1
|
Kudaibergenova Z, Pany S, Placheril E, Jeremic AM. UTRs and Ago-2/miR-335 Complex Restricts Amylin Translation in Insulinoma and Human Pancreatic β-Cells. Int J Mol Sci 2024; 25:9614. [PMID: 39273561 PMCID: PMC11394793 DOI: 10.3390/ijms25179614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Amylin promoter and transcriptional factors are well-established, inducible factors in the production of the main amyloidogenic pancreatic hormone, human islet amyloid peptide (hIAPP) or amylin. However, posttranscriptional mechanisms driving hIAPP expression in pancreas remain enigmatic, and hence were explored here. The translational assay revealed that both 5' and 3' untranslated regions (UTRs) of hIAPP restricted expression of the luciferase constructs only in constructs driven by the hIAPP promoter. Bioinformatics analysis revealed several putative seed sequences for a dozen micro RNAs (miRNAs) in hIAPP's 3' UTR. miR-182, miR-335, and miR-495 were the most downregulated miRNAs in stressed human islets exposed to endoplasmic reticulum (ER) or metabolic stressors, thapsigargin (TG) or high glucose (HG). Correspondingly, miR-335 mimics alone or in combination with miR-495 and miR-182 mimics significantly and potently (>3-fold) reduced hIAPP protein expression in HG-treated cultured human islets. siRNA-mediated silencing of Ago2 but not Ago1 significantly stimulated hIAPP expression and secretion from transfected, HG-treated human islets. Conversely, ectopic expression of Ago2 in hIAPP-expressing RIN-m5F cell line driven by CMV promoter reduced hIAPP intracellular protein levels. Collectively, the results point to a novel and synergistic role for hIAPP promoter, 5/3' UTRs and Ago-2/miR-335 complex in post-transcriptional regulation of hIAPP gene expression in normal and metabolically active β-cells.
Collapse
Affiliation(s)
| | | | | | - Aleksandar M. Jeremic
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA; (Z.K.); (S.P.); (E.P.)
| |
Collapse
|
2
|
Gerling N, Mendez JA, Gomez E, Ruiz-Garcia J. The separation between mRNA-ends is more variable than expected. FEBS Open Bio 2024. [PMID: 39226224 DOI: 10.1002/2211-5463.13877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024] Open
Abstract
Effective circularization of mRNA molecules is a key step for the efficient initiation of translation. Research has shown that the intrinsic separation of the ends of mRNA molecules is rather small, suggesting that intramolecular arrangements could provide this effective circularization. Considering that the innate proximity of RNA ends might have important unknown biological implications, we aimed to determine whether the close proximity of the ends of mRNA molecules is a conserved feature across organisms and gain further insights into the functional effects of the proximity of RNA ends. To do so, we studied the secondary structure of 274 full native mRNA molecules from 17 different organisms to calculate the contour length (CL) of the external loop as an index of their end-to-end separation. Our computational predictions show bigger variations (from 0.59 to 31.8 nm) than previously reported and also than those observed in random sequences. Our results suggest that separations larger than 18.5 nm are not favored, whereas short separations could be related to phenotypical stability. Overall, our work implies the existence of a biological mechanism responsible for the increase in the observed variability, suggesting that the CL features of the exterior loop could be relevant for the initiation of translation and that a short CL could contribute to the stability of phenotypes.
Collapse
Affiliation(s)
- Nancy Gerling
- Institute of Physics, Biological Physics Laboratory, San Luis Potosi, Mexico
| | - J Alfredo Mendez
- Institute of Physics, Laboratory of Molecular Biophysics, San Luis Potosi, Mexico
| | - Eduardo Gomez
- Cold Atoms Laboratory, Institute of Physics, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Jaime Ruiz-Garcia
- Institute of Physics, Biological Physics Laboratory, San Luis Potosi, Mexico
| |
Collapse
|
3
|
Kerkhofs K, Guydosh NR, Bayfield MA. Respiratory Syncytial Virus (RSV) optimizes the translational landscape during infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606199. [PMID: 39131278 PMCID: PMC11312563 DOI: 10.1101/2024.08.02.606199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Viral infection often triggers eukaryotic initiator factor 2α (eIF2α) phosphorylation, leading to global 5'-cap-dependent translation inhibition. RSV encodes messenger RNAs (mRNAs) mimicking 5'-cap structures of host mRNAs and thus inhibition of cap-dependent translation initiation would likely also reduce viral translation. We confirmed that RSV limits widespread translation initiation inhibition and unexpectedly found that the fraction of ribosomes within polysomes increases during infection, indicating higher ribosome loading on mRNAs during infection. We found that AU-rich host transcripts that are less efficiently translated under normal conditions become more efficient at recruiting ribosomes, similar to RSV transcripts. Viral transcripts are transcribed in cytoplasmic inclusion bodies, where the viral AU-rich binding protein M2-1 has been shown to bind viral transcripts and shuttle them into the cytoplasm. We further demonstrated that M2-1 is found on polysomes, and that M2-1 might deliver host AU-rich transcripts for translation.
Collapse
Affiliation(s)
- Kyra Kerkhofs
- Department of Biology, Faculty of Science, York University, Toronto, Ontario N3J 1P3, Canada
| | - Nicholas R. Guydosh
- Section on mRNA Regulation and Translation, Laboratory of Biochemistry & Genetics. National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark A. Bayfield
- Department of Biology, Faculty of Science, York University, Toronto, Ontario N3J 1P3, Canada
| |
Collapse
|
4
|
Dutcher HA, Gasch AP. Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604323. [PMID: 39091809 PMCID: PMC11291059 DOI: 10.1101/2024.07.19.604323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
RNA-binding proteins (RBPs) play critical cellular roles by mediating various stages of RNA life cycles. Ssd1, an RBP with pleiotropic effects, has been implicated in aneuploidy tolerance in Saccharomyces cerevisiae but its mechanistic role remains unclear. Here we used a network-based approach to inform on Ssd1's role in aneuploidy tolerance, by identifying and experimentally perturbing a network of RBPs that share mRNA targets with Ssd1. We identified RBPs whose bound mRNA targets significantly overlap with Ssd1 targets. For 14 identified RBPs, we then used a genetic approach to generate all combinations of genotypes for euploid and aneuploid yeast with an extra copy of chromosome XII, with and without SSD1 and/or the RBP of interest. Deletion of 10 RBPs either exacerbated or alleviated the sensitivity of wild-type and/or ssd1 Δ cells to chromosome XII duplication, in several cases indicating genetic interactions with SSD1 in the context of aneuploidy. We integrated these findings with results from a global over-expression screen that identified genes whose duplication complements ssd1 Δ aneuploid sensitivity. The resulting network points to a sub-group of proteins with shared roles in translational repression and p-body formation, implicating these functions in aneuploidy tolerance. Our results reveal a role for new RBPs in aneuploidy tolerance and support a model in which Ssd1 mitigates translation-related stresses in aneuploid cells.
Collapse
|
5
|
Khan D, Fox PL. Host-like RNA Elements Regulate Virus Translation. Viruses 2024; 16:468. [PMID: 38543832 PMCID: PMC10976276 DOI: 10.3390/v16030468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/01/2024] Open
Abstract
Viruses are obligate, intracellular parasites that co-opt host cell machineries for propagation. Critical among these machineries are those that translate RNA into protein and their mechanisms of control. Most regulatory mechanisms effectuate their activity by targeting sequence or structural features at the RNA termini, i.e., at the 5' or 3' ends, including the untranslated regions (UTRs). Translation of most eukaryotic mRNAs is initiated by 5' cap-dependent scanning. In contrast, many viruses initiate translation at internal RNA regions at internal ribosome entry sites (IRESs). Eukaryotic mRNAs often contain upstream open reading frames (uORFs) that permit condition-dependent control of downstream major ORFs. To offset genome compression and increase coding capacity, some viruses take advantage of out-of-frame overlapping uORFs (oORFs). Lacking the essential machinery of protein synthesis, for example, ribosomes and other translation factors, all viruses utilize the host apparatus to generate virus protein. In addition, some viruses exhibit RNA elements that bind host regulatory factors that are not essential components of the translation machinery. SARS-CoV-2 is a paradigm example of a virus taking advantage of multiple features of eukaryotic host translation control: the virus mimics the established human GAIT regulatory element and co-opts four host aminoacyl tRNA synthetases to form a stimulatory binding complex. Utilizing discontinuous transcription, the elements are present and identical in all SARS-CoV-2 subgenomic RNAs (and the genomic RNA). Thus, the virus exhibits a post-transcriptional regulon that improves upon analogous eukaryotic regulons, in which a family of functionally related mRNA targets contain elements that are structurally similar but lacking sequence identity. This "thrifty" virus strategy can be exploited against the virus since targeting the element can suppress the expression of all subgenomic RNAs as well as the genomic RNA. Other 3' end viral elements include 3'-cap-independent translation elements (3'-CITEs) and 3'-tRNA-like structures. Elucidation of virus translation control elements, their binding proteins, and their mechanisms can lead to novel therapeutic approaches to reduce virus replication and pathogenicity.
Collapse
Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul L. Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| |
Collapse
|
6
|
Ji W, Xu L, Sun X, Xu X, Zhang H, Luo H, Yao B, Zhang W, Su X, Huang H. Exploiting Systematic Engineering of the Expression Cassette as a Powerful Tool to Enhance Heterologous Gene Expression in Trichoderma reesei. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5307-5317. [PMID: 38426871 DOI: 10.1021/acs.jafc.3c07988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Many endeavors in expressing a heterologous gene in microbial hosts rely on simply placing the gene of interest between a selected pair of promoters and terminator. However, although the expression efficiency could be improved by engineering the host cell, how modifying the expression cassette itself systematically would affect heterologous gene expression remains largely unknown. As the promoter and terminator bear plentiful cis-elements, herein using the Aspergillus niger mannanase with high application value in animal feeds and the eukaryotic filamentous fungus workhorse Trichoderma reesei as a model gene/host, systematic engineering of an expression cassette was investigated to decipher the effect of its mutagenesis on heterologous gene expression. Modifying the promoter, signal peptide, the eukaryotic-specific Kozak sequence, and the 3'-UTR could stepwise improve extracellular mannanase production from 17 U/mL to an ultimate 471 U/mL, representing a 27.7-fold increase in expression. The strategies can be generally applied in improving the production of heterologous proteins in eukaryotic microbial hosts.
Collapse
Affiliation(s)
- Wangli Ji
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Haidian District, Beijing 100081, China
| | - Li Xu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Xianhua Sun
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Xinxin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Haidian District, Beijing 100081, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Haidian District, Beijing 100081, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| |
Collapse
|
7
|
Steadman K, You S, Srinivas DV, Mouakkad L, Yan Y, Kim M, Venugopal SV, Tanaka H, Freeman MR. Autonomous action and cooperativity between the ONECUT2 transcription factor and its 3' untranslated region. Front Cell Dev Biol 2023; 11:1206259. [PMID: 37484909 PMCID: PMC10356556 DOI: 10.3389/fcell.2023.1206259] [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: 04/15/2023] [Accepted: 05/16/2023] [Indexed: 07/25/2023] Open
Abstract
The transcription factor ONECUT2 (OC2) is a master transcriptional regulator operating in metastatic castration-resistant prostate cancer that suppresses androgen receptor activity and promotes neural differentiation and tumor cell survival. OC2 mRNA possesses an unusually long (14,575 nt), evolutionarily conserved 3' untranslated region (3' UTR) with many microRNA binding sites, including up to 26 miR-9 sites. This is notable because miR-9 targets many of the same genes regulated by the OC2 protein. Paradoxically, OC2 expression is high in tissues with high miR-9 expression. The length and complex secondary structure of OC2 mRNA suggests that it is a potent master competing endogenous RNA (ceRNA) capable of sequestering miRNAs. Here, we describe a novel role for OC2 3' UTR in lethal prostate cancer consistent with a function as a ceRNA. A plausible ceRNA network in OC2-driven tumors was constructed computationally and then confirmed in prostate cancer cell lines. Genes regulated by OC2 3' UTR exhibited high overlap (up to 45%) with genes driven by the overexpression of the OC2 protein in the absence of 3' UTR, indicating a cooperative functional relationship between the OC2 protein and its 3' UTR. These overlapping networks suggest an evolutionarily conserved mechanism to reinforce OC2 transcription by protection of OC2-regulated mRNAs from miRNA suppression. Both the protein and 3' UTR showed increased polycomb-repressive complex activity. The expression of OC2 3' UTR mRNA alone (without protein) dramatically increased the metastatic potential by in vitro assays. Additionally, OC2 3' UTR increased the expression of Aldo-Keto reductase and UDP-glucuronyl transferase family genes responsible for altering the androgen synthesis pathway. ONECUT2 represents the first-described dual-modality transcript that operates as both a key transcription factor driving castration-resistant prostate cancer and a master ceRNA that promotes and protects the same transcriptional network.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Michael R. Freeman
- Division of Cancer Biology and Therapeutics, Biomedical Sciences and Pathology and Laboratory Medicine, Department of Urology, Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, United States
| |
Collapse
|
8
|
Htet M, Lei S, Bajpayi S, Zoitou A, Chamakioti M, Tampakakis E. The role of noncoding genetic variants in cardiomyopathy. Front Cardiovasc Med 2023; 10:1116925. [PMID: 37283586 PMCID: PMC10239966 DOI: 10.3389/fcvm.2023.1116925] [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: 12/06/2022] [Accepted: 05/04/2023] [Indexed: 06/08/2023] Open
Abstract
Cardiomyopathies remain one of the leading causes of morbidity and mortality worldwide. Environmental risk factors and genetic predisposition account for most cardiomyopathy cases. As with all complex diseases, there are significant challenges in the interpretation of the molecular mechanisms underlying cardiomyopathy-associated genetic variants. Given the technical improvements and reduced costs of DNA sequence technologies, an increasing number of patients are now undergoing genetic testing, resulting in a continuously expanding list of novel mutations. However, many patients carry noncoding genetic variants, and although emerging evidence supports their contribution to cardiac disease, their role in cardiomyopathies remains largely understudied. In this review, we summarize published studies reporting on the association of different types of noncoding variants with various types of cardiomyopathies. We focus on variants within transcriptional enhancers, promoters, intronic sites, and untranslated regions that are likely associated with cardiac disease. Given the broad nature of this topic, we provide an overview of studies that are relatively recent and have sufficient evidence to support a significant degree of causality. We believe that more research with additional validation of noncoding genetic variants will provide further mechanistic insights on the development of cardiac disease, and noncoding variants will be increasingly incorporated in future genetic screening tests.
Collapse
Affiliation(s)
- Myo Htet
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
| | - Shunyao Lei
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Sheetal Bajpayi
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
| | - Asimina Zoitou
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | | | - Emmanouil Tampakakis
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, United States
| |
Collapse
|
9
|
Singhal K, Dhamija S, Mukerji M. Exonized Alu repeats in the 3'UTR of a CYP20A1_Alu-LT transcript act as a miRNA sponge. BMC Res Notes 2023; 16:32. [PMID: 36895043 PMCID: PMC9996890 DOI: 10.1186/s13104-023-06289-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/14/2023] [Indexed: 03/11/2023] Open
Abstract
OBJECTIVE Alu repeats have gained huge importance in the creation and modification of regulatory networks. We previously reported a unique isoform of human CYP20A1 i.e. CYP20A1_Alu-LT with 23 Alu repeats exonized in its 9 kb long 3'UTR with 4742 potential binding sites for 994 miRNAs. The role of this transcript was hypothesized as a potential miRNA sponge in primary neurons as its expression correlated with that of 380 genes having shared miRNA sites and enriched in neuro-coagulopathy. This study provides experimental evidence for the miRNA sponge activity of CYP20A1_Alu-LT in neuronal cell lines. RESULTS We studied the Alu-rich fragment of the CYP20A1_Alu-LT extended 3'UTR with > 10 binding sites for miR-619-5p and miR-3677-3p. Enrichment of the Alu-rich fragment with Ago2 confirmed miRNA association of this transcript. Cloning the fragment downstream of a reporter gene led to a 90% decrease in luciferase activity. Overexpression and knockdown studies revealed a positive correlation between the expression of CYP20A1_Alu-LT and miR-619-5p / miR-3677-3p target genes. GAP43, one of the key modulators of nerve regeneration, was significantly altered by the expression of CYP20A1_Alu-LT. This study, for the first time, provides evidence for a unique regulatory function of exonized Alu repeats as miRNA sponges.
Collapse
Affiliation(s)
- Khushboo Singhal
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, 110025, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, Uttar Pradesh, India
| | - Sonam Dhamija
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, 110025, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, Uttar Pradesh, India
| | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, 110025, New Delhi, India. .,Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, Uttar Pradesh, India. .,Department of Bioscience and Bioengineering, Indian Institute of Technology, 342037, Jodhpur, Rajasthan, India.
| |
Collapse
|
10
|
Soybean product consumption decreases risk of gastric cancer: results from the Health Examinees Study. Eur J Nutr 2023; 62:1743-1753. [PMID: 36820884 DOI: 10.1007/s00394-023-03115-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND Epidemiological findings on the association between soybean product consumption and gastric cancer risk remain inconsistent. We evaluated the relationship between soybean product consumption and the risk of gastric cancer in a prospective cohort study in Korea. METHODS This prospective cohort study included a total of 139,267 participants aged 40-69 years from the Health Examinees-Gem (HEXA-G) study between 2004 and 2013. Information on cancer diagnosis was retrieved from the Korea Central Cancer Registry until 31 December 2018. Multivariate hazard ratios (HRs) and 95% of confidence intervals (CIs) for the risk of gastric cancer according to the consumption of soybean products were estimated using Cox proportional hazards models. RESULTS A total of 767 incident cases of gastric cancer occurred over an average follow-up period of 9.21 years. We found that men who consumed two servings per week had 37% lower risk of gastric cancer compared with who consume those who almost never consumed (HR for tofu consumption of more than two servings/week vs. almost never consumed was 0.63 (95% CI 0.45, 0.89); p for trend = 0.04). Among men with a BMI of less than 25 kg/m2, increased consumption of soybean paste (p for trend = 0.02) and tofu (HR 0.51 (95% CI 0.32, 0.82 for more than two servings/week vs. almost never consumed); p for trend = 0.01) was associated with decreased risk of gastric cancer. CONCLUSION Our results suggest that a high consumption of soybean products has a protective effect against gastric cancer.
Collapse
|
11
|
Vasu K, Ramachandiran I, Chechi A, Khan K, Khan D, Kaufman R, Fox PL. Translational control of murine adiponectin expression by an upstream open reading frame element. RNA Biol 2023; 20:737-749. [PMID: 37702393 PMCID: PMC10501164 DOI: 10.1080/15476286.2023.2256094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023] Open
Abstract
Adiponectin, an adipocyte-specific secretory protein encoded by the ADIPOQ gene has a causal role in insulin resistance. Anti-diabetic drugs increase plasma adiponectin by a poorly understood, post-transcriptional mechanism enhancing insulin sensitivity. Deletion analysis of a reporter bearing the mouse Adipoq mRNA 5'-leader identified an inhibitory cis-regulatory sequence. The 5'-leader harbours two potential upstream open reading frames (uORFs) overlapping the principal downstream ORF. Mutation of the uORF ATGs increased reporter translation ~3-fold, indicative of a functional uORF. uORFs are common in mammalian mRNAs; however, only a select group resist translational repression by the integrated stress response (ISR). Thapsigargin (TG), which induces endoplasmic reticulum (ER) stress and the ISR, enhanced expression of a reporter bearing the Adipoq 5'-leader; polysome profiling verified translation-stimulation. TG-stimulated translation was absent in cells defective in Ser51 phosphorylation of eukaryotic initiation factor 2α (eIF2α), required for the ISR. To determine its role in expression and function of endogenous adiponectin, the upstream uORF was disrupted by CRISPR-Cas9-mediated mutagenesis of differentiated mouse 3T3-L1 adipocytes. uORF disruption in adipocytes increased adiponectin expression, triacylglycerol accumulation, and glucose uptake, and inhibited paracrine muscle and liver cell expression of gluconeogenic enzymes, establishing an important role of the uORF in adiponectin-mediated responses to stress.
Collapse
Affiliation(s)
- Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Aayushi Chechi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Randall Kaufman
- Degenerative Diseases Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Paul L. Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| |
Collapse
|
12
|
Lin J, Chen Y, Zhang Y, Lin H, Ouyang Z. Deciphering the role of RNA structure in translation efficiency. BMC Bioinformatics 2022; 23:559. [PMID: 36564729 PMCID: PMC9783404 DOI: 10.1186/s12859-022-05037-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND RNA secondary structure has broad impact on the fate of RNA metabolism. The reduced stability of secondary structures near the translation initiation site/start codon of the coding region promotes the efficiency of translation in both prokaryotic and eukaryotic species. However, the inaccuracy of in silico folding and the focus on the coding region limit our understanding of the global relationship between the whole mRNA structure and translation efficiency. Leveraging high-throughput RNA structure probing data in the transcriptome, we aim to systematically investigate the role of RNA structure in regulating translation efficiency. RESULTS Here, we analyze the influences of hundreds of sequence and structural features on translation efficiency in the mouse embryonic stem cells (mESCs) and zebrafish developmental stages. Our findings reveal that overall in vivo RNA structure has a higher relative importance in predicting translation efficiency than in vitro RNA structure in both mESCs and zebrafish. Also, RNA structures in 3' untranslated region (UTR) have much stronger influence on translation efficiency compared to those in coding regions or 5' UTR. Furthermore, strong alternation between in vitro and in vivo structures in 3' UTR are detected in highly translated mRNAs in mESCs but not zebrafish. Instead, moderate alteration between in vitro and in vivo RNA structures in the 5' UTR and proximal coding regions are detected in highly translated mRNAs in zebrafish. CONCLUSIONS Our results suggest the openness of the 3' UTR promotes the translation efficiency in both mice and zebrafish, with the in vivo structure in 3' UTR more important in mice than in zebrafish. This reveals a novel role of RNA secondary structure on translational regulation.
Collapse
Affiliation(s)
- Jianan Lin
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Yang Chen
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA
| | - Yuping Zhang
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
- Center for Quantitative Medicine, University of Connecticut, Farmington, CT, 06030, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University, New Haven, CT, 06520, USA
| | - Zhengqing Ouyang
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, 01003, USA.
| |
Collapse
|
13
|
Liang M, Foster CE, Yuan YW. Lost in translation: Molecular basis of reduced flower coloration in a self-pollinated monkeyflower ( Mimulus) species. SCIENCE ADVANCES 2022; 8:eabo1113. [PMID: 36103532 PMCID: PMC9473569 DOI: 10.1126/sciadv.abo1113] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Phenotypic evolution is usually attributed to changes in protein function or gene transcription. In principle, mutations that affect protein abundance through enhancing or attenuating protein translation also could be an important source for phenotypic evolution. However, these types of mutations remain largely unexplored in the studies of phenotypic variation in nature. Through fine-scale genetic mapping and functional interrogation, we identify a single nucleotide substitution in an anthocyanin-activating R2R3-MYB gene causing flower color variation between a pair of closely related monkeyflower (Mimulus) species, the hummingbird-pollinated Mimulus cardinalis, and self-pollinated Mimulus parishii. This causal mutation is located in the 5' untranslated region and generates an upstream ATG start codon, leading to attenuated protein translation and reduced flower coloration in the self-pollinated species. Together, our results provide empirical support for the role of mutations affecting protein translation, as opposed to protein function or transcript level, in natural phenotypic variation.
Collapse
Affiliation(s)
- Mei Liang
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Caitlin E. Foster
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| |
Collapse
|
14
|
Dionisi S, Piera K, Baumschlager A, Khammash M. Implementation of a Novel Optogenetic Tool in Mammalian Cells Based on a Split T7 RNA Polymerase. ACS Synth Biol 2022; 11:2650-2661. [PMID: 35921263 PMCID: PMC9396705 DOI: 10.1021/acssynbio.2c00067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Optogenetic tools are widely used to control gene expression
dynamics
both in prokaryotic and eukaryotic cells. These tools are used in
a variety of biological applications from stem cell differentiation
to metabolic engineering. Despite some tools already available in
bacteria, no light-inducible system currently exists to control gene
expression independently from mammalian transcriptional and/or translational
machineries thus working orthogonally to endogenous regulatory mechanisms.
Such a tool would be particularly important in synthetic biology,
where orthogonality is advantageous to achieve robust activation of
synthetic networks. Here we implement, characterize, and optimize
a new optogenetic tool in mammalian cells based on a previously published
system in bacteria called Opto-T7RNAPs. The tool is orthogonal to
the cellular machinery for transcription and consists of a split T7
RNA polymerase coupled with the blue light-inducible magnets system
(mammalian OptoT7–mOptoT7). In our study we exploited the T7
polymerase’s viral origins to tune our system’s expression
level, reaching up to an almost 20-fold change activation over the
dark control. mOptoT7 is used here to generate mRNA for protein expression,
shRNA for protein inhibition, and Pepper aptamer for RNA visualization.
Moreover, we show that mOptoT7 can mitigate the gene expression burden
when compared to another optogenetic construct. These properties make
mOptoT7 a powerful new tool to use when orthogonality and viral RNA
species (that lack endogenous RNA modifications) are desired.
Collapse
Affiliation(s)
- Sara Dionisi
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Karol Piera
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Armin Baumschlager
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| |
Collapse
|
15
|
Ribbans WJ, September AV, Collins M. Tendon and Ligament Genetics: How Do They Contribute to Disease and Injury? A Narrative Review. Life (Basel) 2022; 12:life12050663. [PMID: 35629331 PMCID: PMC9147569 DOI: 10.3390/life12050663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 12/15/2022] Open
Abstract
A significant proportion of patients requiring musculoskeletal management present with tendon and ligament pathology. Our understanding of the intrinsic and extrinsic mechanisms that lead to such disabilities is increasing. However, the complexity underpinning these interactive multifactorial elements is still not fully characterised. Evidence highlighting the genetic components, either reducing or increasing susceptibility to injury, is increasing. This review examines the present understanding of the role genetic variations contribute to tendon and ligament injury risk. It examines the different elements of tendon and ligament structure and considers our knowledge of genetic influence on form, function, ability to withstand load, and undertake repair or regeneration. The role of epigenetic factors in modifying gene expression in these structures is also explored. It considers the challenges to interpreting present knowledge, the requirements, and likely pathways for future research, and whether such information has reached the point of clinical utility.
Collapse
Affiliation(s)
- William J. Ribbans
- School of Health, The University of Northampton, Northampton NN1 5PH, UK
- The County Clinic, Northampton NN1 5DB, UK
- Correspondence: ; Tel.: +44-1604-795414
| | - Alison V. September
- Division of Physiological Sciences, Department of Human Biology, Health Sciences Faculty, University of Cape Town, Cape Town 7700, South Africa; (A.V.S.); (M.C.)
- Health Through Physical Activity, Lifestyle and Sport Research Centre (HPALS), Department of Human Biology, Health Sciences Faculty, University of Cape Town, Cape Town 7700, South Africa
- International Federation of Sports Medicine (FIMS), Collaborative Centre of Sports Medicine, Department of Human Biology, University of Cape Town, Cape Town 7700, South Africa
| | - Malcolm Collins
- Division of Physiological Sciences, Department of Human Biology, Health Sciences Faculty, University of Cape Town, Cape Town 7700, South Africa; (A.V.S.); (M.C.)
- Health Through Physical Activity, Lifestyle and Sport Research Centre (HPALS), Department of Human Biology, Health Sciences Faculty, University of Cape Town, Cape Town 7700, South Africa
- International Federation of Sports Medicine (FIMS), Collaborative Centre of Sports Medicine, Department of Human Biology, University of Cape Town, Cape Town 7700, South Africa
| |
Collapse
|
16
|
LncRNA SFTA1P mediates positive feedback regulation of the Hippo-YAP/TAZ signaling pathway in non-small cell lung cancer. Cell Death Discov 2021; 7:369. [PMID: 34845189 PMCID: PMC8630011 DOI: 10.1038/s41420-021-00761-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/19/2021] [Accepted: 11/05/2021] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate numerous biological processes involved in both development and carcinogenesis. Hippo-YAP/TAZ signaling, a critical pathway responsible for organ size control, is often dysregulated in a variety of cancers. However, the nature and function of YAP/TAZ-regulated lncRNAs during tumorigenesis remain largely unexplored. By profiling YAP/TAZ-regulated lncRNAs, we identified SFTA1P as a novel transcriptional target and a positive feedback regulator of YAP/TAZ signaling. Using non-small cell lung cancer (NSCLC) cell lines, we show that SFTA1P is transcriptionally activated by YAP/TAZ in a TEAD-dependent manner. Functionally, knockdown of SFTA1P in NSCLC cell lines inhibited proliferation, induced programmed cell death, and compromised their tumorigenic potential. Mechanistically, SFTA1P knockdown decreased TAZ protein abundance and consequently, the expression of YAP/TAZ transcriptional targets. We provide evidence that this phenomenon could potentially be mediated via its interaction with TAZ mRNA to regulate TAZ translation. Our results reveal SFTA1P as a positive feedback regulator of Hippo-YAP/TAZ signaling, which may serve as the molecular basis for lncRNA-based therapies against YAP/TAZ-driven cancers.
Collapse
|
17
|
A structurally conserved RNA element within SARS-CoV-2 ORF1a RNA and S mRNA regulates translation in response to viral S protein-induced signaling in human lung cells. J Virol 2021; 96:e0167821. [PMID: 34757848 PMCID: PMC8791291 DOI: 10.1128/jvi.01678-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The positive-sense, single-stranded RNA genome SARS-CoV-2 harbors functionally important cis-acting elements governing critical aspects of viral gene expression. However, insights on how these elements sense various signals from the host cell and regulate viral protein synthesis are lacking. Here, we identified two novel cis-regulatory elements in SARS-CoV-2 ORF1a and S RNAs and describe their role in translational control of SARS-CoV-2. These elements are sequence-unrelated but form conserved hairpin structures (validated by NMR) resembling Gamma Activated Inhibitor of Translation (GAIT) elements that are found in a cohort of human mRNAs directing translational suppression in myeloid cells in response to IFN-γ. Our studies show that treatment of human lung cells with receptor-binding S1 subunit, S protein pseudotyped lentivirus, and S protein-containing virus-like particles triggers a signaling pathway involving DAP-kinase1 that leads to phosphorylation and release of the ribosomal protein L13a from the large ribosomal subunit. Released L13a forms a Virus Activated Inhibitor of Translation (VAIT) complex that binds to ORF1a and S VAIT elements, causing translational silencing. Translational silencing requires extracellular S protein (and its interaction with host ACE2 receptor), but not its intracellular synthesis. RNA-protein interaction analyses and in vitro translation experiments showed that GAIT and VAIT elements do not compete with each other, highlighting differences between the two pathways. Sequence alignments of SARS-CoV-2 genomes showed a high level of conservation of VAIT elements, suggesting their functional importance. This VAIT-mediated translational control mechanism of SARS-CoV-2 may provide novel targets for small molecule intervention and/or facilitate development of more effective mRNA vaccines. Importance Specific RNA elements in the genomes of RNA viruses play important roles in host-virus interaction. For SARS-CoV-2, the mechanistic insights on how these RNA elements could sense the signals from the host cell are lacking. Here we report a novel relationship between the GAIT-like SARS-CoV-2 RNA element (called VAITs) and the signal generated from the host cell. We show that for SARS-CoV-2, the interaction of spike protein with ACE2 not only serves the purpose for viral entry into the host cell, but also transduces signals that culminate into the phosphorylation and the release of L13a from the large ribosomal subunit. We also show that this event leads to the translational arrest of ORF1a and S mRNAs in a manner dependent on the structure of the RNA elements. Translational control of viral mRNA by a host-cell generated signal triggered by viral protein is a new paradigm in the host-virus relationship.
Collapse
|
18
|
Kaleta B, Lachota M, Łukaszkiewicz J, Woźniacka A, Bogaczewicz J. Osteopontin Gene Polymorphisms rs1126616 C>T and rs1126772 A>G are Associated with Atopic Dermatitis in Polish Population. APPLICATION OF CLINICAL GENETICS 2021; 14:417-425. [PMID: 34675603 PMCID: PMC8502056 DOI: 10.2147/tacg.s323735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/27/2021] [Indexed: 11/24/2022]
Abstract
Purpose Atopic dermatitis (AD) is a chronic, relapsing inflammatory disease, caused by environmental and genetic factors, which lead to immunological abnormalities. Osteopontin (OPN), also named secreted phosphoprotein 1 (SPP1), is a protein involved in the pathogenesis of numerous autoimmune and inflammatory conditions. However, its role in AD has not been fully elucidated. Therefore, we aim to gain an insight into the role of OPN in AD pathogenesis through investigating its gene single nucleotide polymorphisms (SNPs) and their possible associations with disease clinical features. Patients and Methods A total of 182 Caucasian participants (45 AD patients and 137 gender- and age-matched controls) were studied. Genomic DNA was isolated from peripheral blood samples. Genotyping for the rs1126616 C>T, rs1126772 A>G, rs9138 A>C, and rs3841116 T>G SNPs was performed by real time polymerase chain reaction (RT-PCR). Results The frequency of the minor TT genotype and the T allele of rs1126616 C>T was higher in AD patients compared to controls (P = 0.019, OD = 4.86, 95% CI = 1.46–16.20, and P = 0.047, OR = 1.77, 95% CI = 1.04–3.00, respectively) and was associated with the higher prevalence of asthma (P = 0.017, OR = 3.73, 95% CI = 0.71–19.67, and P = 0.004, OR = 3.96, 95% CI = 1.53–10.25, respectively). Likewise, the minor GG genotype and the G allele of rs1126772 A>G were more frequent in AD patients (P = 0.026, OR = 3.27, 95% CI = 1.29–8.33, and P = 0.013, OR = 1.94, 95% CI = 1.18–3.21, respectively) and were associated with the increased incidence of asthma (P = 0.016, OR = 5.06, 95% CI = 1.14–22.49, and P = 0.002, OR = 4.40, 95% CI = 1.71–11.35, respectively). Furthermore, haplotype frequency estimation determined the four-loci haplotype TGCT, as a significant risk factor for AD compared to controls (P = 0.031, OR = 9.48, 95% CI = 1.23–71.91). Conclusion Our results suggest that the variation in the OPN gene might be associated with AD and increased incidence of asthma in Caucasians. Further studies should be conducted to look into the possible role of OPN as a biomarker for AD.
Collapse
Affiliation(s)
- Beata Kaleta
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Mieszko Lachota
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland.,Doctoral School, Medical University of Warsaw, Warsaw, Poland
| | - Jacek Łukaszkiewicz
- Department of Biochemistry and Clinical Chemistry, Medical University of Warsaw, Warsaw, Poland
| | - Anna Woźniacka
- Department of Dermatology and Venereology, Medical University of Lodz, Lodz, Poland
| | | |
Collapse
|
19
|
Takakura Y, Hori N, Terada N, Machida M, Yamaguchi N, Takano H, Yamaguchi N. VGLL3 activates inflammatory responses by inducing interleukin-1α secretion. FASEB J 2021; 35:e21996. [PMID: 34679187 DOI: 10.1096/fj.202100679rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 09/05/2021] [Accepted: 10/04/2021] [Indexed: 01/10/2023]
Abstract
Vestigial-like family member 3 (VGLL3), a member of the vestigial-like family, is a cofactor of the TEA-domain-containing transcription factor (TEAD). Although elevation in VGLL3 expression is associated with inflammatory diseases, such as inflammatory sarcomas and autoimmune diseases, the molecular mechanisms underlying VGLL3-mediated inflammation remain largely unknown. In this study, we analyzed the relationship between elevated VGLL3 expression and the levels of NF-κB, a transcription factor that plays a pivotal role in inflammation. NF-κB was found to be activated in a cell line stably expressing VGLL3. Mechanistically, VGLL3 was shown to promote the expression and secretion of the potent NF-κB-activating cytokine interleukin (IL)-1α, probably through its association with TEADs. As VGLL3 is a target of transforming growth factor β (TGF-β) signaling, we analyzed IL-1α induction upon TGF-β stimulation. TGF-β stimulation was observed to induce IL-1α secretion and NF-κB activation, and VGLL3 was associated with this phenomenon. The TGF-β transcription factors Smad3 and Smad4 were shown to be necessary for inducing VGLL3 and IL-1α expression. Lastly, we found that VGLL3-dependent IL-1α secretion is involved in constitutive NF-κB activation in highly malignant breast cancer cells. Collectively, the findings suggested that VGLL3 expression and TGF-β stimulation activate the inflammatory response by inducing IL-1α secretion.
Collapse
Affiliation(s)
- Yuki Takakura
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Naoto Hori
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.,Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Natsumi Terada
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Moeka Machida
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.,Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Naoto Yamaguchi
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Hiroyuki Takano
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Noritaka Yamaguchi
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.,Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| |
Collapse
|
20
|
Wang Y, Guo J, Yu F, Tian Y, Wu Y, Cui L, Liu LE. The association between soy-based food and soy isoflavone intake and the risk of gastric cancer: a systematic review and meta-analysis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:5314-5324. [PMID: 34032287 DOI: 10.1002/jsfa.11334] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/14/2021] [Accepted: 06/25/2021] [Indexed: 06/12/2023]
Abstract
Soy contains many bioactive phytochemicals, such as isoflavones, which have the effect of preventing many cancers. Some studies have shown the beneficial effect of soy-based food and isoflavone intake on gastric cancer (GC), while others claimed no effect. Therefore, whether the beneficial effect of soy-based food is related to its fermentation or whether its protective effect comes from isoflavones still remains inconclusive. Our aim was to investigate the relationship between total soybean, fermented soybean, non-fermented soybean and isoflavone intake, and the risk of GC. Ten cohort studies and 21 case-control studies involving 916 354 participants were included. The association between soy-based food and isoflavone intake and the risk of GC was calculated with the pooled relative risks (RRs) for the highest versus lowest intake categories. The results showed that isoflavone intake might be a protective factor to GC, but the result was not statistically significant (RR = 0.92; 95% CI: 0.79-1.07). However, total soybean intake could significantly decrease the risk of GC by 36% (RR = 0.64; 95% CI: 0.51-0.80), which might be credited to non-fermented soybean products (RR = 0.79; 95% CI: 0.71-0.87). In contrast, high intake of fermented soybean products could increase the risk of GC (RR = 1.19; 95% CI: 1.02-1.38). High intake of total soybean and non-fermented soybean products could reduce the risk of GC, and high intake of fermented soybean products could increase the risk, which indicated that the beneficial effect of soy-based food might be related to its non-fermentation. However, high intake of isoflavones may not be associated with the incidence of GC. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Yameng Wang
- College of Public Health, Zhengzhou University, Zhengzhou City, People's Republic of China
| | - Jiaping Guo
- College of Public Health, Zhengzhou University, Zhengzhou City, People's Republic of China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou City, People's Republic of China
| | - Yongmei Tian
- College of Public Health, Zhengzhou University, Zhengzhou City, People's Republic of China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou City, People's Republic of China
- Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou City, People's Republic of China
| | - Lingling Cui
- College of Public Health, Zhengzhou University, Zhengzhou City, People's Republic of China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou City, People's Republic of China
- Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou City, People's Republic of China
| |
Collapse
|
21
|
Xu Y, Huangyang P, Wang Y, Xue L, Devericks E, Nguyen HG, Yu X, Oses-Prieto JA, Burlingame AL, Miglani S, Goodarzi H, Ruggero D. ERα is an RNA-binding protein sustaining tumor cell survival and drug resistance. Cell 2021; 184:5215-5229.e17. [PMID: 34559986 PMCID: PMC8547373 DOI: 10.1016/j.cell.2021.08.036] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 06/28/2021] [Accepted: 08/29/2021] [Indexed: 12/15/2022]
Abstract
Estrogen receptor α (ERα) is a hormone receptor and key driver for over 70% of breast cancers that has been studied for decades as a transcription factor. Unexpectedly, we discover that ERα is a potent non-canonical RNA-binding protein. We show that ERα RNA binding function is uncoupled from its activity to bind DNA and critical for breast cancer progression. Employing genome-wide cross-linking immunoprecipitation (CLIP) sequencing and a functional CRISPRi screen, we find that ERα-associated mRNAs sustain cancer cell fitness and elicit cellular responses to stress. Mechanistically, ERα controls different steps of RNA metabolism. In particular, we demonstrate that ERα RNA binding mediates alternative splicing of XBP1 and translation of the eIF4G2 and MCL1 mRNAs, which facilitates survival upon stress conditions and sustains tamoxifen resistance of cancer cells. ERα is therefore a multifaceted RNA-binding protein, and this activity transforms our knowledge of post-transcriptional regulation underlying cancer development and drug response.
Collapse
Affiliation(s)
- Yichen Xu
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Peiwei Huangyang
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ying Wang
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lingru Xue
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Emily Devericks
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hao G Nguyen
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Xiuyan Yu
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sohit Miglani
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hani Goodarzi
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
22
|
Challa S, Khulpateea BR, Nandu T, Camacho CV, Ryu KW, Chen H, Peng Y, Lea JS, Kraus WL. Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers. Cell 2021; 184:4531-4546.e26. [PMID: 34314702 PMCID: PMC8380725 DOI: 10.1016/j.cell.2021.07.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/11/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Defects in translation lead to changes in the expression of proteins that can serve as drivers of cancer formation. Here, we show that cytosolic NAD+ synthesis plays an essential role in ovarian cancer by regulating translation and maintaining protein homeostasis. Expression of NMNAT-2, a cytosolic NAD+ synthase, is highly upregulated in ovarian cancers. NMNAT-2 supports the catalytic activity of the mono(ADP-ribosyl) transferase (MART) PARP-16, which mono(ADP-ribosyl)ates (MARylates) ribosomal proteins. Depletion of NMNAT-2 or PARP-16 leads to inhibition of MARylation, increased polysome association and enhanced translation of specific mRNAs, aggregation of their translated protein products, and reduced growth of ovarian cancer cells. Furthermore, MARylation of the ribosomal proteins, such as RPL24 and RPS6, inhibits polysome assembly by stabilizing eIF6 binding to ribosomes. Collectively, our results demonstrate that ribosome MARylation promotes protein homeostasis in cancers by fine-tuning the levels of protein synthesis and preventing toxic protein aggregation.
Collapse
Affiliation(s)
- Sridevi Challa
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Beman R Khulpateea
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cristel V Camacho
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Keun W Ryu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yan Peng
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jayanthi S Lea
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
23
|
Jiao J, Kavdia K, Pagala V, Palmer L, Finkelstein D, Fan Y, Peng J, Demontis F. An age-downregulated ribosomal RpS28 protein variant regulates the muscle proteome. G3-GENES GENOMES GENETICS 2021; 11:6273667. [PMID: 33974070 PMCID: PMC8495913 DOI: 10.1093/g3journal/jkab165] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/06/2021] [Indexed: 11/14/2022]
Abstract
Recent evidence indicates that the composition of the ribosome is heterogeneous and that multiple types of specialized ribosomes regulate the synthesis of specific protein subsets. In Drosophila, we find that expression of the ribosomal RpS28 protein variants RpS28a and RpS28-like preferentially occurs in the germline, a tissue resistant to aging and that it significantly declines in skeletal muscle during aging. Muscle-specific overexpression of RpS28a at levels similar to those seen in the germline decreases early mortality and promotes the synthesis of a subset of proteins with known anti-aging roles, some of which have preferential expression in the germline. These findings indicate a contribution of specialized ribosomal proteins to the regulation of the muscle proteome during aging.
Collapse
Affiliation(s)
- Jianqin Jiao
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Kanisha Kavdia
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Vishwajeeth Pagala
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lance Palmer
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| |
Collapse
|
24
|
Extrinsic Regulators of mRNA Translation in Developing Brain: Story of WNTs. Cells 2021; 10:cells10020253. [PMID: 33525513 PMCID: PMC7911671 DOI: 10.3390/cells10020253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/16/2021] [Accepted: 01/21/2021] [Indexed: 12/30/2022] Open
Abstract
Extrinsic molecules such as morphogens can regulate timed mRNA translation events in developing neurons. In particular, Wingless-type MMTV integration site family, member 3 (Wnt3), was shown to regulate the translation of Foxp2 mRNA encoding a Forkhead transcription factor P2 in the neocortex. However, the Wnt receptor that possibly mediates these translation events remains unknown. Here, we report Frizzled member 7 (Fzd7) as the Wnt3 receptor that lays downstream in Wnt3-regulated mRNA translation. Fzd7 proteins co-localize with Wnt3 ligands in developing neocortices. In addition, the Fzd7 proteins overlap in layer-specific neuronal subpopulations expressing different transcription factors, Foxp1 and Foxp2. When Fzd7 was silenced, we found decreased Foxp2 protein expression and increased Foxp1 protein expression, respectively. The Fzd7 silencing also disrupted the migration of neocortical glutamatergic neurons. In contrast, Fzd7 overexpression reversed the pattern of migratory defects and Foxp protein expression that we found in the Fzd7 silencing. We further discovered that Fzd7 is required for Wnt3-induced Foxp2 mRNA translation. Surprisingly, we also determined that the Fzd7 suppression of Foxp1 protein expression is not Wnt3 dependent. In conclusion, it is exhibited that the interaction between Wnt3 and Fzd7 regulates neuronal identity and the Fzd7 receptor functions as a downstream factor in ligand Wnt3 signaling for mRNA translation. In particular, the Wnt3-Fzd7 signaling axis determines the deep layer Foxp2-expressing neurons of developing neocortices. Our findings also suggest that Fzd7 controls the balance of the expression for Foxp transcription factors in developing neocortical neurons. These discoveries are presented in our manuscript within a larger framework of this review on the role of extrinsic factors in regulating mRNA translation.
Collapse
|
25
|
Menendez-Gil P, Toledo-Arana A. Bacterial 3'UTRs: A Useful Resource in Post-transcriptional Regulation. Front Mol Biosci 2021; 7:617633. [PMID: 33490108 PMCID: PMC7821165 DOI: 10.3389/fmolb.2020.617633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022] Open
Abstract
Bacterial messenger RNAs (mRNAs) are composed of 5′ and 3′ untranslated regions (UTRs) that flank the coding sequences (CDSs). In eukaryotes, 3′UTRs play key roles in post-transcriptional regulatory mechanisms. Shortening or deregulation of these regions is associated with diseases such as cancer and metabolic disorders. Comparatively, little is known about the functions of 3′UTRs in bacteria. Over the past few years, 3′UTRs have emerged as important players in the regulation of relevant bacterial processes such as virulence, iron metabolism, and biofilm formation. This MiniReview is an update for the different 3′UTR-mediated mechanisms that regulate gene expression in bacteria. Some of these include 3′UTRs that interact with the 5′UTR of the same transcript to modulate translation, 3′UTRs that are targeted by specific ribonucleases, RNA-binding proteins and small RNAs (sRNAs), and 3′UTRs that act as reservoirs of trans-acting sRNAs, among others. In addition, recent findings regarding a differential evolution of bacterial 3′UTRs and its impact in the species-specific expression of orthologous genes are also discussed.
Collapse
Affiliation(s)
- Pilar Menendez-Gil
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC) - Gobierno de Navarra, Navarra, Spain
| | - Alejandro Toledo-Arana
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC) - Gobierno de Navarra, Navarra, Spain
| |
Collapse
|
26
|
Sayadi M, Rostami S, Nadali F, Fathabad ME, Riazi-Rad F, Sayadi K, Ajdary S. miR-192 overexpression effect on DHFR and TYMS in acute lymphoblastic leukemia. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
27
|
Levin M, Zalts H, Mostov N, Hashimshony T, Yanai I. Gene expression dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms. Nucleic Acids Res 2020; 48:5926-5938. [PMID: 32421815 PMCID: PMC7293032 DOI: 10.1093/nar/gkaa359] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/11/2020] [Accepted: 04/27/2020] [Indexed: 01/08/2023] Open
Abstract
Alternative polyadenylation (APA) produces isoforms with distinct 3′-ends, yet their functional differences remain largely unknown. Here, we introduce the APA-seq method to detect the expression levels of APA isoforms from 3′-end RNA-Seq data by exploiting both paired-end reads for gene isoform identification and quantification. We detected the expression levels of APA isoforms in individual Caenorhabditis elegans embryos at different stages throughout embryogenesis. Examining the correlation between the temporal profiles of isoforms led us to distinguish two classes of genes: those with highly correlated isoforms (HCI) and those with lowly correlated isoforms (LCI) across time. We hypothesized that variants with similar expression profiles may be the product of biological noise, while the LCI variants may be under tighter selection and consequently their distinct 3′ UTR isoforms are more likely to have functional consequences. Supporting this notion, we found that LCI genes have significantly more miRNA binding sites, more correlated expression profiles with those of their targeting miRNAs and a relative lack of correspondence between their transcription and protein abundances. Collectively, our results suggest that a lack of coherence among the regulation of 3′ UTR isoforms is a proxy for selective pressures acting upon APA usage and consequently for their functional relevance.
Collapse
Affiliation(s)
- Michal Levin
- Quantitative Proteomics, Institute of Molecular Biology, Mainz 55128, Germany
| | - Harel Zalts
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Natalia Mostov
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Itai Yanai
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York 10016, USA
| |
Collapse
|
28
|
Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020; 21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
Collapse
Affiliation(s)
- Boris Slobodin
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Rivka Dikstein
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| |
Collapse
|
29
|
Abstract
Aminoacyl-tRNA synthetases (ARSs) are a family of essential "housekeeping" enzymes ubiquitous in the three major domains of life. ARSs uniquely connect the essential minimal units of both major oligomer classes-the 3-nucleotide codons of oligonucleotides and the amino acids of proteins. They catalyze the esterification of amino acids to the 3'-end of cognate transfer RNAs (tRNAs) bearing the correct anticodon triplet to ensure accurate transfer of information from mRNA to protein according to the genetic code. As an essential translation factor responsible for the first biochemical reaction in protein biosynthesis, ARSs control protein production by catalyzing aminoacylation, and by editing of mischarged aminoacyl-tRNAs to maintain translational fidelity. In addition to their primary enzymatic activities, many ARSs have noncanonical functions unrelated to their catalytic activity in protein synthesis. Among the ARSs with "moonlighting" activities, several, including GluProRS (or EPRS), LeuRS, LysRS, SerRS, TyrRS, and TrpRS, exhibit cell signaling-related activities that sense environmental signals, regulate gene expression, and modulate cellular functions. ARS signaling functions generally depend on catalytically-inactive, appended domains not present in ancient enzyme forms, and are activated by stimulus-dependent post-translational modification. Activation often results in cellular re-localization and gain of new interacting partners. The newly formed ARS-bearing complexes conduct a host of signal transduction functions, including immune response, mTORC1 pathway signaling, and fibrogenic and angiogenic signaling, among others. Because noncanonical functions of ARSs in signal transduction are uncoupled from canonical aminoacylation functions, function-specific inhibitors can be developed, thus providing promising opportunities and therapeutic targets for treatment of human disease.
Collapse
Affiliation(s)
- Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine and Department of Biochemistry & Biophysics, The Center for RNA Biology, The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, United States.
| | - Paul L Fox
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States.
| |
Collapse
|
30
|
The Complex Relationship between HTLV-1 and Nonsense-Mediated mRNA Decay (NMD). Pathogens 2020; 9:pathogens9040287. [PMID: 32326562 PMCID: PMC7238105 DOI: 10.3390/pathogens9040287] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Accepted: 04/12/2020] [Indexed: 02/07/2023] Open
Abstract
Before the establishment of an adaptive immune response, retroviruses can be targeted by several cellular host factors at different stages of the viral replication cycle. This intrinsic immunity relies on a large diversity of antiviral processes. In the case of HTLV-1 infection, these active innate host defense mechanisms are debated. Among these mechanisms, we focused on an RNA decay pathway called nonsense-mediated mRNA decay (NMD), which can target multiple viral RNAs, including HTLV-1 unspliced RNA, as has been recently demonstrated. NMD is a co-translational process that depends on the RNA helicase UPF1 and regulates the expression of multiple types of host mRNAs. RNA sensitivity to NMD depends on mRNA organization and the ribonucleoprotein (mRNP) composition. HTLV-1 has evolved several means to evade the NMD threat, leading to NMD inhibition. In the early steps of infection, NMD inhibition favours the production of HTLV-1 infectious particles, which may contribute to the survival of the fittest clones despite genome instability; however, its direct long-term impact remains to be investigated.
Collapse
|
31
|
Menendez-Gil P, Caballero CJ, Catalan-Moreno A, Irurzun N, Barrio-Hernandez I, Caldelari I, Toledo-Arana A. Differential evolution in 3'UTRs leads to specific gene expression in Staphylococcus. Nucleic Acids Res 2020; 48:2544-2563. [PMID: 32016395 PMCID: PMC7049690 DOI: 10.1093/nar/gkaa047] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 12/05/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
The evolution of gene expression regulation has contributed to species differentiation. The 3' untranslated regions (3'UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3'UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3'UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3'UTR of orthologous genes and demonstrated that 3'UTR sequence variations affect protein production. This suggested that species-specific functional 3'UTRs might be specifically selected during evolution. 3'UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3'UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3'UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3'UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.
Collapse
Affiliation(s)
- Pilar Menendez-Gil
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Carlos J Caballero
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Arancha Catalan-Moreno
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Naiara Irurzun
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000-Strasbourg, France
| | - Alejandro Toledo-Arana
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| |
Collapse
|
32
|
Woo YM, Kwak Y, Namkoong S, Kristjánsdóttir K, Lee SH, Lee JH, Kwak H. TED-Seq Identifies the Dynamics of Poly(A) Length during ER Stress. Cell Rep 2019; 24:3630-3641.e7. [PMID: 30257221 DOI: 10.1016/j.celrep.2018.08.084] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 07/02/2018] [Accepted: 08/28/2018] [Indexed: 12/31/2022] Open
Abstract
Post-transcriptional RNA processing is a core mechanism of gene expression control in cell stress response. The poly(A) tail influences mRNA translation and stability, but it is unclear whether there are global roles of poly(A)-tail lengths in cell stress. To address this, we developed tail-end displacement sequencing (TED-seq) for an efficient transcriptome-wide profiling of poly(A) lengths and applied it to endoplasmic reticulum (ER) stress in human cells. ER stress induced increases in the poly(A) lengths of certain mRNAs, including known ER stress regulators, XBP1, DDIT3, and HSPA5. Importantly, the mRNAs with increased poly(A) lengths are both translationally de-repressed and stabilized. Furthermore, mRNAs in stress-induced RNA granules have shorter poly(A) tails than in the cytoplasm, supporting the view that RNA processing is compartmentalized. In conclusion, TED-seq reveals that poly(A) length is dynamically regulated upon ER stress, with potential consequences for both translation and mRNA turnover.
Collapse
Affiliation(s)
- Yu Mi Woo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Yeonui Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sim Namkoong
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katla Kristjánsdóttir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seung Ha Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
33
|
Venkata Subbaiah KC, Hedaya O, Wu J, Jiang F, Yao P. Mammalian RNA switches: Molecular rheostats in gene regulation, disease, and medicine. Comput Struct Biotechnol J 2019; 17:1326-1338. [PMID: 31741723 PMCID: PMC6849081 DOI: 10.1016/j.csbj.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 01/12/2023] Open
Abstract
Alteration of RNA structure by environmental signals is a fundamental mechanism of gene regulation. For example, the riboswitch is a noncoding RNA regulatory element that binds a small molecule and causes a structural change in the RNA, thereby regulating transcription, splicing, or translation of an mRNA. The role of riboswitches in metabolite sensing and gene regulation in bacteria and other lower species was reported almost two decades ago, but riboswitches have not yet been discovered in mammals. An analog of the riboswitch, the protein-directed RNA switch (PDRS), has been identified as an important regulatory mechanism of gene expression in mammalian cells. RNA-binding proteins and microRNAs are two major executors of PDRS via their interaction with target transcripts in mammals. These protein-RNA interactions influence cellular functions by integrating environmental signals and intracellular pathways from disparate stimuli to modulate stability or translation of specific mRNAs. The discovery of a riboswitch in eukaryotes that is composed of a single class of thiamine pyrophosphate (TPP) suggests that additional ligand-sensing RNAs may be present to control eukaryotic or mammalian gene expression. In this review, we focus on protein-directed RNA switch mechanisms in mammals. We offer perspectives on the potential discovery of mammalian protein-directed and compound-dependent RNA switches that are related to human disease and medicine.
Collapse
Affiliation(s)
- Kadiam C Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Omar Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| |
Collapse
|
34
|
Dvorak P, Leupen S, Soucek P. Functionally Significant Features in the 5' Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates. Cells 2019; 8:cells8060623. [PMID: 31234415 PMCID: PMC6627321 DOI: 10.3390/cells8060623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023] Open
Abstract
Single nucleotide polymorphisms located in 5′ untranslated regions (5′UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5′UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5′UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5′UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5′UTRs, such as GC content variation, hairpin structure conservation or 5′UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.
Collapse
Affiliation(s)
- Pavel Dvorak
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
| | - Sarah Leupen
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
- Toxicogenomics Unit, National Institute of Public Health, Srobarova 48, 100 42 Prague 10, Czech Republic.
| |
Collapse
|
35
|
de la Peña JBI, Song JJ, Campbell ZT. RNA control in pain: Blame it on the messenger. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1546. [PMID: 31090211 DOI: 10.1002/wrna.1546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/17/2019] [Accepted: 04/22/2019] [Indexed: 12/12/2022]
Abstract
mRNA function is meticulously controlled. We provide an overview of the integral role that posttranscriptional controls play in the perception of painful stimuli by sensory neurons. These specialized cells, termed nociceptors, precisely regulate mRNA polarity, translation, and stability. A growing body of evidence has revealed that targeted disruption of mRNAs and RNA-binding proteins robustly diminishes pain-associated behaviors. We propose that the use of multiple independent regulatory paradigms facilitates robust temporal and spatial precision of protein expression in response to a range of pain-promoting stimuli. This article is categorized under: RNA in Disease and Development > RNA in Disease Translation > Translation Regulation RNA Turnover and Surveillance > Regulation of RNA Stability.
Collapse
Affiliation(s)
- June Bryan I de la Peña
- Department of Biological Sciences and the Center for Advanced Pain Studies, University of Texas, Dallas, Richardson, Texas
| | - Jane J Song
- Department of Biological Sciences and the Center for Advanced Pain Studies, University of Texas, Dallas, Richardson, Texas
| | - Zachary T Campbell
- Department of Biological Sciences and the Center for Advanced Pain Studies, University of Texas, Dallas, Richardson, Texas
| |
Collapse
|
36
|
Tooth agenesis-related GLI2 and GLI3 genes may contribute to craniofacial skeletal morphology in humans. Arch Oral Biol 2019; 103:12-18. [PMID: 31112935 DOI: 10.1016/j.archoralbio.2019.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/03/2019] [Accepted: 05/09/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The present cross-sectional, multi-centre, genetic study aimed to determine, whether single nucleotide polymorphisms (SNPs) in tooth agenesis (TA)-associated GLI2 and GLI3 genes contribute to the development of craniofacial skeletal morphology in humans. DESIGN Orthodontic patients from an ethnically heterogeneous population were selected for the present study (n = 594). The presence or absence of TA was determined by analysis of panoramic radiography and dental records. The subjects were classified according to their skeletal malocclusion and facial growth pattern by means of digital cephalometric analysis. Genomic DNA was extracted from squamous epithelial cells of the buccal mucosa and SNPs in GLI2 (rs3738880, rs2278741) and GLI3 (rs929387, rs846266) were analysed by polymerase chain reaction using TaqMan chemistry and end-point analysis. RESULTS Class II skeletal malocclusion presented a significantly lower frequency of TA (P < 0.05). Subjects without TA showed significantly higher ANB angles (P < 0.05). Genotype and/or allele distributions of the SNPs in GLI2 (rs3738880, rs2278741) and GLI3 (rs846266) were associated with the presence of TA (P < 0.05). The SNPs rs3738880, rs2278741 and rs929387 were also associated with some type of skeletal malocclusion (P < 0.05), but not with the facial growth pattern (P > 0.05). The G allele for TA-related GLI2 rs3738880 was strongly linked to the presence of Class III skeletal malocclusion (OR = 2.03; 95% CI = 1.37-3.03; P<3125 × 10-6). GLI2 rs2278741 C allele was overrepresented in individuals without TA, suggesting it as a protective factor for this dental phenotype (OR = 0.43; 95% CI = 0.24-0.78; P<625 × 10-5). CONCLUSION The present study suggests that SNPs in TA-associated GLI2 and GLI3 genes may also play a role in the development of skeletal malocclusions. rs3738880 and rs2278741 in GLI2 seems to contribute to the genetic background for skeletal Class III and TA, respectively. TA could be an additional predictor of craniofacial morphology in some cases. Further research replicating the reported associations should be performed.
Collapse
|
37
|
Zhang LS, Liu C, Ma H, Dai Q, Sun HL, Luo G, Zhang Z, Zhang L, Hu L, Dong X, He C. Transcriptome-wide Mapping of Internal N 7-Methylguanosine Methylome in Mammalian mRNA. Mol Cell 2019; 74:1304-1316.e8. [PMID: 31031084 DOI: 10.1016/j.molcel.2019.03.036] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 02/26/2019] [Accepted: 03/27/2019] [Indexed: 01/05/2023]
Abstract
N7-methylguanosine (m7G) is a positively charged, essential modification at the 5' cap of eukaryotic mRNA, regulating mRNA export, translation, and splicing. m7G also occurs internally within tRNA and rRNA, but its existence and distribution within eukaryotic mRNA remain to be investigated. Here, we show the presence of internal m7G sites within mammalian mRNA. We then performed transcriptome-wide profiling of internal m7G methylome using m7G-MeRIP sequencing (MeRIP-seq). To map this modification at base resolution, we developed a chemical-assisted sequencing approach that selectively converts internal m7G sites into abasic sites, inducing misincorporation at these sites during reverse transcription. This base-resolution m7G-seq enabled transcriptome-wide mapping of m7G in human tRNA and mRNA, revealing distribution features of the internal m7G methylome in human cells. We also identified METTL1 as a methyltransferase that installs a subset of m7G within mRNA and showed that internal m7G methylation could affect mRNA translation.
Collapse
Affiliation(s)
- Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Chang Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Honghui Ma
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qing Dai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Hui-Lung Sun
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Guanzheng Luo
- The State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Zijie Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Linda Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Lulu Hu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Xueyang Dong
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
38
|
Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation. Sci Rep 2019; 9:6127. [PMID: 30992521 PMCID: PMC6467909 DOI: 10.1038/s41598-019-42511-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/02/2019] [Indexed: 01/05/2023] Open
Abstract
Leishmania donovani is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of L. donovani is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an L. donovani genome attained to date. The use of a combination of sequencing platforms enabled to assemble, without any sequence gap, the 36 chromosomes for this species. Additionally, based on this assembly and using RNA-seq reads derived from poly-A + RNA, the transcriptome for this species, not yet available, was delineated. Alternative SL addition sites and heterogeneity in the poly-A addition sites were commonly observed for most of the genes. After a complete annotation of the transcriptome, 2,410 novel transcripts were defined. Additionally, the relative expression for all transcripts present in the promastigote stage was determined. Events of cis-splicing have been documented to occur during the maturation of the transcripts derived from genes LDHU3_07.0430 and LDHU3_29.3990. The complete genome assembly and the availability of the gene models (including annotation of untranslated regions) are important pieces to understand how differential gene expression occurs in this pathogen, and to decipher phenotypic peculiarities like tissue tropism, clinical disease, and drug susceptibility.
Collapse
|
39
|
Murai K, Honda M, Shirasaki T, Shimakami T, Omura H, Misu H, Kita Y, Takeshita Y, Ishii KA, Takamura T, Urabe T, Shimizu R, Okada H, Yamashita T, Sakai Y, Kaneko S. Induction of Selenoprotein P mRNA during Hepatitis C Virus Infection Inhibits RIG-I-Mediated Antiviral Immunity. Cell Host Microbe 2019; 25:588-601.e7. [PMID: 30974086 DOI: 10.1016/j.chom.2019.02.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 12/13/2017] [Accepted: 02/26/2019] [Indexed: 12/16/2022]
Abstract
Patients infected with hepatitis C virus (HCV) have an increased risk of developing type 2 diabetes. HCV infection is linked to various liver abnormalities, potentially contributing to this association. We show that HCV infection increases the levels of hepatic selenoprotein P (SeP) mRNA (SEPP1 mRNA) and serum SeP, a hepatokine linked to insulin resistance. SEPP1 mRNA inhibits type I interferon responses by limiting the function of retinoic-acid-inducible gene I (RIG-I), a sensor of viral RNA. SEPP1 mRNA binds directly to RIG-I and inhibits its activity. SEPP1 mRNA knockdown in hepatocytes causes a robust induction of interferon-stimulated genes and decreases HCV replication. Clinically, high SeP serum levels are significantly associated with treatment failure of direct-acting antivirals in HCV-infected patients. Thus, SeP regulates insulin resistance and innate immunity, possibly inducing immune tolerance in the liver, and its upregulation may explain the increased risk of type 2 diabetes in HCV-infected patients.
Collapse
Affiliation(s)
- Kazuhisa Murai
- Department of Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Japan
| | - Masao Honda
- Department of Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Japan; Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan.
| | - Takayoshi Shirasaki
- Department of Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Japan
| | - Tetsuro Shimakami
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Hitoshi Omura
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Hirofumi Misu
- Department of Endocrinology and Metabolism, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Yuki Kita
- Department of Endocrinology and Metabolism, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Yumie Takeshita
- Department of Endocrinology and Metabolism, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Kiyo-Aki Ishii
- Department of Endocrinology and Metabolism, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Toshinari Takamura
- Department of Endocrinology and Metabolism, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Takeshi Urabe
- Public Central Hospital of Matto Ishikawa, Hakusan, Ishikawa, Japan
| | - Ryogo Shimizu
- Department of Laboratory Medicine, Kanazawa University Graduate School of Health Medicine, Kanazawa, Japan
| | - Hikari Okada
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Taro Yamashita
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Yoshio Sakai
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| |
Collapse
|
40
|
Yun D, Wang H, Wang Y, Chen Y, Zhao Z, Ma J, Ji Y, Huang Q, Chen J, Chen H, Lu D. Shuttling SLC2A4RG is regulated by 14-3-3θ to modulate cell survival via caspase-3 and caspase-6 in human glioma. EBioMedicine 2019; 40:163-175. [PMID: 30686753 PMCID: PMC6413354 DOI: 10.1016/j.ebiom.2019.01.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 12/27/2022] Open
Abstract
Background Glioma is the most common and aggressive primary brain tumor with polygenic susceptibility. The cytoplasmic/nuclear shuttling protein, SLC2A4RG (SLC2A4 regulator), has been identified in the 20q13.33 region influencing glioma susceptibility by genome-wide association studies (GWAS) and fine mapping analyses. Methods To discover the expression of SLC2A4RG and its relationship with patient prognosis, tissue microarray containing glioma samples and normal brains was constructed followed by immunohistochemical staining. The role of SLC2A4RG on cell proliferation, cell cycle, and apoptosis was evaluated by gain- and loss-of-function assays in vivo, and subcutaneous and intracranial xenografts were performed to assess its functional effects. The mechanism underlying SLC2A4RG was further investigated via luciferase reporter analyses, ChIP, mass spectrometry, Co-IP, immunofluorescence, etc. Findings The potential tumor suppressor role of SLC2A4RG was further validated by in vitro and in vivo experiments that SLC2A4RG could attenuate cell proliferation via G2/M phase arrest and induce glioma cell apoptosis by direct transactivation of caspase-3 and caspase-6. Moreover, its function displaying showed to depend on the nuclear transportation of SLC2A4RG, however, bound with 14-3-3θ, it would be sequestered in the cytoplasm followed by reversal effect. Interpretation We identify a new pro-oncogenic mechanism whereby 14-3-3θ negatively regulates the nuclear function of the tumor suppressor SLC2A4RG, with significant therapeutic implications for the intervention of human glioma. Fund This work was supported by the National Natural Science Foundation of China (81372706, 81572501, and 81372235).
Collapse
Affiliation(s)
- Dapeng Yun
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Hongxiang Wang
- Department of Neurosurgery, Shanghai Institute of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Yuqi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Yuanyuan Chen
- Department of Critical Care Medicine, Wuxi No'2 People's Hospital, Wuxi, Jiangsu Province, China
| | - Zhipeng Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Jiawei Ma
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yuanyuan Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Qilin Huang
- Department of Neurosurgery, Shanghai Institute of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Juxiang Chen
- Department of Neurosurgery, Shanghai Institute of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Hongyan Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, 2005 Songhu Road, Shanghai 200438, China.
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, 2005 Songhu Road, Shanghai 200438, China.
| |
Collapse
|
41
|
Abstract
BACKGROUND AND OBJECTIVE Insulin-like growth factor 1 (IGF1) gene three prime untranslated region (3'-UTR) polymorphisms have been reported to be associated with cancer risk. However, the conclusions of the relevant studies are not consistent. The present meta-analysis evaluates the relationship between IGF1 gene 3'-UTR polymorphisms (rs5742714, rs6214, and rs6220) and cancer risk. METHODS Articles regarding the relationship between IGF1 rs5742714, rs6214, and rs6220 polymorphisms and cancer risk were selected by searching the PubMed, Embase, and Web of Science databases before April 30, 2018. Altogether, we obtained 34 case-controlled studies from 20 articles, including 21,568 cases and 31,199 controls. The strength of associations was quantified using odds ratios (ORs) and the corresponding 95% confidence intervals (CIs). RESULTS In the present meta-analysis, no significant associations were detected between rs5742714, rs6214, and rs6220 and overall cancer risk. Thus, in stratified analyses, we found that rs6214 was associated with a significantly reduced risk of breast cancer under the allele, heterozygote, and dominant models (A vs G: OR, 0.94, 95% CI,0.88-1.00, P = .044; GA vs GG: OR, 0.88, 95% CI, 0.80-0.97, P = .012; AA + GA vs GG: OR, 0.89, 95% CI, 0.81-0.97, P = .011), as well as pancreatic cancer under the recessive model (AA vs GA + GG: OR, 0.68, 95% CI,0.53-0.87, P = .003). Also, rs6220 was associated with a significantly increased risk of breast cancer under the homozygote model (GG vs AA: OR, 1.23, 95% CI, 1.02-1.48, P = .031). In addition, rs6220 was found to increase overall cancer risk among Caucasians under the allele model (G vs A: OR, 1.06, 95% CI, 1.00-1.13, P = .043). CONCLUSIONS In this meta-analysis, we investigated and reviewed the relationship between IGF1 gene 3'-UTR polymorphisms (rs5742714, rs6214, and rs6220) and cancer risk based on present epidemiological studies. Further studies are needed to draw more precise conclusions in the future.
Collapse
Affiliation(s)
| | | | - Wen-Yue Xie
- Department of Oncology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | | |
Collapse
|
42
|
Meyer KD. m 6A-mediated translation regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:301-309. [PMID: 30342175 DOI: 10.1016/j.bbagrm.2018.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States of America.
| |
Collapse
|
43
|
Guo H, Zhao L, Shi B, Bao J, Zheng D, Zhou B, Shi J. GALNT5 uaRNA promotes gastric cancer progression through its interaction with HSP90. Oncogene 2018; 37:4505-4517. [PMID: 29743591 DOI: 10.1038/s41388-018-0266-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 03/23/2018] [Accepted: 03/25/2018] [Indexed: 12/24/2022]
Abstract
Recently, long noncoding RNAs (lncRNAs) have been reported to play a pivotal role in the occurrence and progression of cancer because of their unique characteristics and have therefore become an active area of cancer research. The object of this study was to screen lncRNAs that are dysregulated in gastric cancer and to investigate their potential functions. Global expression of lncRNAs in gastric cancer and adjacent normal tissues of patients was profiled using a microarray assay. We identified an lncRNA (GALNT5 uaRNA, UTR-associated RNA) that is derived from the 3'-UTR of GALNT5. This lncRNA was transcribed independently of the coding region of GALNT5 and was determined to be markedly upregulated in human gastric carcinoma relative to their corresponding normal gastric tissues by quantitative RT-PCR (qRT-PCR) analysis of tissues from 122 gastric carcinoma patients. The expression of GALNT5 uaRNA was significantly correlated with the TNM stage and with lymph node metastasis. Further results demonstrated that GALNT5 uaRNA facilitated the proliferation and migration of gastric cancer cells in vitro and promoted tumor growth in a mouse model of human gastric cancer. Our results also indicated that GALNT5 uaRNA might function in gastric cancer by binding with HSP90. Further studies indicated that the 5'-end stem-loop motifs of GALNT5 uaRNA promoted the binding of HSP90 and its client proteins, and thus inhibited ubiquitination of the clients. These results expanded our understanding of GALNT5 uaRNA as a new avenue for therapeutic intervention against gastric cancer progression.
Collapse
Affiliation(s)
- Hui Guo
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Lianmei Zhao
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Research Center, the Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Bianhua Shi
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Jiayu Bao
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Dexian Zheng
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Baoguo Zhou
- Department of General Surgery, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China.
| | - Juan Shi
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
| |
Collapse
|
44
|
You M, Yang Y, Zhong C, Chen F, Wang X, Jia T, Chen Y, Zhou B, Mi Q, Zhao Q, An Z, Luo W, Xia N. Efficient mAb production in CHO cells with optimized signal peptide, codon, and UTR. Appl Microbiol Biotechnol 2018; 102:5953-5964. [PMID: 29740673 DOI: 10.1007/s00253-018-8986-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022]
Abstract
Antibody drugs have been used to treat a number of diseases successfully. Producing antibodies with high yield and quality is necessary for clinical applications of antibodies. For a candidate molecule, optimization of a vector to produce sufficient yield and an accurate primary structure is indispensable in the early stage of the production process development. It is especially important to maintain the fidelity of N-terminal sequence. In order to produce antibodies with a high yield and accurate N-terminal, the expression vector was systematically optimized in this study. First, the heavy chain and light chain were co-expressed in Chinese hamster ovary (CHO) cells with different signal peptides. Mass spectrometry (MS) revealed that signal peptides Esp-K, Bsp-H, and 8Hsp-H were accurately deleted from mature antibodies. Further, the yield was doubled by codon optimization and increased by 50% with the presence of untranslated regions (UTR). The combination of UTR with optimal codon and signal peptide to form an expression vector resulted in yield improvement of 150% and correct N-terminal sequences. Moreover, the main product peak was above 98% as assessed by size-exclusion chromatography (SEC). Additionally, the bioactivity of products made from optimized transient gene expression (TGE) was almost identical to the standard sample. The production efficiency and product quality from the identified TGE optimization strategy was further demonstrated through application to two other antibodies. The expression level of SGE (stable gene expression) can also be improved effectively with this optimization strategy. In conclusion, vector optimization via combination of optimized signal peptide, codon, and UTR is an alternative approach for efficient antibody production with high fidelity N-terminal sequence in CHO cells.
Collapse
Affiliation(s)
- Min You
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Yi Yang
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Chuanqi Zhong
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, 361102, China
| | - Fentian Chen
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Xin Wang
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Tianrong Jia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Yuanzhi Chen
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Bing Zhou
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Qingyu Mi
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Qinjian Zhao
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Zhiqiang An
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
- Texas Therapeutics Institute, The Brown Foundation of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Wenxin Luo
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China.
| | - Ningshao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| |
Collapse
|
45
|
Ozturk S, Uysal F. Potential roles of the poly(A)-binding proteins in translational regulation during spermatogenesis. J Reprod Dev 2018; 64:289-296. [PMID: 29780056 PMCID: PMC6105736 DOI: 10.1262/jrd.2018-026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Spermatogenesis is briefly defined as the production of mature spermatozoa from spermatogonial stem cells at the end of a strictly regulated process. It is well known that, to a large
extent, transcriptional activity ceases at mid-spermiogenesis. Several mRNAs transcribed during early stages of spermatogenesis are stored as ribonucleoproteins (RNPs). During the later
stages, translational control of these mRNAs is mainly carried out in a time dependent-manner by poly(A)-binding proteins (PABPs) in cooperation with other RNA-binding proteins and
translation-related factors. Conserved PABPs specifically bind to poly(A) tails at the 3′ ends of mRNAs to regulate their translational activity in spermatogenic cells. Studies in this field
have revealed that PABPs, particularly poly(A)-binding protein cytoplasmic 1 (Pabpc1), Pabpc2, and the embryonic poly(A)-binding protein (Epab), play roles in the translational regulation of
mRNAs required at later stages of spermatogenesis. In this review article, we evaluated the spatial and temporal expression patterns and potential functions of these PABPs in spermatogenic
cells during spermatogenesis. The probable relationship between alterations in PABP expression and the development of male infertility is also reviewed.
Collapse
Affiliation(s)
- Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey
| | - Fatma Uysal
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey
| |
Collapse
|
46
|
Jiang B, Zhao W, Shi M, Zhang J, Chen A, Ma H, Suleman M, Lin F, Zhou L, Wang J, Zhang Y, Liu M, Wen S, Ouyang C, Wang H, Huang X, Zhou H, Li Q. IDH1 Arg-132 mutant promotes tumor formation through down-regulating p53. J Biol Chem 2018; 293:9747-9758. [PMID: 29743236 DOI: 10.1074/jbc.ra117.001385] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 04/30/2018] [Indexed: 11/06/2022] Open
Abstract
Resistance to apoptosis and uncontrolled proliferation are two hallmarks of cancer cells. p53 is crucial for apoptosis triggered by a broad range of stresses and a well-known gatekeeper for neoplastic transformation. Here we show that oncogenic IDH1 R132H/R132Q mutants robustly inhibit p53 expression and such an effect is attributed to 2-HG production. Mechanistically, 2-hydroxyglutarate (2-HG) stabilizes hypoxia-inducible factor-2α, which in turn activates the expression of miR-380-5p, a characterized microRNA against p53 expression. Rescue expression of p53 can inhibit the proliferation rate and impair the resistance of apoptosis induced by doxorubicin in IDH1 R132Q mouse embryonic fibroblast cells. Furthermore, p53 protein levels correlates negatively with IDH1 R132H levels in human glioma samples. Our results thus shed a new light on how p53 is down-regulated by 2-HG and suggests that impairment of p53-mediated apoptosis contributes to the tumorigenesis driven by IDH1 mutants.
Collapse
Affiliation(s)
- Bin Jiang
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Wentao Zhao
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Minggang Shi
- the Department of Neurosurgery, Huanhu Hospital, No. 6 Jizhao Road, Jinnan District, Tianjin 30050, China, and
| | - Jia Zhang
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Ai Chen
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Huanhuan Ma
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Muhammad Suleman
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Furong Lin
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Lin Zhou
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jinyang Wang
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yan Zhang
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Mengjue Liu
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Shixiong Wen
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Cong Ouyang
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Huihui Wang
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiumin Huang
- the Department of Gynecology and Obstetrics, the Zhongshan Hospital, Xiamen University, Xiamen 361004, China
| | - Huamin Zhou
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China,
| | - Qinxi Li
- From the State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China,
| |
Collapse
|
47
|
Zhang JJ, Yano H, Sasaki T, Matsuo N, Yoshioka H. The pro-α1(V) collagen gene (Col5a1) is coordinately regulated by miR-29b with core promoter in cultured cells. Connect Tissue Res 2018; 59:263-273. [PMID: 28829698 DOI: 10.1080/03008207.2017.1370465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AIMS Col5a1 encodes the α1 chain of type V collagen, a quantitatively minor fibrillar collagen that is critical for the formation and function of the organs in the body. MicroRNAs (miRNAs) are small noncoding RNAs that posttranscriptionally regulate biological functions by binding to the 3'-untranslated region (3'UTR) of specific target mRNA. In this study, we investigated the posttranscriptional regulation of miRNAs on the Col5a1 gene expression. MATERIALS AND METHODS We cultured osteoblasts and fibroblasts of cell lines. To examine the 3'UTR activity of the Col5a1 gene, chimeric plasmids constructs containing the core promoter and 3'UTR of Col5a1 were generated and luciferase assays were performed. We also evaluated the role of miRNA using constructs that were mutated at the putative binding sites of miRNA. In addition, we evaluated the endogenous mRNA and protein, and luciferase activity of the Col5a1 gene after miRNA overexpression/knockdown or CRISPR/Cas9-induced knockout. RESULTS The luciferase assay showed a decreased activity of the 3'UTR of Col5a1 gene. However, the expression of the mutant constructs of miRNA-binding sites was restored. The overexpression of miRNA inhibited the Col5a1 gene not only with regard to the luciferase activity and endogenous mRNA but also at the protein level. In contrast, the RNAi-mediated knockdown or CRISPR/Cas9 system increased the expression of the Col5a1 gene. CONCLUSION These results provided evidence that miR-29b regulates the Col5a1 gene expression through binding to the 3'UTR, which might play an important role in the pathogenesis of disease related to bone metabolism and fibrogenic reactions.
Collapse
Affiliation(s)
- Juan Juan Zhang
- a Department of Matrix Medicine, Faculty of Medicine , Oita University , Oita , Japan
| | - Hiroyuki Yano
- b Research Promotion Institute , Oita University , Oita , Japan
| | - Takako Sasaki
- a Department of Matrix Medicine, Faculty of Medicine , Oita University , Oita , Japan
| | - Noritaka Matsuo
- a Department of Matrix Medicine, Faculty of Medicine , Oita University , Oita , Japan
| | - Hidekatsu Yoshioka
- a Department of Matrix Medicine, Faculty of Medicine , Oita University , Oita , Japan
| |
Collapse
|
48
|
Kajiwara S, Yamada R, Ogino H. Secretory Overexpression of Bacillus thermocatenulatus Lipase in Saccharomyces cerevisiae Using Combinatorial Library Strategy. Biotechnol J 2018; 13:e1700409. [PMID: 29637708 DOI: 10.1002/biot.201700409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 03/23/2018] [Indexed: 01/17/2023]
Abstract
Simple and cost-effective lipase expression host microorganisms are highly desirable. A combinatorial library strategy is used to improve the secretory expression of lipase from Bacillus thermocatenulatus (BTL2) in the culture supernatant of Saccharomyces cerevisiae. A plasmid library including expression cassettes composed of sequences encoding one of each 15 promoters, 15 secretion signals, and 15 terminators derived from yeast species, S. cerevisiae, Pichia pastoris, and Hansenula polymorpha, is constructed. The S. cerevisiae transformant YPH499/D4, comprising H. polymorpha GAP promoter, S. cerevisiae SAG1 secretion signal, and P. pastoris AOX1 terminator, is selected by high-throughput screening. This transformant expresses BTL2 extra-cellularly with a 130-fold higher than the control strain, comprising S. cerevisiae PGK1 promoter, S. cerevisiae α-factor secretion signal, and S. cerevisiae PGK1 terminator, after cultivation for 72 h. This combinatorial library strategy holds promising potential for application in the optimization of the secretory expression of proteins in yeast.
Collapse
Affiliation(s)
- Shota Kajiwara
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Ryosuke Yamada
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| |
Collapse
|
49
|
Kordaß T, Osen W, Eichmüller SB. Controlling the Immune Suppressor: Transcription Factors and MicroRNAs Regulating CD73/NT5E. Front Immunol 2018; 9:813. [PMID: 29720980 PMCID: PMC5915482 DOI: 10.3389/fimmu.2018.00813] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/04/2018] [Indexed: 01/27/2023] Open
Abstract
The NT5E (CD73) molecule represents an ecto-5′-nucleotidase expressed on the cell surface of various cell types. Hydrolyzing extracellular adenosine monophosphate into adenosine and inorganic phosphate, NT5E performs numerous homeostatic functions in healthy organs and tissues. Importantly, NT5E can act as inhibitory immune checkpoint molecule, since free adenosine generated by NT5E inhibits cellular immune responses, thereby promoting immune escape of tumor cells. MicroRNAs (miRNAs) are small non-coding RNA molecules regulating gene expression on posttranscriptional level through binding to mRNAs, resulting in translational repression or degradation of the targeted mRNA molecule. In tumor cells, miRNA expression patterns are often altered which in turn might affect NT5E surface expression and eventually influence the efficacy of antitumor immune responses. This review describes the diverse roles of NT5E, summarizes current knowledge about transcription factors controlling NT5E expression, and highlights the significance of miRNAs involved in the posttranscriptional regulation of NT5E expression.
Collapse
Affiliation(s)
- Theresa Kordaß
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, University Heidelberg, Heidelberg, Germany
| | - Wolfram Osen
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan B Eichmüller
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
50
|
Wanke KA, Devanna P, Vernes SC. Understanding Neurodevelopmental Disorders: The Promise of Regulatory Variation in the 3'UTRome. Biol Psychiatry 2018; 83:548-557. [PMID: 29289333 DOI: 10.1016/j.biopsych.2017.11.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 11/02/2017] [Accepted: 11/02/2017] [Indexed: 01/28/2023]
Abstract
Neurodevelopmental disorders have a strong genetic component, but despite widespread efforts, the specific genetic factors underlying these disorders remain undefined for a large proportion of affected individuals. Given the accessibility of exome sequencing, this problem has thus far been addressed from a protein-centric standpoint; however, protein-coding regions only make up ∼1% to 2% of the human genome. With the advent of whole genome sequencing we are in the midst of a paradigm shift as it is now possible to interrogate the entire sequence of the human genome (coding and noncoding) to fill in the missing heritability of complex disorders. These new technologies bring new challenges, as the number of noncoding variants identified per individual can be overwhelming, making it prudent to focus on noncoding regions of known function, for which the effects of variation can be predicted and directly tested to assess pathogenicity. The 3'UTRome is a region of the noncoding genome that perfectly fulfills these criteria and is of high interest when searching for pathogenic variation related to complex neurodevelopmental disorders. Herein, we review the regulatory roles of the 3'UTRome as binding sites for microRNAs or RNA binding proteins, or during alternative polyadenylation. We detail existing evidence that these regions contribute to neurodevelopmental disorders and outline strategies for identification and validation of novel putatively pathogenic variation in these regions. This evidence suggests that studying the 3'UTRome will lead to the identification of new risk factors, new candidate disease genes, and a better understanding of the molecular mechanisms contributing to neurodevelopmental disorders.
Collapse
Affiliation(s)
- Kai A Wanke
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Paolo Devanna
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands.
| |
Collapse
|