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Mohanan NK, Shaji F, Sudheesh AP, Bangalore Prabhashankar A, Sundaresan NR, Laishram RS. Star-PAP controls oncogene expression through primary miRNA 3'-end formation to regulate cellular proliferation and tumour formation. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167080. [PMID: 38364942 DOI: 10.1016/j.bbadis.2024.167080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/04/2024] [Accepted: 02/10/2024] [Indexed: 02/18/2024]
Abstract
Star-PAP is a non-canonical poly(A) polymerase that is down regulated in breast cancer. While Star-PAP down regulation impairs target mRNA polyadenylation, paradoxically, we see up regulation of a large number of oncogenes on Star-PAP knockdown. Using two breast cancer cells (MCF7 with high Star-PAP, and MDA-MB-231 with negligible Star-PAP level), we discover that Star-PAP negatively regulates oncogene expression and subsequently cellular proliferation. This regulation is compromised with Star-PAP mutant of 3'-end processing function (serine 6 to alanine, S6A phospho-mutation). Concomitantly, xenograft mice model using MDA-MB-231 cells reveals a reduction in the tumour formation on ectopic Star-PAP expression that is ameliorated by S6A mutation. We find that Star-PAP control of target oncogene expression is independent of Star-PAP-mediated alternative polyadenylation or target mRNA 3'-end formation. We demonstrate that Star-PAP regulates target oncogenes through cellular miRNAs (miR-421, miR-335, miR-424, miR-543, miR-205, miR-34a, and miR-26a) that are down regulated in breast cancer. Analysis of various steps in miRNA biogenesis pathway reveals that Star-PAP regulates 3'-end formation and synthesis of primary miRNA (host) transcripts that is dependent on S6 phosphorylation thus controlling mature miRNA generation. Using mimics and inhibitors of two target miRNAs (miR-421 and miR-424) after Star-PAP depletion in MCF7 or ectopic expression in MDA-MB-231 cells, we demonstrate that Star-PAP controls oncogene expression and cellular proliferation through targeting miRNAs that regulates tumour formation. Our study establishes a novel mechanism of oncogene expression independent of alternative polyadenylation through Star-PAP-mediated miRNA host transcript polyadenylation that regulates breast cancer progression.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; Manipal Academy of Higher Education, Manipal 576104, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; Regional Centre for Biotechnology, Faridabad 121001, India
| | - A P Sudheesh
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | | | - Nagalingam R Sundaresan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India.
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2
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Shaji F, Mohanan NK, Shahzad S, V P G, Bangalore Prabhashankar A, Sundaresan NR, Laishram RS. Proto-oncogene cSrc-mediated RBM10 phosphorylation arbitrates anti-hypertrophy gene program in the heart and controls cardiac hypertrophy. Life Sci 2024; 341:122482. [PMID: 38309577 DOI: 10.1016/j.lfs.2024.122482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/20/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
AIMS RBM10 is a well-known RNA binding protein that regulates alternative splicing in various disease states. We have shown a splicing-independent function of RBM10 that regulates heart failure. This study aims to unravel a new biological function of RBM10 phosphorylation by proto-oncogene cSrc that enables anti-hypertrophy gene program and controls cardiac hypertrophy. MATERIALS AND METHODS We employ in vitro and in vivo approaches to characterise RBM10 phosphorylation at three-tyrosine residues (Y81, Y500, and Y971) by cSrc and target mRNA regulation. We also use isoproterenol induced rat heart and cellular hypertrophy model to determine role of cSrc-mediated RBM10 phosphorylation. KEY FINDINGS We show that RBM10 phosphorylation is induced in cellular and animal heart model of cardiac hypertrophy and regulates target mRNA expression and 3'-end formation. Inhibition of cSrc kinase or mutation of the three-tyrosine phosphorylation sites to phenylalanine accentuates myocyte hypertrophy, and results in advancement and an early attainment of hypertrophy in the heart. RBM10 is down regulated in the hypertrophic myocyte and that its re-expression reverses cellular and molecular changes in the myocyte. However, in the absence of phosphorylation (cSrc inhibition or phospho-deficient mutation), restoration of endogenous RBM10 level in the hypertrophic heart or ectopic re-expression in vitro failed to reverse cardiomyocyte hypertrophy. Mechanistically, loss of RBM10 phosphorylation inhibits nuclear localisation and interaction with Star-PAP compromising anti-hypertrophy gene expression. SIGNIFICANCE Our study establishes that cSrc-mediated RBM10 phosphorylation arbitrates anti-hypertrophy gene program. We also report a new functional regulation of RBM10 by phosphorylation that is poised to control heart failure.
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Affiliation(s)
- Feba Shaji
- Rajiv Gandhi Centre for Biotechnology, Cardiovascular Diseases and Diabetes Biology Group, Thiruvananthapuram, 695014, India; Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Neeraja K Mohanan
- Rajiv Gandhi Centre for Biotechnology, Cardiovascular Diseases and Diabetes Biology Group, Thiruvananthapuram, 695014, India; Manipal Academy of Higher Education, 576104, India
| | - Sumayya Shahzad
- Rajiv Gandhi Centre for Biotechnology, Cardiovascular Diseases and Diabetes Biology Group, Thiruvananthapuram, 695014, India
| | - Gowri V P
- Rajiv Gandhi Centre for Biotechnology, Cardiovascular Diseases and Diabetes Biology Group, Thiruvananthapuram, 695014, India
| | | | | | - Rakesh S Laishram
- Rajiv Gandhi Centre for Biotechnology, Cardiovascular Diseases and Diabetes Biology Group, Thiruvananthapuram, 695014, India.
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3
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Vidalle MC, Sheth B, Fazio A, Marvi MV, Leto S, Koufi FD, Neri I, Casalin I, Ramazzotti G, Follo MY, Ratti S, Manzoli L, Gehlot S, Divecha N, Fiume R. Nuclear Phosphoinositides as Key Determinants of Nuclear Functions. Biomolecules 2023; 13:1049. [PMID: 37509085 PMCID: PMC10377365 DOI: 10.3390/biom13071049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Polyphosphoinositides (PPIns) are signalling messengers representing less than five per cent of the total phospholipid concentration within the cell. Despite their low concentration, these lipids are critical regulators of various cellular processes, including cell cycle, differentiation, gene transcription, apoptosis and motility. PPIns are generated by the phosphorylation of the inositol head group of phosphatidylinositol (PtdIns). Different pools of PPIns are found at distinct subcellular compartments, which are regulated by an array of kinases, phosphatases and phospholipases. Six of the seven PPIns species have been found in the nucleus, including the nuclear envelope, the nucleoplasm and the nucleolus. The identification and characterisation of PPIns interactor and effector proteins in the nucleus have led to increasing interest in the role of PPIns in nuclear signalling. However, the regulation and functions of PPIns in the nucleus are complex and are still being elucidated. This review summarises our current understanding of the localisation, biogenesis and physiological functions of the different PPIns species in the nucleus.
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Affiliation(s)
- Magdalena C Vidalle
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Bhavwanti Sheth
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Antonietta Fazio
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Vittoria Marvi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Leto
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Foteini-Dionysia Koufi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Neri
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Casalin
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Giulia Ramazzotti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Matilde Y Follo
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Ratti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Lucia Manzoli
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Sonakshi Gehlot
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Roberta Fiume
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
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4
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Francis N, Behera MR, Natarajan K, Laishram RS. Tyrosine phosphorylation controlled poly(A) polymerase I activity regulates general stress response in bacteria. Life Sci Alliance 2023; 6:6/3/e202101148. [PMID: 36535710 PMCID: PMC9764084 DOI: 10.26508/lsa.202101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
RNA 3'-end polyadenylation that marks transcripts for degradation is implicated in general stress response in Escherichia coli Yet, the mechanism and regulation of poly(A) polymerase I (PAPI) in stress response are obscure. We show that pcnB (that encodes PAPI)-null mutation widely stabilises stress response mRNAs and imparts cellular tolerance to multiple stresses, whereas PAPI ectopic expression renders cells stress-sensitive. We demonstrate that there is a substantial loss of PAPI activity on stress exposure that functionally phenocopies pcnB-null mutation stabilising target mRNAs. We identify PAPI tyrosine phosphorylation at the 202 residue (Y202) that is enormously enhanced on stress exposure. This phosphorylation inhibits PAPI polyadenylation activity under stress. Consequentially, PAPI phosphodeficient mutation (tyrosine 202 to phenylalanine, Y202F) fails to stimulate mRNA expression rendering cells stress-sensitive. Bacterial tyrosine kinase Wzc phosphorylates PAPI-Y202 residue, and that wzc-null mutation renders cells stress-sensitive. Accordingly, wzc-null mutation has no effect on stress sensitivity in the presence of pcnB-null or pcnB-Y202F mutation. We also establish that PAPI phosphorylation-dependent stress tolerance mechanism is distinct and operates downstream of the primary stress regulator RpoS.
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Affiliation(s)
- Nimmy Francis
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Malaya R Behera
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.,Regional Centre for Biotechnology, Faridabad, India
| | - Kathiresan Natarajan
- Transdisciplinary Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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5
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Koshre GR, Shaji F, Mohanan NK, Mohan N, Ali J, Laishram RS. Star-PAP RNA Binding Landscape Reveals Novel Role of Star-PAP in mRNA Metabolism That Requires RBM10-RNA Association. Int J Mol Sci 2021; 22:9980. [PMID: 34576144 PMCID: PMC8469156 DOI: 10.3390/ijms22189980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/08/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022] Open
Abstract
Star-PAP is a non-canonical poly(A) polymerase that selects mRNA targets for polyadenylation. Yet, genome-wide direct Star-PAP targets or the mechanism of specific mRNA recognition is still vague. Here, we employ HITS-CLIP to map the cellular Star-PAP binding landscape and the mechanism of global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP that is diminished on Star-PAP depletion. Consistent with its role in the 3'-UTR processing, we observed a high association of Star-PAP at the 3'-UTR region. Strikingly, there is an enrichment of Star-PAP at the coding region exons (CDS) in 42% of target mRNAs. We demonstrate that Star-PAP binding de-stabilises these mRNAs indicating a new role of Star-PAP in mRNA metabolism. Comparison with earlier microarray data reveals that while UTR-associated transcripts are down-regulated, CDS-associated mRNAs are largely up-regulated on Star-PAP depletion. Strikingly, the knockdown of a Star-PAP coregulator RBM10 resulted in a global loss of Star-PAP association on target mRNAs. Consistently, RBM10 depletion compromises 3'-end processing of a set of Star-PAP target mRNAs, while regulating stability/turnover of a different set of mRNAs. Our results establish a global profile of Star-PAP mRNA association and a novel role of Star-PAP in the mRNA metabolism that requires RBM10-mRNA association in the cell.
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Affiliation(s)
- Ganesh R. Koshre
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; (G.R.K.); (F.S.); (N.K.M.); (N.M.)
- Manipal Academy of Higher Education, Manipal 576104, India
| | - Feba Shaji
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; (G.R.K.); (F.S.); (N.K.M.); (N.M.)
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Neeraja K. Mohanan
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; (G.R.K.); (F.S.); (N.K.M.); (N.M.)
- Manipal Academy of Higher Education, Manipal 576104, India
| | - Nimmy Mohan
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; (G.R.K.); (F.S.); (N.K.M.); (N.M.)
| | - Jamshaid Ali
- Bioinformatics Facility, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695585, India;
| | - Rakesh S. Laishram
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; (G.R.K.); (F.S.); (N.K.M.); (N.M.)
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6
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Sudheesh AP, Mohan N, Francis N, Laishram RS, Anderson RA. Star-PAP controlled alternative polyadenylation coupled poly(A) tail length regulates protein expression in hypertrophic heart. Nucleic Acids Res 2020; 47:10771-10787. [PMID: 31598705 PMCID: PMC6847588 DOI: 10.1093/nar/gkz875] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 09/08/2019] [Accepted: 10/05/2019] [Indexed: 12/31/2022] Open
Abstract
Alternative polyadenylation (APA)-mediated 3′-untranslated region (UTR) shortening is known to increase protein expression due to the loss of miRNA regulatory sites. Yet, mRNAs with longer 3′-UTR also show enhanced protein expression. Here, we identify a mechanism by which longer transcripts generated by the distal-most APA site leads to increased protein expression compared to the shorter transcripts and the longer transcripts are positioned to regulate heart failure (HF). A Star-PAP target gene, NQO1 has three poly(A) sites (PA-sites) at the terminal exon on the pre-mRNA. Star-PAP selects the distal-most site that results in the expression of the longest isoform. We show that the NQO1 distal-specific mRNA isoform accounts for the majority of cellular NQO1 protein. Star-PAP control of the distal-specific isoform is stimulated by oxidative stress and the toxin dioxin. The longest NQO1 transcript has increased poly(A) tail (PA-tail) length that accounts for the difference in translation potentials of the three NQO1 isoforms. This mechanism is involved in the regulation of cardiac hypertrophy (CH), an antecedent condition to HF where NQO1 downregulation stems from the loss of the distal-specific transcript. The loss of NQO1 during hypertrophy was rescued by ectopic expression of the distal- but not the proximal- or middle-specific NQO1 mRNA isoforms in the presence of Star-PAP expression, and reverses molecular events of hypertrophy in cardiomyocytes.
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Affiliation(s)
- A P Sudheesh
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Nimmy Mohan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Nimmy Francis
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India
| | - Richard A Anderson
- School of Medicine and Public Health, University of Wisconsin, MD 53726, USA
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7
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Chung CZ, Jaramillo JE, Ellis MJ, Bour DYN, Seidl LE, Jo DHS, Turk MA, Mann MR, Bi Y, Haniford DB, Duennwald ML, Heinemann IU. RNA surveillance by uridylation-dependent RNA decay in Schizosaccharomyces pombe. Nucleic Acids Res 2019; 47:3045-3057. [PMID: 30715470 PMCID: PMC6451125 DOI: 10.1093/nar/gkz043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 12/14/2022] Open
Abstract
Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In this study, we investigate the prevalence and impact of uridylation-dependent RNA decay in S. pombe by transcriptionally profiling cid1 and dis3L2 deletion strains. We found that the exonuclease Dis3L2 represents a bottleneck in uridylation-dependent mRNA decay, whereas Cid1 plays a redundant role that can be complemented by other Tutases. Deletion of dis3L2 elicits a cellular stress response, upregulating transcription of genes involved in protein folding and degradation. Misfolded proteins accumulate in both deletion strains, yet only trigger a strong stress response in dis3L2 deficient cells. While a deletion of cid1 increases sensitivity to protein misfolding stress, a dis3L2 deletion showed no increased sensitivity or was even protective. We furthermore show that uridylyl- and adenylyltransferases cooperate to generate a 5'-NxAUUAAAA-3' RNA motif on dak2 mRNA. Our studies elucidate the role of uridylation-dependent RNA decay as part of a global mRNA surveillance, and we found that perturbation of this pathway leads to the accumulation of misfolded proteins and elicits cellular stress responses.
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Affiliation(s)
- Christina Z Chung
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Julia E Jaramillo
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Michael J Ellis
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Daniel Y N Bour
- Department of Pathology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Lauren E Seidl
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - David H S Jo
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Matthew A Turk
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Mitchell R Mann
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Yumin Bi
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - David B Haniford
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Martin L Duennwald
- Department of Pathology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
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8
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Chung CZ, Balasuriya N, Manni E, Liu X, Li SSC, O'Donoghue P, Heinemann IU. Gld2 activity is regulated by phosphorylation in the N-terminal domain. RNA Biol 2019; 16:1022-1033. [PMID: 31057087 DOI: 10.1080/15476286.2019.1608754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The de-regulation of microRNAs (miRNAs) is associated with multiple human diseases, yet cellular mechanisms governing miRNA abundance remain largely elusive. Human miR-122 is required for Hepatitis C proliferation, and low miR-122 abundance is associated with hepatic cancer. The adenylyltransferase Gld2 catalyses the post-transcriptional addition of a single adenine residue (A + 1) to the 3'-end of miR-122, enhancing its stability. Gld2 activity is inhibited by binding to the Hepatitis C virus core protein during HepC infection, but no other mechanisms of Gld2 regulation are known. We found that Gld2 activity is regulated by site-specific phosphorylation in its disordered N-terminal domain. We identified two phosphorylation sites (S62, S110) where phosphomimetic substitutions increased Gld2 activity and one site (S116) that markedly reduced activity. Using mass spectrometry, we confirmed that HEK 293 cells readily phosphorylate the N-terminus of Gld2. We identified protein kinase A (PKA) and protein kinase B (Akt1) as the kinases that site-specifically phosphorylate Gld2 at S116, abolishing Gld2-mediated nucleotide addition. The data demonstrate a novel phosphorylation-dependent mechanism to regulate Gld2 activity, revealing tumour suppressor miRNAs as a previously unknown target of Akt1-dependent signalling.
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Affiliation(s)
- Christina Z Chung
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | - Nileeka Balasuriya
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | - Emad Manni
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | - Xuguang Liu
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | - Shawn Shun-Cheng Li
- a Department of Biochemistry , The University of Western Ontario , London , Canada.,b Department of Oncology and Child Health Research Institute , The University of Western Ontario , London , Canada
| | - Patrick O'Donoghue
- a Department of Biochemistry , The University of Western Ontario , London , Canada.,c Department of Chemistry , The University of Western Ontario , London , Canada
| | - Ilka U Heinemann
- a Department of Biochemistry , The University of Western Ontario , London , Canada
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9
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Nomura Y, Roston D, Montemayor EJ, Cui Q, Butcher SE. Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1. Nucleic Acids Res 2018; 46:11488-11501. [PMID: 30215753 PMCID: PMC6265477 DOI: 10.1093/nar/gky812] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 01/08/2023] Open
Abstract
Post-transcriptional modification of snRNA is central to spliceosome function. Usb1 is an exoribonuclease that shortens the oligo-uridine tail of U6 snRNA, resulting in a terminal 2',3' cyclic phosphate group in most eukaryotes, including humans. Loss of function mutations in human Usb1 cause the rare disorder poikiloderma with neutropenia (PN), and result in U6 snRNAs with elongated 3' ends that are aberrantly adenylated. Here, we show that human Usb1 removes 3' adenosines with 20-fold greater efficiency than uridines, which explains the presence of adenylated U6 snRNAs in cells lacking Usb1. We determined three high-resolution co-crystal structures of Usb1: wild-type Usb1 bound to the substrate analog adenosine 5'-monophosphate, and an inactive mutant bound to RNAs with a 3' terminal adenosine and uridine. These structures, along with QM/MM MD simulations of the catalytic mechanism, illuminate the molecular basis for preferential deadenylation of U6 snRNA. The extent of Usb1 processing is influenced by the secondary structure of U6 snRNA.
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Affiliation(s)
- Yuichiro Nomura
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Daniel Roston
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Eric J Montemayor
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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10
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Yashiro Y, Tomita K. Function and Regulation of Human Terminal Uridylyltransferases. Front Genet 2018; 9:538. [PMID: 30483311 PMCID: PMC6240794 DOI: 10.3389/fgene.2018.00538] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/24/2018] [Indexed: 11/21/2022] Open
Abstract
RNA uridylylation plays a pivotal role in the biogenesis and metabolism of functional RNAs, and regulates cellular gene expression. RNA uridylylation is catalyzed by a subset of proteins from the non-canonical terminal nucleotidyltransferase family. In human, three proteins (TUT1, TUT4, and TUT7) have been shown to exhibit template-independent uridylylation activity at 3′-end of specific RNAs. TUT1 catalyzes oligo-uridylylation of U6 small nuclear (sn) RNA, which catalyzes mRNA splicing. Oligo-uridylylation of U6 snRNA is required for U6 snRNA maturation, U4/U6-di-snRNP formation, and U6 snRNA recycling during mRNA splicing. TUT4 and TUT7 catalyze mono- or oligo-uridylylation of precursor let-7 (pre–let-7). Let-7 RNA is broadly expressed in somatic cells and regulates cellular proliferation and differentiation. Mono-uridylylation of pre–let-7 by TUT4/7 promotes subsequent Dicer processing to up-regulate let-7 biogenesis. Oligo-uridylylation of pre–let-7 by TUT4/7 is dependent on an RNA-binding protein, Lin28. Oligo-uridylylated pre–let-7 is less responsive to processing by Dicer and degraded by an exonuclease DIS3L2. As a result, let-7 expression is repressed. Uridylylation of pre–let-7 depends on the context of the 3′-region of pre–let-7 and cell type. In this review, we focus on the 3′ uridylylation of U6 snRNA and pre-let-7, and describe the current understanding of mechanism of activity and regulation of human TUT1 and TUT4/7, based on their crystal structures that have been recently solved.
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Affiliation(s)
- Yuka Yashiro
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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11
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Mohan N, Kumar V, Kandala DT, Kartha CC, Laishram RS. A Splicing-Independent Function of RBM10 Controls Specific 3′ UTR Processing to Regulate Cardiac Hypertrophy. Cell Rep 2018; 24:3539-3553. [DOI: 10.1016/j.celrep.2018.08.077] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/09/2018] [Accepted: 08/24/2018] [Indexed: 10/28/2022] Open
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12
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Jiang S, Zhang M, Sun J, Yang X. Casein kinase 1α: biological mechanisms and theranostic potential. Cell Commun Signal 2018; 16:23. [PMID: 29793495 PMCID: PMC5968562 DOI: 10.1186/s12964-018-0236-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/16/2018] [Indexed: 02/07/2023] Open
Abstract
Casein kinase 1α (CK1α) is a multifunctional protein belonging to the CK1 protein family that is conserved in eukaryotes from yeast to humans. It regulates signaling pathways related to membrane trafficking, cell cycle progression, chromosome segregation, apoptosis, autophagy, cell metabolism, and differentiation in development, circadian rhythm, and the immune response as well as neurodegeneration and cancer. Given its involvement in diverse cellular, physiological, and pathological processes, CK1α is a promising therapeutic target. In this review, we summarize what is known of the biological functions of CK1α, and provide an overview of existing challenges and potential opportunities for advancing theranostics.
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Affiliation(s)
- Shaojie Jiang
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Zhejiang, 310016, Hangzhou, China
| | - Miaofeng Zhang
- Department of Orthopaedics, Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, 310009, Hangzhou, China
| | - Jihong Sun
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Zhejiang, 310016, Hangzhou, China
| | - Xiaoming Yang
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Zhejiang, 310016, Hangzhou, China. .,Image-Guided Bio-Molecular Intervention Research, Department of Radiology, University of Washington School of Medicine, Seattle, WA, 98109, USA.
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13
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Nuclear Phosphatidylinositol-Phosphate Type I Kinase α-Coupled Star-PAP Polyadenylation Regulates Cell Invasion. Mol Cell Biol 2018; 38:MCB.00457-17. [PMID: 29203642 PMCID: PMC5809686 DOI: 10.1128/mcb.00457-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/27/2017] [Indexed: 01/15/2023] Open
Abstract
Star-PAP, a nuclear phosphatidylinositol (PI) signal-regulated poly(A) polymerase (PAP), couples with type I PI phosphate kinase α (PIPKIα) and controls gene expression. We show that Star-PAP and PIPKIα together regulate 3′-end processing and expression of pre-mRNAs encoding key anti-invasive factors (KISS1R, CDH1, NME1, CDH13, FEZ1, and WIF1) in breast cancer. Consistently, the endogenous Star-PAP level is negatively correlated with the cellular invasiveness of breast cancer cells. While silencing Star-PAP or PIPKIα increases cellular invasiveness in low-invasiveness MCF7 cells, Star-PAP overexpression decreases invasiveness in highly invasive MDA-MB-231 cells in a cellular Star-PAP level-dependent manner. However, expression of the PIPKIα-noninteracting Star-PAP mutant or the phosphodeficient Star-PAP (S6A mutant) has no effect on cellular invasiveness. These results strongly indicate that PIPKIα interaction and Star-PAP S6 phosphorylation are required for Star-PAP-mediated regulation of cancer cell invasion and give specificity to target anti-invasive gene expression. Our study establishes Star-PAP–PIPKIα-mediated 3′-end processing as a key anti-invasive mechanism in breast cancer.
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14
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Yamashita S, Takagi Y, Nagaike T, Tomita K. Crystal structures of U6 snRNA-specific terminal uridylyltransferase. Nat Commun 2017; 8:15788. [PMID: 28589955 PMCID: PMC5467268 DOI: 10.1038/ncomms15788] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/27/2017] [Indexed: 02/06/2023] Open
Abstract
The terminal uridylyltransferase, TUT1, builds or repairs the 3′-oligo-uridylylated tail of U6 snRNA. The 3′-oligo-uridylylated tail is the Lsm-binding site for U4/U6 di-snRNP formation and U6 snRNA recycling for pre-mRNA splicing. Here, we report crystallographic and biochemical analyses of human TUT1, which revealed the mechanisms for the specific uridylylation of the 3′-end of U6 snRNA by TUT1. The O2 and O4 atoms of the UTP base form hydrogen bonds with the conserved His and Asn in the catalytic pocket, respectively, and TUT1 preferentially incorporates UMP onto the 3′-end of RNAs. TUT1 recognizes the entire U6 snRNA molecule by its catalytic domains, N-terminal RNA-recognition motifs and a previously unidentified C-terminal RNA-binding domain. Each domain recognizes specific regions within U6 snRNA, and the recognition is coupled with the domain movements and U6 snRNA structural changes. Hence, TUT1 functions as the U6 snRNA-specific terminal uridylyltransferase required for pre-mRNA splicing. After transcription the 3′-end of U6 snRNA is oligo-uridylylated by the terminal uridylyltransferase TUT1. Here the authors present the crystal structure of human TUT1 and give insights into the mechanism of 3′-end uridylylation by the enzyme.
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Affiliation(s)
- Seisuke Yamashita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Yuko Takagi
- National Institute of Advanced Industrial Science and Technology, Biomedical Research Institute, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Takashi Nagaike
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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15
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Chung CZ, Seidl LE, Mann MR, Heinemann IU. Tipping the balance of RNA stability by 3' editing of the transcriptome. Biochim Biophys Acta Gen Subj 2017; 1861:2971-2979. [PMID: 28483641 DOI: 10.1016/j.bbagen.2017.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/02/2017] [Indexed: 11/26/2022]
Abstract
BACKGROUND The regulation of active microRNAs (miRNAs) and maturation of messenger RNAs (mRNAs) that are competent for translation is a crucial point in the control of all cellular processes, with established roles in development and differentiation. Terminal nucleotidyltransferases (TNTases) are potent regulators of RNA metabolism. TNTases promote the addition of single or multiple nucleotides to an RNA transcript that can rapidly alter transcript stability. The well-known polyadenylation promotes transcript stability while the newly discovered but ubiquitious 3'-end polyuridylation marks RNA for degradation. Monoadenylation and uridylation are essential control mechanisms balancing mRNA and miRNA homeostasis. SCOPE OF REVIEW This review discusses the multiple functions of non-canonical TNTases, focusing on their substrate range, biological functions, and evolution. TNTases directly control mRNA and miRNA levels, with diverse roles in transcriptome stabilization, maturation, silencing, or degradation. We will summarize the current state of knowledge on non-canonical nucleotidyltransferases and their function in regulating miRNA and mRNA metabolism. We will review the discovery of uridylation as an RNA degradation pathway and discuss the evolution of nucleotidyltransferases along with their use in RNA labeling and future applications as therapeutic targets. MAJOR CONCLUSIONS The biochemically and evolutionarily highly related adenylyl- and uridylyltransferases play antagonizing roles in the cell. In general, RNA adenylation promotes stability, while uridylation marks RNA for degradation. Uridylyltransferases evolved from adenylyltransferases in multiple independent evolutionary events by the insertion of a histidine residue into the active site, altering nucleotide, but not RNA specificity. GENERAL SIGNIFICANCE Understanding the mechanisms regulating RNA stability in the cell and controlling the transcriptome is essential for efforts aiming to influence cellular fate. Selectively enhancing or reducing RNA stability allows for alterations in the transcriptome, proteome, and downstream cellular processes. Genetic, biochemical, and clinical data suggest TNTases are potent targets for chemotherapeutics and have been exploited for RNA labeling applications. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Christina Z Chung
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Lauren E Seidl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Mitchell R Mann
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
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16
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Haas G, Cetin S, Messmer M, Chane-Woon-Ming B, Terenzi O, Chicher J, Kuhn L, Hammann P, Pfeffer S. Identification of factors involved in target RNA-directed microRNA degradation. Nucleic Acids Res 2016; 44:2873-87. [PMID: 26809675 PMCID: PMC4824107 DOI: 10.1093/nar/gkw040] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 01/13/2016] [Indexed: 12/18/2022] Open
Abstract
The mechanism by which micro (mi)RNAs control their target gene expression is now well understood. It is however less clear how the level of miRNAs themselves is regulated. Under specific conditions, abundant and highly complementary target RNA can trigger miRNA degradation by a mechanism involving nucleotide addition and exonucleolytic degradation. One such mechanism has been previously observed to occur naturally during viral infection. To date, the molecular details of this phenomenon are not known. We report here that both the degree of complementarity and the ratio of miRNA/target abundance are crucial for the efficient decay of the small RNA. Using a proteomic approach based on the transfection of biotinylated antimiRNA oligonucleotides, we set to identify the factors involved in target-mediated miRNA degradation. Among the retrieved proteins, we identified members of the RNA-induced silencing complex, but also RNA modifying and degradation enzymes. We further validate and characterize the importance of one of these, the Perlman Syndrome 3′-5′ exonuclease DIS3L2. We show that this protein interacts with Argonaute 2 and functionally validate its role in target-directed miRNA degradation both by artificial targets and in the context of mouse cytomegalovirus infection.
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Affiliation(s)
- Gabrielle Haas
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Semih Cetin
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Mélanie Messmer
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Béatrice Chane-Woon-Ming
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Olivier Terenzi
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Johana Chicher
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Lauriane Kuhn
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Philippe Hammann
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Sébastien Pfeffer
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
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17
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Kandala DT, Mohan N, A V, A P S, G R, Laishram RS. CstF-64 and 3'-UTR cis-element determine Star-PAP specificity for target mRNA selection by excluding PAPα. Nucleic Acids Res 2015; 44:811-23. [PMID: 26496945 PMCID: PMC4737136 DOI: 10.1093/nar/gkv1074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/06/2015] [Indexed: 01/02/2023] Open
Abstract
Almost all eukaryotic mRNAs have a poly (A) tail at the 3′-end. Canonical PAPs (PAPα/γ) polyadenylate nuclear pre-mRNAs. The recent identification of the non-canonical Star-PAP revealed specificity of nuclear PAPs for pre-mRNAs, yet the mechanism how Star-PAP selects mRNA targets is still elusive. Moreover, how Star-PAP target mRNAs having canonical AAUAAA signal are not regulated by PAPα is unclear. We investigate specificity mechanisms of Star-PAP that selects pre-mRNA targets for polyadenylation. Star-PAP assembles distinct 3′-end processing complex and controls pre-mRNAs independent of PAPα. We identified a Star-PAP recognition nucleotide motif and showed that suboptimal DSE on Star-PAP target pre-mRNA 3′-UTRs inhibit CstF-64 binding, thus preventing PAPα recruitment onto it. Altering 3′-UTR cis-elements on a Star-PAP target pre-mRNA can switch the regulatory PAP from Star-PAP to PAPα. Our results suggest a mechanism of poly (A) site selection that has potential implication on the regulation of alternative polyadenylation.
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Affiliation(s)
- Divya T Kandala
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Nimmy Mohan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Vivekanand A
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Sudheesh A P
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Reshmi G
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Rakesh S Laishram
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
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