and EsCSDP1 demonstrated DNA-melting activity at 4 °C. The presented experimental data indicate that i: interaction of EsCSDP1-3 with beacon single-stranded region is obligatory for efficient melting; ii: cold shock domain and C-terminal domain with zinc finger motifs should be present in one protein molecule to have high melting activity.
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Affiliation(s)
- Nikolai Zlobin
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Russia
| | - Konstantin Evlakov
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Russia
| | - Yakov Alekseev
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Russia
| | - Konstantin Blagodatskikh
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Russia
| | - Aleksei Babakov
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Russia
| | - Vasiliy Taranov
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Russia
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