1
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Neumann DP, Pillman KA, Dredge BK, Bert AG, Phillips CA, Lumb R, Ramani Y, Bracken CP, Hollier BG, Selth LA, Beilharz TH, Goodall GJ, Gregory PA. The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking. RNA Biol 2024; 21:1-11. [PMID: 38112323 PMCID: PMC10732628 DOI: 10.1080/15476286.2023.2294222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. Using 3' end anchored RNA sequencing, we mapped the alternative polyadenylation (APA) landscape following Transforming Growth Factor (TGF)-β-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3'UTR lengthening during this cell state transition. Investigation of potential mediators of APA indicated the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, regulates a subset of events including the length of its own transcript. Analysis of QKI crosslinked immunoprecipitation (CLIP)-sequencing data identified the binding of QKI within 3' untranslated regions (UTRs) was enriched near cleavage and polyadenylation sites. Following QKI knockdown, APA of many transcripts is altered to produce predominantly shorter 3'UTRs associated with reduced gene expression. These findings reveal the changes in APA that occur during EMT and identify a potential role for QKI in this process.
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Affiliation(s)
- Daniel P. Neumann
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Katherine A. Pillman
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - B. Kate Dredge
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Andrew G. Bert
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Caroline A. Phillips
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Rachael Lumb
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Yesha Ramani
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Cameron P. Bracken
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Brett G. Hollier
- Australian Prostate Cancer Research Centre - Queensland, Centre for Genomics and Personalised Health, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Luke A. Selth
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Traude H. Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Gregory J. Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Philip A. Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
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2
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McCrory C, Verma J, Tucey TM, Turner R, Weerasinghe H, Beilharz TH, Traven A. The short-chain fatty acid crotonate reduces invasive growth and immune escape of Candida albicans by regulating hyphal gene expression. mBio 2023; 14:e0260523. [PMID: 37929941 PMCID: PMC10746253 DOI: 10.1128/mbio.02605-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Microbes are exposed to nutritional and stress challenges in their environmental and host niches. To rise to these challenges, they regulate transcriptional programs that enable cellular adaptation. For instance, metabolite concentrations regulate post-translational modifications of chromatin, such as histone acetylation. In this way, metabolic signals are integrated with transcription. Over the last decade, several histone acylations have been discovered, including histone crotonylation. Their roles in microbial biology, environmental adaptation, and microbe-host interactions are incompletely defined. Here we show that the short-chain fatty acid crotonate, which is used to study histone crotonylation, changes cell morphology and immune interactions of Candida albicans. Crotonate reduces invasive hyphal morphogenesis of C. albicans within macrophages, thereby delaying macrophage killing and pathogen escape, as well as reducing inflammatory cytokine maturation. Crotonate's ability to reduce hyphal growth is environmentally contingent and pronounced within macrophages. Moreover, crotonate is a stronger hyphal inhibitor than butyrate under the conditions that we tested. Crotonate causes increased histone crotonylation in C. albicans under hyphal growth conditions and reduces transcription of hyphae-induced genes in a manner that involves the Nrg1 repressor pathway. Increasing histone acetylation by histone deacetylase inhibition partially rescues hyphal growth and gene transcription in the presence of crotonate. These results indicate that histone crotonylation might compete with acetylation in the regulation of hyphal morphogenesis. Based on our findings, we propose that diverse acylations of histones (and likely also non-histone proteins) enable C. albicans to respond to environmental signals, which in turn regulate its cell morphology and host-pathogen interactions.IMPORTANCEMacrophages curtail the proliferation of the pathogen Candida albicans within human body niches. Within macrophages, C. albicans adapts its metabolism and switches to invasive hyphal morphology. These adaptations enable fungal growth and immune escape by triggering macrophage lysis. Transcriptional programs regulate these metabolic and morphogenetic adaptations. Here we studied the roles of chromatin in these processes and implicate lysine crotonylation, a histone mark regulated by metabolism, in hyphal morphogenesis and macrophage interactions by C. albicans. We show that the short-chain fatty acid crotonate increases histone crotonylation, reduces hyphal formation within macrophages, and slows macrophage lysis and immune escape of C. albicans. Crotonate represses hyphal gene expression, and we propose that C. albicans uses diverse acylation marks to regulate its cell morphology in host environments. Hyphal formation is a virulence property of C. albicans. Therefore, a further importance of our study stems from identifying crotonate as a hyphal inhibitor.
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Affiliation(s)
- Christopher McCrory
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Jiyoti Verma
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Timothy M. Tucey
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Rachael Turner
- Department of Biochemistry and Molecular Biology and Stem Cells and Development Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Harshini Weerasinghe
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Traude H. Beilharz
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Department of Biochemistry and Molecular Biology and Stem Cells and Development Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Ana Traven
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
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3
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Fernando CD, Jayasekara WSN, Inampudi C, Kohonen-Corish MRJ, Cooper WA, Beilharz TH, Josephs TM, Garama DJ, Gough DJ. A STAT3 protein complex required for mitochondrial mRNA stability and cancer. Cell Rep 2023; 42:113033. [PMID: 37703176 DOI: 10.1016/j.celrep.2023.113033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/16/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) is a potent transcription factor necessary for life whose activity is corrupted in diverse diseases, including cancer. STAT3 biology was presumed to be entirely dependent on its activity as a transcription factor until the discovery of a mitochondrial pool of STAT3, which is necessary for normal tissue function and tumorigenesis. However, the mechanism of this mitochondrial activity remained elusive. This study uses immunoprecipitation and mass spectrometry to identify a complex containing STAT3, leucine-rich pentatricopeptide repeat containing (LRPPRC), and SRA stem-loop-interacting RNA-binding protein (SLIRP) that is required for the stability of mature mitochondrially encoded mRNAs and transport to the mitochondrial ribosome. Moreover, we show that this complex is enriched in patients with lung adenocarcinoma and that its deletion inhibits the growth of lung cancer in vivo, providing therapeutic opportunities through the specific targeting of the mitochondrial activity of STAT3.
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Affiliation(s)
- C Dilanka Fernando
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - W Samantha N Jayasekara
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Chaitanya Inampudi
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Maija R J Kohonen-Corish
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Woolcock Institute of Medical Research, Glebe, NSW 2037, Australia; School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; Faculty of Science, UTS Sydney, Ultimo, NSW 2007, Australia
| | - Wendy A Cooper
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW 2006, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Tracy M Josephs
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Daniel J Garama
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia.
| | - Daniel J Gough
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia.
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4
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Yau KPS, Weerasinghe H, Olivier FAB, Lo TL, Powell DR, Koch B, Beilharz TH, Traven A. The proteasome regulator Rpn4 controls antifungal drug tolerance by coupling protein homeostasis with metabolic responses to drug stress. PLoS Pathog 2023; 19:e1011338. [PMID: 37075064 PMCID: PMC10150987 DOI: 10.1371/journal.ppat.1011338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/01/2023] [Accepted: 03/31/2023] [Indexed: 04/20/2023] Open
Abstract
Fungal pathogens overcome antifungal drug therapy by classic resistance mechanisms, such as increased efflux or changes to the drug target. However, even when a fungal strain is susceptible, trailing or persistent microbial growth in the presence of an antifungal drug can contribute to therapeutic failure. This trailing growth is caused by adaptive physiological changes that enable the growth of a subpopulation of fungal cells in high drug concentrations, in what is described as drug tolerance. Mechanistically, antifungal drug tolerance is not well understood. Here we report that the transcriptional activator Rpn4 is important for drug tolerance in the human fungal pathogen Candida albicans. Deletion of RPN4 eliminates tolerance to the commonly used antifungal drug fluconazole. We defined the mechanism and show that Rpn4 controls fluconazole tolerance via two target pathways. First, Rpn4 activates proteasome gene expression, which enables sufficient proteasome capacity to overcome fluconazole-induced proteotoxicity and the accumulation of ubiquitinated proteins targeted for degradation. Consistently, inhibition of the proteasome with MG132 eliminates fluconazole tolerance and resistance, and phenocopies the rpn4Δ/Δ mutant for loss of tolerance. Second, Rpn4 is required for wild type expression of the genes required for the synthesis of the membrane lipid ergosterol. Our data indicates that this function of Rpn4 is required for mitigating the inhibition of ergosterol biosynthesis by fluconazole. Based on our findings, we propose that Rpn4 is a central hub for fluconazole tolerance in C. albicans by coupling the regulation of protein homeostasis (proteostasis) and lipid metabolism to overcome drug-induced proteotoxicity and membrane stress.
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Affiliation(s)
- Ka Pui Sharon Yau
- Infection Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
| | - Harshini Weerasinghe
- Infection Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
| | - Francios A B Olivier
- Infection Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
| | - Tricia L Lo
- Infection Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Clayton, Victoria, Australia
| | - Barbara Koch
- Infection Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ana Traven
- Infection Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
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5
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Simm C, Weerasinghe H, Thomas DR, Harrison PF, Newton HJ, Beilharz TH, Traven A. Disruption of Iron Homeostasis and Mitochondrial Metabolism Are Promising Targets to Inhibit Candida auris. Microbiol Spectr 2022; 10:e0010022. [PMID: 35412372 PMCID: PMC9045333 DOI: 10.1128/spectrum.00100-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/21/2022] [Indexed: 11/20/2022] Open
Abstract
Fungal infections are a global threat, but treatments are limited due to a paucity in antifungal drug targets and the emergence of drug-resistant fungi such as Candida auris. Metabolic adaptations enable microbial growth in nutrient-scarce host niches, and they further control immune responses to pathogens, thereby offering opportunities for therapeutic targeting. Because it is a relatively new pathogen, little is known about the metabolic requirements for C. auris growth and its adaptations to counter host defenses. Here, we establish that triggering metabolic dysfunction is a promising strategy against C. auris. Treatment with pyrvinium pamoate (PP) induced metabolic reprogramming and mitochondrial dysfunction evident in disrupted mitochondrial morphology and reduced tricarboxylic acid (TCA) cycle enzyme activity. PP also induced changes consistent with disrupted iron homeostasis. Nutrient supplementation experiments support the proposition that PP-induced metabolic dysfunction is driven by disrupted iron homeostasis, which compromises carbon and lipid metabolism and mitochondria. PP inhibited C. auris replication in macrophages, which is a relevant host niche for this yeast pathogen. We propose that PP causes a multipronged metabolic hit to C. auris: it restricts the micronutrient iron to potentiate nutritional immunity imposed by immune cells, and it further causes metabolic dysfunction that compromises the utilization of macronutrients, thereby curbing the metabolic plasticity needed for growth in host environments. Our study offers a new avenue for therapeutic development against drug-resistant C. auris, shows how complex metabolic dysfunction can be caused by a single compound triggering antifungal inhibition, and provides insights into the metabolic needs of C. auris in immune cell environments. IMPORTANCE Over the last decade, Candida auris has emerged as a human pathogen around the world causing life-threatening infections with wide-spread antifungal drug resistance, including pandrug resistance in some cases. In this study, we addressed the mechanism of action of the antiparasitic drug pyrvinium pamoate against C. auris and show how metabolism could be inhibited to curb C. auris proliferation. We show that pyrvinium pamoate triggers sweeping metabolic and mitochondrial changes and disrupts iron homeostasis. PP-induced metabolic dysfunction compromises the utilization of both micro- and macronutrients by C. auris and reduces its growth in vitro and in immune phagocytes. Our findings provide insights into the metabolic requirements for C. auris growth and define the mechanisms of action of pyrvinium pamoate against C. auris, demonstrating how this compound works by inhibiting the metabolic flexibility of the pathogen. As such, our study characterizes credible avenues for new antifungal approaches against C. auris.
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Affiliation(s)
- Claudia Simm
- Infection Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
- Centre to Impact AMR, Monash University, Victoria, Australia
| | - Harshini Weerasinghe
- Infection Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
- Centre to Impact AMR, Monash University, Victoria, Australia
| | - David R. Thomas
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | | | - Hayley J. Newton
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Traude H. Beilharz
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
| | - Ana Traven
- Infection Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
- Centre to Impact AMR, Monash University, Victoria, Australia
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6
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Turner RE, Harrison PF, Swaminathan A, Kraupner-Taylor CA, Goldie BJ, See M, Peterson AL, Schittenhelm RB, Powell DR, Creek DJ, Dichtl B, Beilharz TH. Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast. eLife 2021; 10:65331. [PMID: 34232857 PMCID: PMC8263057 DOI: 10.7554/elife.65331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/22/2021] [Indexed: 01/23/2023] Open
Abstract
Most eukaryotic mRNAs accommodate alternative sites of poly(A) addition in the 3’ untranslated region in order to regulate mRNA function. Here, we present a systematic analysis of 3’ end formation factors, which revealed 3’UTR lengthening in response to a loss of the core machinery, whereas a loss of the Sen1 helicase resulted in shorter 3’UTRs. We show that the anti-cancer drug cordycepin, 3’ deoxyadenosine, caused nucleotide accumulation and the usage of distal poly(A) sites. Mycophenolic acid, a drug which reduces GTP levels and impairs RNA polymerase II (RNAP II) transcription elongation, promoted the usage of proximal sites and reversed the effects of cordycepin on alternative polyadenylation. Moreover, cordycepin-mediated usage of distal sites was associated with a permissive chromatin template and was suppressed in the presence of an rpb1 mutation, which slows RNAP II elongation rate. We propose that alternative polyadenylation is governed by temporal coordination of RNAP II transcription and 3’ end processing and controlled by the availability of 3’ end factors, nucleotide levels and chromatin landscape.
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Affiliation(s)
- Rachael Emily Turner
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Paul F Harrison
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Angavai Swaminathan
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Calvin A Kraupner-Taylor
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Belinda J Goldie
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Michael See
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Amanda L Peterson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Bernhard Dichtl
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
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7
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Kandhari N, Kraupner-Taylor CA, Harrison PF, Powell DR, Beilharz TH. The Detection and Bioinformatic Analysis of Alternative 3 ' UTR Isoforms as Potential Cancer Biomarkers. Int J Mol Sci 2021; 22:5322. [PMID: 34070203 PMCID: PMC8158509 DOI: 10.3390/ijms22105322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 12/17/2022] Open
Abstract
Alternative transcript cleavage and polyadenylation is linked to cancer cell transformation, proliferation and outcome. This has led researchers to develop methods to detect and bioinformatically analyse alternative polyadenylation as potential cancer biomarkers. If incorporated into standard prognostic measures such as gene expression and clinical parameters, these could advance cancer prognostic testing and possibly guide therapy. In this review, we focus on the existing methodologies, both experimental and computational, that have been applied to support the use of alternative polyadenylation as cancer biomarkers.
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Affiliation(s)
- Nitika Kandhari
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia; (N.K.); (C.A.K.-T.); (P.F.H.)
| | - Calvin A. Kraupner-Taylor
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia; (N.K.); (C.A.K.-T.); (P.F.H.)
| | - Paul F. Harrison
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia; (N.K.); (C.A.K.-T.); (P.F.H.)
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia;
| | - David R. Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia;
| | - Traude H. Beilharz
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia; (N.K.); (C.A.K.-T.); (P.F.H.)
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8
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Arthur JW, Pickett HA, Barbaro PM, Kilo T, Vasireddy RS, Beilharz TH, Powell DR, Hackett EL, Bennetts B, Curtin JA, Jones K, Christodoulou J, Reddel RR, Teo J, Bryan TM. A novel cause of DKC1-related bone marrow failure: Partial deletion of the 3' untranslated region. EJHaem 2021; 2:157-166. [PMID: 35845273 PMCID: PMC9175968 DOI: 10.1002/jha2.165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
Telomere biology disorders (TBDs), including dyskeratosis congenita (DC), are a group of rare inherited diseases characterized by very short telomeres. Mutations in the components of the enzyme telomerase can lead to insufficient telomere maintenance in hematopoietic stem cells, resulting in the bone marrow failure that is characteristic of these disorders. While an increasing number of genes are being linked to TBDs, the causative mutation remains unidentified in 30‐40% of patients with DC. There is therefore a need for whole genome sequencing (WGS) in these families to identify novel genes, or mutations in regulatory regions of known disease‐causing genes. Here we describe a family in which a partial deletion of the 3′ untranslated region (3′ UTR) of DKC1, encoding the protein dyskerin, was identified by WGS, despite being missed by whole exome sequencing. The deletion segregated with disease across the family and resulted in reduced levels of DKC1 mRNA in the proband. We demonstrate that the DKC1 3′ UTR contains two polyadenylation signals, both of which were removed by this deletion, likely causing mRNA instability. Consistent with the major function of dyskerin in stabilization of the RNA subunit of telomerase, hTR, the level of hTR was also reduced in the proband, providing a molecular basis for his very short telomeres. This study demonstrates that the terminal region of the 3′ UTR of the DKC1 gene is essential for gene function and illustrates the importance of analyzing regulatory regions of the genome for molecular diagnosis of inherited disease.
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Affiliation(s)
- Jonathan W Arthur
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Hilda A Pickett
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Pasquale M Barbaro
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Tatjana Kilo
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Raja S Vasireddy
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Traude H Beilharz
- Monash Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria Australia
| | - David R Powell
- Monash Bioinformatics Platform Monash University Clayton Victoria Australia
| | - Emma L Hackett
- Department of Molecular Genetics Children's Hospital Westmead Westmead New South Wales Australia
| | - Bruce Bennetts
- Department of Molecular Genetics Children's Hospital Westmead Westmead New South Wales Australia.,Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health University of Sydney Westmead New South Wales Australia
| | - Julie A Curtin
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Kristi Jones
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health University of Sydney Westmead New South Wales Australia.,Department of Clinical Genetics Children's Hospital Westmead Westmead New South Wales Australia
| | - John Christodoulou
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health University of Sydney Westmead New South Wales Australia.,Murdoch Children's Research Institute and Department of Paediatrics Melbourne Medical School Parkville Victoria Australia
| | - Roger R Reddel
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Juliana Teo
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Tracy M Bryan
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
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9
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Turner RE, Henneken LM, Liem-Weits M, Harrison PF, Swaminathan A, Vary R, Nikolic I, Simpson KJ, Powell DR, Beilharz TH, Dichtl B. Requirement for cleavage factor II m in the control of alternative polyadenylation in breast cancer cells. RNA 2020; 26:969-981. [PMID: 32295865 PMCID: PMC7373993 DOI: 10.1261/rna.075226.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Alternative polyadenylation (APA) determines stability, localization and translation potential of the majority of mRNA in eukaryotic cells. The heterodimeric mammalian cleavage factor II (CF IIm) is required for pre-mRNA 3' end cleavage and is composed of the RNA kinase hClp1 and the termination factor hPcf11; the latter protein binds to RNA and the RNA polymerase II carboxy-terminal domain. Here, we used siRNA mediated knockdown and poly(A) targeted RNA sequencing to analyze the role of CF IIm in gene expression and APA in estrogen receptor positive MCF7 breast cancer cells. Identified gene ontology terms link CF IIm function to regulation of growth factor activity, protein heterodimerization and the cell cycle. An overlapping requirement for hClp1 and hPcf11 suggested that CF IIm protein complex was involved in the selection of proximal poly(A) sites. In addition to APA shifts within 3' untranslated regions (3'-UTRs), we observed shifts from promoter proximal regions to the 3'-UTR facilitating synthesis of full-length mRNAs. Moreover, we show that several truncated mRNAs that resulted from APA within introns in MCF7 cells cosedimented with ribosomal components in an EDTA sensitive manner suggesting that those are translated into protein. We propose that CF IIm contributes to the regulation of mRNA function in breast cancer.
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Affiliation(s)
- Rachael E Turner
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Lee M Henneken
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
| | - Marije Liem-Weits
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
| | - Paul F Harrison
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
- Monash Bioinformatics Platform, Monash University, Melbourne, Victoria 3800, Australia
| | - Angavai Swaminathan
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Robert Vary
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Iva Nikolic
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, Victoria 3800, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Bernhard Dichtl
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
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10
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Swaminathan A, Harrison PF, Preiss T, Beilharz TH. PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A)-Length Distribution in Yeast Transcriptomes. Methods Mol Biol 2020; 2049:141-164. [PMID: 31602610 DOI: 10.1007/978-1-4939-9736-7_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Next-generation sequencing (NGS) and its application to RNA (RNA-seq) has opened up multiple aspects of RNA processing to deep transcriptome-wide analysis at nucleotide resolution. This has been useful in delineating the transcribed areas of the genome, and in quantitation of RNA isoforms. Such isoforms can diversify the regulatory repertoire of mRNAs. For example, the 3'-end of mRNA can vary in two important ways, in the position chosen for cleavage and polyadenylation, and in the length of the poly(A)-tail. Accordingly, the step-up in resolution made possible by NGS has revealed an unexpectedly high level of alternative polyadenylation (APA). Moreover, it has massively simplified the transcriptome-wide detection of poly(A)-tail length changes. Here we present our approach to the study of 3'-end dynamics using a 3'-focused RNA-seq method called PAT-seq (for poly(A)-test sequencing). The approach records gene expression, APA, and poly(A)-tail changes between transcriptomes to reveal complex interplay between transcriptional and posttranscriptional control mechanisms.
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Affiliation(s)
- Angavai Swaminathan
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia
| | - Thomas Preiss
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia.
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11
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Fan Z, Devlin JR, Hogg SJ, Doyle MA, Harrison PF, Todorovski I, Cluse LA, Knight DA, Sandow JJ, Gregory G, Fox A, Beilharz TH, Kwiatkowski N, Scott NE, Vidakovic AT, Kelly GP, Svejstrup JQ, Geyer M, Gray NS, Vervoort SJ, Johnstone RW. CDK13 cooperates with CDK12 to control global RNA polymerase II processivity. Sci Adv 2020; 6:eaaz5041. [PMID: 32917631 PMCID: PMC7190357 DOI: 10.1126/sciadv.aaz5041] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/10/2020] [Indexed: 05/04/2023]
Abstract
The RNA polymerase II (POLII)-driven transcription cycle is tightly regulated at distinct checkpoints by cyclin-dependent kinases (CDKs) and their cognate cyclins. The molecular events underpinning transcriptional elongation, processivity, and the CDK-cyclin pair(s) involved remain poorly understood. Using CRISPR-Cas9 homology-directed repair, we generated analog-sensitive kinase variants of CDK12 and CDK13 to probe their individual and shared biological and molecular roles. Single inhibition of CDK12 or CDK13 induced transcriptional responses associated with cellular growth signaling pathways and/or DNA damage, with minimal effects on cell viability. In contrast, dual kinase inhibition potently induced cell death, which was associated with extensive genome-wide transcriptional changes including widespread use of alternative 3' polyadenylation sites. At the molecular level, dual kinase inhibition resulted in the loss of POLII CTD phosphorylation and greatly reduced POLII elongation rates and processivity. These data define substantial redundancy between CDK12 and CDK13 and identify both as fundamental regulators of global POLII processivity and transcription elongation.
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Affiliation(s)
- Zheng Fan
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Jennifer R Devlin
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Simon J Hogg
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Maria A Doyle
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Paul F Harrison
- Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia
- Monash Bioinformatics Platform, Monash University, Clayton, 3800 VIC, Australia
| | - Izabela Todorovski
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Leonie A Cluse
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Deborah A Knight
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3052 VIC, Australia
| | - Gareth Gregory
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Andrew Fox
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Traude H Beilharz
- Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia
| | - Nicholas Kwiatkowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nichollas E Scott
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Parkville, 3052 VIC, Australia
| | | | - Gavin P Kelly
- Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Stephin J Vervoort
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Ricky W Johnstone
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
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12
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Wang Q, Verma J, Vidan N, Wang Y, Tucey TM, Lo TL, Harrison PF, See M, Swaminathan A, Kuchler K, Tscherner M, Song J, Powell DR, Sopta M, Beilharz TH, Traven A. The YEATS Domain Histone Crotonylation Readers Control Virulence-Related Biology of a Major Human Pathogen. Cell Rep 2020; 31:107528. [PMID: 32320659 DOI: 10.1016/j.celrep.2020.107528] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/31/2020] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
Identification of multiple histone acylations diversifies transcriptional control by metabolism, but their functions are incompletely defined. Here we report evidence of histone crotonylation in the human fungal pathogen Candida albicans. We define the enzymes that regulate crotonylation and show its dynamic control by environmental signals: carbon sources, the short-chain fatty acids butyrate and crotonate, and cell wall stress. Crotonate regulates stress-responsive transcription and rescues C. albicans from cell wall stress, indicating broad impact on cell biology. The YEATS domain crotonylation readers Taf14 and Yaf9 are required for C. albicans virulence, and Taf14 controls gene expression, stress resistance, and invasive growth via its chromatin reader function. Blocking the Taf14 C terminus with a tag reduced virulence, suggesting that inhibiting Taf14 interactions with chromatin regulators impairs function. Our findings shed light on the regulation of histone crotonylation and the functions of the YEATS proteins in eukaryotic pathogen biology and fungal infections.
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Affiliation(s)
- Qi Wang
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Jiyoti Verma
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Nikolina Vidan
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia; Department of Molecular Biology, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Yanan Wang
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Timothy M Tucey
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Tricia L Lo
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Paul F Harrison
- Bioinformatics Platform, Monash University, Clayton 3800 VIC, Australia
| | - Michael See
- Bioinformatics Platform, Monash University, Clayton 3800 VIC, Australia
| | - Angavai Swaminathan
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Karl Kuchler
- Medical University of Vienna, Center for Medical Biochemistry, Max Perutz Labs, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/2, Vienna, Austria
| | - Michael Tscherner
- Medical University of Vienna, Center for Medical Biochemistry, Max Perutz Labs, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/2, Vienna, Austria
| | - Jiangning Song
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Clayton 3800 VIC, Australia
| | - Mary Sopta
- Department of Molecular Biology, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Traude H Beilharz
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Ana Traven
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia.
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13
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Formosa LE, Muellner-Wong L, Reljic B, Sharpe AJ, Jackson TD, Beilharz TH, Stojanovski D, Lazarou M, Stroud DA, Ryan MT. Dissecting the Roles of Mitochondrial Complex I Intermediate Assembly Complex Factors in the Biogenesis of Complex I. Cell Rep 2020; 31:107541. [DOI: 10.1016/j.celrep.2020.107541] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/17/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022] Open
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14
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Johnstone CN, Pattison AD, Harrison PF, Powell DR, Lock P, Ernst M, Anderson RL, Beilharz TH. FGF13 promotes metastasis of triple-negative breast cancer. Int J Cancer 2020; 147:230-243. [PMID: 31957002 DOI: 10.1002/ijc.32874] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 12/01/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022]
Abstract
Triple-negative breast cancer (TNBC) represents 10-20% of all human ductal adenocarcinomas and has a poor prognosis relative to other subtypes, due to the high propensity to develop distant metastases. Hence, new molecular targets for therapeutic intervention are needed for TNBC. We recently conducted a rigorous phenotypic and genomic characterization of four isogenic populations of MDA-MB-231 human triple-negative breast cancer cells that possess a range of intrinsic spontaneous metastatic capacities in vivo, ranging from nonmetastatic (MDA-MB-231_ATCC) to highly metastatic to lung, liver, spleen and spine (MDA-MB-231_HM). Gene expression profiling of primary tumours by RNA-Seq identified the fibroblast growth factor homologous factor, FGF13, as highly upregulated in aggressively metastatic MDA-MB-231_HM tumours. Clinically, higher FGF13 mRNA expression was associated with significantly worse relapse free survival in both luminal A and basal-like human breast cancers but was not associated with other clinical variables and was not upregulated in primary tumours relative to normal mammary gland. Stable FGF13 depletion restricted in vitro colony forming ability in MDA-MB-231_HM TNBC cells but not in oestrogen receptor (ER)-positive MCF-7 or MDA-MB-361 cells. However, despite augmenting MDA-MB-231_HM cell migration and invasion in vitro, FGF13 suppression almost completely blocked the spontaneous metastasis of MDA-MB-231_HM orthotopic xenografts to both lung and liver while having negligible impact on primary tumour growth. Together, these data indicate that FGF13 may represent a therapeutic target for blocking metastatic outgrowth of certain TNBCs. Further evaluation of the roles of individual FGF13 protein isoforms in progression of the different subtypes of breast cancer is warranted.
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Affiliation(s)
- Cameron N Johnstone
- Cancer Research Division, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia.,Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Andrew D Pattison
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.,Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Clayton, VIC, Australia
| | - David R Powell
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Monash Bioinformatics Platform, Monash University, Clayton, VIC, Australia
| | - Peter Lock
- LIMS Bioimaging Facility, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, VIC, Australia
| | - Robin L Anderson
- Cancer Research Division, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia.,Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, VIC, Australia
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.,Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Monash Bioinformatics Platform, Monash University, Clayton, VIC, Australia
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15
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Koch B, Barugahare AA, Lo TL, Huang C, Schittenhelm RB, Powell DR, Beilharz TH, Traven A. A Metabolic Checkpoint for the Yeast-to-Hyphae Developmental Switch Regulated by Endogenous Nitric Oxide Signaling. Cell Rep 2019; 25:2244-2258.e7. [PMID: 30463019 DOI: 10.1016/j.celrep.2018.10.080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/31/2018] [Accepted: 10/22/2018] [Indexed: 12/13/2022] Open
Abstract
The yeast Candida albicans colonizes several sites in the human body and responds to metabolic signals in commensal and pathogenic states. The yeast-to-hyphae transition correlates with virulence, but how metabolic status is integrated with this transition is incompletely understood. We used the putative mitochondrial fission inhibitor mdivi-1 to probe the crosstalk between hyphal signaling and metabolism. Mdivi-1 repressed C. albicans hyphal morphogenesis, but the mechanism was independent of its presumed target, the mitochondrial fission GTPase Dnm1. Instead, mdivi-1 triggered extensive metabolic reprogramming, consistent with metabolic stress, and reduced endogenous nitric oxide (NO) levels. Limiting endogenous NO stabilized the transcriptional repressor Nrg1 and inhibited the yeast-to-hyphae transition. We establish a role for endogenous NO signaling in C. albicans hyphal morphogenesis and suggest that NO regulates a metabolic checkpoint for hyphal growth. Furthermore, identifying NO signaling as an mdivi-1 target could inform its therapeutic applications in human diseases.
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Affiliation(s)
- Barbara Koch
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Adele A Barugahare
- Bioinformatics Platform, Monash University, Clayton, VIC 3800, Australia
| | - Tricia L Lo
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Cheng Huang
- Biomedical Proteomics Facility and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ralf B Schittenhelm
- Biomedical Proteomics Facility and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Clayton, VIC 3800, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ana Traven
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
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16
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Johnstone CN, Pattison AD, Gorringe KL, Harrison PF, Powell DR, Lock P, Baloyan D, Ernst M, Stewart AG, Beilharz TH, Anderson RL. Functional and genomic characterisation of a xenograft model system for the study of metastasis in triple-negative breast cancer. Dis Model Mech 2018; 11:dmm032250. [PMID: 29720474 PMCID: PMC5992606 DOI: 10.1242/dmm.032250] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 04/13/2018] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) represents 10-20% of all human ductal adenocarcinomas and has a poor prognosis relative to other subtypes. Hence, new molecular targets for therapeutic intervention are necessary. Analyses of panels of human or mouse cancer lines derived from the same individual that differ in their cellular phenotypes but not in genetic background have been instrumental in defining the molecular players that drive the various hallmarks of cancer. To determine the molecular regulators of metastasis in TNBC, we completed a rigorous in vitro and in vivo characterisation of four populations of the MDA-MB-231 human breast cancer line ranging in aggressiveness from non-metastatic to spontaneously metastatic to lung, liver, spleen and lymph node. Single nucleotide polymorphism (SNP) array analyses and genome-wide mRNA expression profiles of tumour cells isolated from orthotopic mammary xenografts were compared between the four lines to define both cell autonomous pathways and genes associated with metastatic proclivity. Gene set enrichment analysis (GSEA) demonstrated an unexpected association between both ribosome biogenesis and mRNA metabolism and metastatic capacity. Differentially expressed genes or families of related genes were allocated to one of four categories, associated with either metastatic initiation (e.g. CTSC, ENG, BMP2), metastatic virulence (e.g. ADAMTS1, TIE1), metastatic suppression (e.g. CST1, CST2, CST4, CST6, SCNNA1, BMP4) or metastatic avirulence (e.g. CD74). Collectively, this model system based on MDA-MB-231 cells should be useful for the assessment of gene function in the metastatic cascade and also for the testing of novel experimental therapeutics for the treatment of TNBC.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Cameron N Johnstone
- Cancer Research Division, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3050, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3050, Australia
- Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Department of Pharmacology & Therapeutics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew D Pattison
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Kylie L Gorringe
- Cancer Research Division, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3050, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Clayton, Victoria 3800, Australia
| | - David R Powell
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Monash Bioinformatics Platform, Monash University, Clayton, Victoria 3800, Australia
| | - Peter Lock
- LIMS Bioimaging Facility, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - David Baloyan
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Alastair G Stewart
- Department of Pharmacology & Therapeutics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Robin L Anderson
- Cancer Research Division, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Parkville, Victoria 3050, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3050, Australia
- Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia
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17
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Ratnadiwakara M, Archer SK, Dent CI, Ruiz De Los Mozos I, Beilharz TH, Knaupp AS, Nefzger CM, Polo JM, Anko ML. SRSF3 promotes pluripotency through Nanog mRNA export and coordination of the pluripotency gene expression program. eLife 2018; 7:37419. [PMID: 29741478 PMCID: PMC5963917 DOI: 10.7554/elife.37419] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/05/2018] [Indexed: 12/28/2022] Open
Abstract
The establishment and maintenance of pluripotency depend on precise coordination of gene expression. We establish serine-arginine-rich splicing factor 3 (SRSF3) as an essential regulator of RNAs encoding key components of the mouse pluripotency circuitry, SRSF3 ablation resulting in the loss of pluripotency and its overexpression enhancing reprogramming. Strikingly, SRSF3 binds to the core pluripotency transcription factor Nanog mRNA to facilitate its nucleo-cytoplasmic export independent of splicing. In the absence of SRSF3 binding, Nanog mRNA is sequestered in the nucleus and protein levels are severely downregulated. Moreover, SRSF3 controls the alternative splicing of the export factor Nxf1 and RNA regulators with established roles in pluripotency, and the steady-state levels of mRNAs encoding chromatin modifiers. Our investigation links molecular events to cellular functions by demonstrating how SRSF3 regulates the pluripotency genes and uncovers SRSF3-RNA interactions as a critical means to coordinate gene expression during reprogramming, stem cell self-renewal and early development.
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Affiliation(s)
- Madara Ratnadiwakara
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Stuart K Archer
- Bioinformatics Platform, Monash University, Clayton, Australia
| | - Craig I Dent
- School of Biological Sciences, Monash University, Melbourne, Australia
| | | | - Traude H Beilharz
- Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Anja S Knaupp
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Minna-Liisa Anko
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
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18
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Tucey TM, Verma J, Harrison PF, Snelgrove SL, Lo TL, Scherer AK, Barugahare AA, Powell DR, Wheeler RT, Hickey MJ, Beilharz TH, Naderer T, Traven A. Glucose Homeostasis Is Important for Immune Cell Viability during Candida Challenge and Host Survival of Systemic Fungal Infection. Cell Metab 2018; 27:988-1006.e7. [PMID: 29719235 PMCID: PMC6709535 DOI: 10.1016/j.cmet.2018.03.019] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/18/2017] [Accepted: 03/26/2018] [Indexed: 12/20/2022]
Abstract
To fight infections, macrophages undergo a metabolic shift whereby increased glycolysis fuels antimicrobial inflammation and killing of pathogens. Here we demonstrate that the pathogen Candida albicans turns this metabolic reprogramming into an Achilles' heel for macrophages. During Candida-macrophage interactions intertwined metabolic shifts occur, with concomitant upregulation of glycolysis in both host and pathogen setting up glucose competition. Candida thrives on multiple carbon sources, but infected macrophages are metabolically trapped in glycolysis and depend on glucose for viability: Candida exploits this limitation by depleting glucose, triggering rapid macrophage death. Using pharmacological or genetic means to modulate glucose metabolism of host and/or pathogen, we show that Candida infection perturbs host glucose homeostasis in the murine candidemia model and demonstrate that glucose supplementation improves host outcomes. Our results support the importance of maintaining glucose homeostasis for immune cell survival during Candida challenge and for host survival in systemic infection.
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Affiliation(s)
- Timothy M Tucey
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
| | - Jiyoti Verma
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
| | - Paul F Harrison
- Bioinformatics Platform, Monash University, Clayton 3800, VIC, Australia
| | - Sarah L Snelgrove
- Centre for Inflammatory Diseases, Monash University Department of Medicine, Monash Medical Centre, Clayton 3168, VIC, Australia
| | - Tricia L Lo
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
| | - Allison K Scherer
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Adele A Barugahare
- Bioinformatics Platform, Monash University, Clayton 3800, VIC, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Clayton 3800, VIC, Australia
| | - Robert T Wheeler
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Michael J Hickey
- Centre for Inflammatory Diseases, Monash University Department of Medicine, Monash Medical Centre, Clayton 3168, VIC, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
| | - Thomas Naderer
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia.
| | - Ana Traven
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia.
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19
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Nejad C, Pillman KA, Siddle KJ, Pépin G, Änkö ML, McCoy CE, Beilharz TH, Quintana-Murci L, Goodall GJ, Bracken CP, Gantier MP. miR-222 isoforms are differentially regulated by type-I interferon. RNA 2018; 24:332-341. [PMID: 29263133 PMCID: PMC5824353 DOI: 10.1261/rna.064550.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/18/2017] [Indexed: 06/07/2023]
Abstract
Endogenous microRNAs (miRNAs) often exist as multiple isoforms (known as "isomiRs") with predominant variation around their 3'-end. Increasing evidence suggests that different isomiRs of the same family can have diverse functional roles, as recently demonstrated with the example of miR-222-3p 3'-end variants. While isomiR levels from a same miRNA family can vary between tissues and cell types, change of templated isomiR stoichiometry to stimulation has not been reported to date. Relying on small RNA-sequencing analyses, we demonstrate here that miR-222-3p 3'-end variants >23 nt are specifically decreased upon interferon (IFN) β stimulation of human fibroblasts, while shorter isoforms are spared. This length-dependent dynamic regulation of long miR-222-3p 3'-isoforms and >40 other miRNA families was confirmed in human monocyte-derived dendritic cells following infection with Salmonella Typhimurium, underlining the breadth of 3'-length regulation by infection, beyond the example of miR-222-3p. We further show that stem-loop miRNA Taqman RT-qPCR exhibits selectivity between 3'-isoforms, according to their length, and that this can lead to misinterpretation of results when these isoforms are differentially regulated. Collectively, and to our knowledge, this work constitutes the first demonstration that the stoichiometry of highly abundant templated 3'-isoforms of a same miRNA family can be dynamically regulated by a stimulus. Given that such 3'-isomiRs can have different functions, our study underlines the need to consider isomiRs when investigating miRNA-based regulation.
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Affiliation(s)
- Charlotte Nejad
- Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia 5000, Australia
| | - Katherine J Siddle
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Geneviève Pépin
- Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Minna-Liisa Änkö
- Department of Anatomy and Developmental Biology, Monash University, Victoria 3800, Australia
- Development and Stem Cells Program, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
| | - Claire E McCoy
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Traude H Beilharz
- Development and Stem Cells Program, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Lluís Quintana-Murci
- Institut Pasteur, Unit of Human Evolutionary Genetics, CNRS URA3012, Paris 75015, France
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia
- Department of Medicine, University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia
- Department of Medicine, University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
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20
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Dufourt J, Bontonou G, Chartier A, Jahan C, Meunier AC, Pierson S, Harrison PF, Papin C, Beilharz TH, Simonelig M. piRNAs and Aubergine cooperate with Wispy poly(A) polymerase to stabilize mRNAs in the germ plasm. Nat Commun 2017; 8:1305. [PMID: 29101389 PMCID: PMC5670238 DOI: 10.1038/s41467-017-01431-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 09/18/2017] [Indexed: 11/12/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) and PIWI proteins play a crucial role in germ cells by repressing transposable elements and regulating gene expression. In Drosophila, maternal piRNAs are loaded into the embryo mostly bound to the PIWI protein Aubergine (Aub). Aub targets maternal mRNAs through incomplete base-pairing with piRNAs and can induce their destabilization in the somatic part of the embryo. Paradoxically, these Aub-dependent unstable mRNAs encode germ cell determinants that are selectively stabilized in the germ plasm. Here we show that piRNAs and Aub actively protect germ cell mRNAs in the germ plasm. Aub directly interacts with the germline-specific poly(A) polymerase Wispy, thus leading to mRNA polyadenylation and stabilization in the germ plasm. These results reveal a role for piRNAs in mRNA stabilization and identify Aub as an interactor of Wispy for mRNA polyadenylation. They further highlight the role of Aub and piRNAs in embryonic patterning through two opposite functions.
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Affiliation(s)
- Jérémy Dufourt
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Gwénaëlle Bontonou
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Aymeric Chartier
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Camille Jahan
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Anne-Cécile Meunier
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Stéphanie Pierson
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, 3800, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Catherine Papin
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Traude H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Martine Simonelig
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier Cedex 5, France.
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21
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Stroud DA, Surgenor EE, Formosa LE, Reljic B, Frazier AE, Dibley MG, Osellame LD, Stait T, Beilharz TH, Thorburn DR, Salim A, Ryan MT. Accessory subunits are integral for assembly and function of human mitochondrial complex I. Nature 2016; 538:123-126. [PMID: 27626371 DOI: 10.1038/nature19754] [Citation(s) in RCA: 338] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/22/2016] [Indexed: 01/02/2023]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the mitochondrial respiratory chain and is composed of 45 subunits in humans, making it one of the largest known multi-subunit membrane protein complexes. Complex I exists in supercomplex forms with respiratory chain complexes III and IV, which are together required for the generation of a transmembrane proton gradient used for the synthesis of ATP. Complex I is also a major source of damaging reactive oxygen species and its dysfunction is associated with mitochondrial disease, Parkinson's disease and ageing. Bacterial and human complex I share 14 core subunits that are essential for enzymatic function; however, the role and necessity of the remaining 31 human accessory subunits is unclear. The incorporation of accessory subunits into the complex increases the cellular energetic cost and has necessitated the involvement of numerous assembly factors for complex I biogenesis. Here we use gene editing to generate human knockout cell lines for each accessory subunit. We show that 25 subunits are strictly required for assembly of a functional complex and 1 subunit is essential for cell viability. Quantitative proteomic analysis of cell lines revealed that loss of each subunit affects the stability of other subunits residing in the same structural module. Analysis of proteomic changes after the loss of specific modules revealed that ATP5SL and DMAC1 are required for assembly of the distal portion of the complex I membrane arm. Our results demonstrate the broad importance of accessory subunits in the structure and function of human complex I. Coupling gene-editing technology with proteomics represents a powerful tool for dissecting large multi-subunit complexes and enables the study of complex dysfunction at a cellular level.
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Affiliation(s)
- David A Stroud
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Elliot E Surgenor
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University 3086, Melbourne, Australia
| | - Boris Reljic
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University 3086, Melbourne, Australia
| | - Ann E Frazier
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia.,Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - Marris G Dibley
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Laura D Osellame
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Tegan Stait
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - David R Thorburn
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne 3052, Australia.,Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital 3052, Melbourne, Australia
| | - Agus Salim
- Department of Mathematics and Statistics, La Trobe University 3086, Melbourne Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
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22
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Soetanto R, Hynes CJ, Patel HR, Humphreys DT, Evers M, Duan G, Parker BJ, Archer SK, Clancy JL, Graham RM, Beilharz TH, Smith NJ, Preiss T. Role of miRNAs and alternative mRNA 3'-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy. Biochim Biophys Acta 2016; 1859:744-56. [PMID: 27032571 DOI: 10.1016/j.bbagrm.2016.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 02/25/2016] [Accepted: 03/20/2016] [Indexed: 12/19/2022]
Abstract
miRNAs play critical roles in heart disease. In addition to differential miRNA expression, miRNA-mediated control is also affected by variable miRNA processing or alternative 3'-end cleavage and polyadenylation (APA) of their mRNA targets. To what extent these phenomena play a role in the heart remains unclear. We sought to explore miRNA processing and mRNA APA in cardiomyocytes, and whether these change during cardiac hypertrophy. Thoracic aortic constriction (TAC) was performed to induce hypertrophy in C57BL/6J mice. RNA extracted from cardiomyocytes of sham-treated, pre-hypertrophic (2 days post-TAC), and hypertrophic (7 days post-TAC) mice was subjected to small RNA- and poly(A)-test sequencing (PAT-Seq). Differential expression analysis matched expectations; nevertheless we identified ~400 mRNAs and hundreds of noncoding RNA loci as altered with hypertrophy for the first time. Although multiple processing variants were observed for many miRNAs, there was little change in their relative proportions during hypertrophy. PAT-Seq mapped ~48,000 mRNA 3'-ends, identifying novel 3' untranslated regions (3'UTRs) for over 7000 genes. Importantly, hypertrophy was associated with marked changes in APA with a net shift from distal to more proximal mRNA 3'-ends, which is predicted to decrease overall miRNA repression strength. We independently validated several examples of 3'UTR proportion change and showed that alternative 3'UTRs associate with differences in mRNA translation. Our work suggests that APA contributes to altered gene expression with the development of cardiomyocyte hypertrophy and provides a rich resource for a systems-level understanding of miRNA-mediated regulation in physiological and pathological states of the heart.
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Affiliation(s)
- R Soetanto
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - C J Hynes
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - H R Patel
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - D T Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - M Evers
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - G Duan
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - B J Parker
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - S K Archer
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia; Monash Bioinformatics Platform, Monash University, Melbourne, Victoria 3800, Australia
| | - J L Clancy
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - R M Graham
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - T H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - N J Smith
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - T Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia; Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.
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23
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Abstract
The mRNA closed-loop, formed through interactions between the cap structure, poly(A) tail, eIF4E, eIF4G and PAB, features centrally in models of eukaryotic translation initiation, although direct support for its existence in vivo is not well established. Here, we investigated the closed-loop using a combination of mRNP isolation from rapidly cross-linked cells and high-throughput qPCR. Using the interaction between these factors and the opposing ends of mRNAs as a proxy for the closed-loop, we provide evidence that it is prevalent for eIF4E/4G-bound but unexpectedly sparse for PAB1-bound mRNAs, suggesting it primarily occurs during a distinct phase of polysome assembly. We observed mRNA-specific variation in the extent of closed-loop formation, consistent with a role for polysome topology in the control of gene expression.
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Affiliation(s)
- Stuart K Archer
- a Genome Biology Department; The John Curtin School of Medical Research (JCSMR); The Australian National University ; Acton (Canberra), Australian Capital Territory , Australia
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24
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Swaminathan A, Beilharz TH. Epitope-tagged yeast strains reveal promoter driven changes to 3'-end formation and convergent antisense-transcription from common 3' UTRs. Nucleic Acids Res 2015; 44:377-86. [PMID: 26481348 PMCID: PMC4705644 DOI: 10.1093/nar/gkv1022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/29/2015] [Indexed: 12/15/2022] Open
Abstract
Epitope-tagging by homologous recombination is ubiquitously used to study gene expression, protein localization and function in yeast. This is generally thought to insulate the regulation of gene expression to that mediated by the promoter and coding regions because native 3′ UTR are replaced. Here we show that the 3′ UTRs, CYC1 and ADH1, contain cryptic promoters that generate abundant convergent antisense-transcription in Saccharomyces cerevisiae. Moreover we show that aberrant, truncating 3′ –end formation is often associated with regulated transcription in TAP-tagged strains. Importantly, the steady-state level of both 3′ –truncated and antisense transcription products is locus dependent. Using TAP and GFP-tagged strains we show that the transcriptional state of the gene-of-interest induces changes to 3′ –end formation by alternative polyadenylation and antisense transcription from a universal 3′ UTR. This means that these 3′ UTRs contains plastic features that can be molded to reflect the regulatory architecture of the locus rather than bringing their own regulatory paradigm to the gene-fusions as would be expected. Our work holds a cautionary note for studies utilizing tagged strains for quantitative biology, but also provides a new model for the study of promoter driven rewiring of 3′ –end formation and regulatory non-coding transcription.
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Affiliation(s)
- Angavai Swaminathan
- Development and stem cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Traude H Beilharz
- Development and stem cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
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25
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Verma-Gaur J, Qu Y, Harrison PF, Lo TL, Quenault T, Dagley MJ, Bellousoff M, Powell DR, Beilharz TH, Traven A. Integration of Posttranscriptional Gene Networks into Metabolic Adaptation and Biofilm Maturation in Candida albicans. PLoS Genet 2015; 11:e1005590. [PMID: 26474309 PMCID: PMC4608769 DOI: 10.1371/journal.pgen.1005590] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/17/2015] [Indexed: 11/19/2022] Open
Abstract
The yeast Candida albicans is a human commensal and opportunistic pathogen. Although both commensalism and pathogenesis depend on metabolic adaptation, the regulatory pathways that mediate metabolic processes in C. albicans are incompletely defined. For example, metabolic change is a major feature that distinguishes community growth of C. albicans in biofilms compared to suspension cultures, but how metabolic adaptation is functionally interfaced with the structural and gene regulatory changes that drive biofilm maturation remains to be fully understood. We show here that the RNA binding protein Puf3 regulates a posttranscriptional mRNA network in C. albicans that impacts on mitochondrial biogenesis, and provide the first functional data suggesting evolutionary rewiring of posttranscriptional gene regulation between the model yeast Saccharomyces cerevisiae and C. albicans. A proportion of the Puf3 mRNA network is differentially expressed in biofilms, and by using a mutant in the mRNA deadenylase CCR4 (the enzyme recruited to mRNAs by Puf3 to control transcript stability) we show that posttranscriptional regulation is important for mitochondrial regulation in biofilms. Inactivation of CCR4 or dis-regulation of mitochondrial activity led to altered biofilm structure and over-production of extracellular matrix material. The extracellular matrix is critical for antifungal resistance and immune evasion, and yet of all biofilm maturation pathways extracellular matrix biogenesis is the least understood. We propose a model in which the hypoxic biofilm environment is sensed by regulators such as Ccr4 to orchestrate metabolic adaptation, as well as the regulation of extracellular matrix production by impacting on the expression of matrix-related cell wall genes. Therefore metabolic changes in biofilms might be intimately linked to a key biofilm maturation mechanism that ultimately results in untreatable fungal disease. Metabolism is a master regulator of cell biology, including gene regulation, developmental switches and cellular life-death decisions, with the mitochondrion playing a central role in eukaryotes. For the yeast Candida albicans mitochondrial functions have been implicated in host-pathogen interactions, but the regulatory mechanism that control mitochondrial biogenesis are poorly described. We identified the RNA binding protein Puf3 as a new mitochondrial regulator in C. albicans, and show that posttranscriptional regulation and mitochondrial function have important roles during community growth in biofilms. Perturbation of mitochondrial activity or inactivation of a key posttranscriptional regulator, CCR4, led to changes in biofilm maturation, shedding light on the interface between metabolic reprogramming and biofilm developmental pathways. We illuminate a new mechanism that regulates extracellular matrix production, an essential biofilm feature that mediates the notorious drug resistance and immune evasion properties of the biofilm growth mode.
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Affiliation(s)
- Jiyoti Verma-Gaur
- Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Yue Qu
- Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Paul F. Harrison
- Monash Bioinformatics Platform, Monash University, Clayton, Victoria, Australia
| | - Tricia L. Lo
- Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Tara Quenault
- Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Michael J. Dagley
- Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Matthew Bellousoff
- Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - David R. Powell
- Monash Bioinformatics Platform, Monash University, Clayton, Victoria, Australia
| | - Traude H. Beilharz
- Development and Stem Cells Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail: (THB); (AT)
| | - Ana Traven
- Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail: (THB); (AT)
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26
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Harrison PF, Powell DR, Clancy JL, Preiss T, Boag PR, Traven A, Seemann T, Beilharz TH. PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA 2015; 21:1502-10. [PMID: 26092945 PMCID: PMC4509939 DOI: 10.1261/rna.048355.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 04/20/2015] [Indexed: 05/21/2023]
Abstract
A major objective of systems biology is to quantitatively integrate multiple parameters from genome-wide measurements. To integrate gene expression with dynamics in poly(A) tail length and adenylation site, we developed a targeted next-generation sequencing approach, Poly(A)-Test RNA-sequencing. PAT-seq returns (i) digital gene expression, (ii) polyadenylation site/s, and (iii) the polyadenylation-state within and between eukaryotic transcriptomes. PAT-seq differs from previous 3' focused RNA-seq methods in that it depends strictly on 3' adenylation within total RNA samples and that the full-native poly(A) tail is included in the sequencing libraries. Here, total RNA samples from budding yeast cells were analyzed to identify the intersect between adenylation state and gene expression in response to loss of the major cytoplasmic deadenylase Ccr4. Furthermore, concordant changes to gene expression and adenylation-state were demonstrated in the classic Crabtree-Warburg metabolic shift. Because all polyadenylated RNA is interrogated by the approach, alternative adenylation sites, noncoding RNA and RNA-decay intermediates were also identified. Most important, the PAT-seq approach uses standard sequencing procedures, supports significant multiplexing, and thus replication and rigorous statistical analyses can for the first time be brought to the measure of 3'-UTR dynamics genome wide.
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Affiliation(s)
- Paul F Harrison
- Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton 3053, Australia Monash Bioinformatics Platform, Monash University, Clayton 3800, Australia
| | - David R Powell
- Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton 3053, Australia Monash Bioinformatics Platform, Monash University, Clayton 3800, Australia
| | - Jennifer L Clancy
- EMBL-Australia Collaborating Laboratory, Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) 2601, Australian Capital Territory, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Laboratory, Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) 2601, Australian Capital Territory, Australia Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia
| | - Peter R Boag
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Ana Traven
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton 3053, Australia
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
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Elewa A, Shirayama M, Kaymak E, Harrison PF, Powell DR, Du Z, Chute CD, Woolf H, Yi D, Ishidate T, Srinivasan J, Bao Z, Beilharz TH, Ryder SP, Mello CC. POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA. Dev Cell 2015; 34:108-18. [PMID: 26096734 DOI: 10.1016/j.devcel.2015.05.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/17/2015] [Accepted: 05/27/2015] [Indexed: 12/01/2022]
Abstract
The regulation of mRNA translation is of fundamental importance in biological mechanisms ranging from embryonic axis specification to the formation of long-term memory. POS-1 is one of several CCCH zinc-finger RNA-binding proteins that regulate cell fate specification during C. elegans embryogenesis. Paradoxically, pos-1 mutants exhibit striking defects in endo-mesoderm development but have wild-type distributions of SKN-1, a key determinant of endo-mesoderm fates. RNAi screens for pos-1 suppressors identified genes encoding the cytoplasmic poly(A)-polymerase homolog GLD-2, the Bicaudal-C homolog GLD-3, and the protein NEG-1. We show that NEG-1 localizes in anterior nuclei, where it negatively regulates endo-mesoderm fates. In posterior cells, POS-1 binds the neg-1 3' UTR to oppose GLD-2 and GLD-3 activities that promote NEG-1 expression and cytoplasmic lengthening of the neg-1 mRNA poly(A) tail. Our findings uncover an intricate series of post-transcriptional regulatory interactions that, together, achieve precise spatial expression of endo-mesoderm fates in C. elegans embryos.
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Affiliation(s)
- Ahmed Elewa
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Masaki Shirayama
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ebru Kaymak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul F Harrison
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria 3800, Australia; Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3053, Australia
| | - David R Powell
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria 3800, Australia; Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3053, Australia
| | - Zhuo Du
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Christopher D Chute
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Life Science and Bioengineering Center, Gateway Park, 60 Prescott Street, Worcester, MA 01605, USA
| | - Hannah Woolf
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dongni Yi
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Takao Ishidate
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Jagan Srinivasan
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Life Science and Bioengineering Center, Gateway Park, 60 Prescott Street, Worcester, MA 01605, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Sean P Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig C Mello
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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Goebels C, Thonn A, Gonzalez-Hilarion S, Rolland O, Moyrand F, Beilharz TH, Janbon G. Introns regulate gene expression in Cryptococcus neoformans in a Pab2p dependent pathway. PLoS Genet 2013; 9:e1003686. [PMID: 23966870 PMCID: PMC3744415 DOI: 10.1371/journal.pgen.1003686] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 06/17/2013] [Indexed: 11/18/2022] Open
Abstract
Most Cryptococccus neoformans genes are interrupted by introns, and alternative splicing occurs very often. In this study, we examined the influence of introns on C. neoformans gene expression. For most tested genes, elimination of introns greatly reduces mRNA accumulation. Strikingly, the number and the position of introns modulate the gene expression level in a cumulative manner. A screen for mutant strains able to express functionally an intronless allele revealed that the nuclear poly(A) binding protein Pab2 modulates intron-dependent regulation of gene expression in C. neoformans. PAB2 deletion partially restored accumulation of intronless mRNA. In addition, our results demonstrated that the essential nucleases Rrp44p and Xrn2p are implicated in the degradation of mRNA transcribed from an intronless allele in C. neoformans. Double mutant constructions and over-expression experiments suggested that Pab2p and Xrn2p could act in the same pathway whereas Rrp44p appears to act independently. Finally, deletion of the RRP6 or the CID14 gene, encoding the nuclear exosome nuclease and the TRAMP complex associated poly(A) polymerase, respectively, has no effect on intronless allele expression. Cryptococcus neoformans is a major human pathogen responsible for deadly infection in immunocompromised patients. The analysis of its genome previously revealed that most of its genes are interrupted by introns. Here, we demonstrate that introns modulate gene expression in a cumulative manner. We also demonstrate that introns can play a positive or a negative role in this process. We identify a nuclear poly(A) binding protein (Pab2p) as implicated in the intron-dependent control of gene expression in C. neoformans. We also demonstrate that the essential nucleases Rrp44p and Xrn2p are implicated in two independent pathways controlling the intron-dependent regulation of gene expression in C. neoformans. Xrn2p regulation seems to depend on Pab2p whereas Rrp44p acts independently. In contrast, the other exosome nuclease Rrp6p and the TRAMP associated poly(A) polymerase Cid14p do not appear to be implicated in this regulation. Our results provide new insights into the regulation of gene expression in eukaryotes and more specifically into the biology and virulence of C. neoformans.
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Affiliation(s)
- Carolin Goebels
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
| | - Aline Thonn
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
| | - Sara Gonzalez-Hilarion
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
| | - Olga Rolland
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
| | - Frederique Moyrand
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
| | - Traude H. Beilharz
- Monash University, Department of Biochemistry and Molecular Biology, Clayton, Australia
| | - Guilhem Janbon
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
- * E-mail:
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Sengupta MS, Low WY, Patterson JR, Kim HM, Traven A, Beilharz TH, Colaiácovo MP, Schisa JA, Boag PR. ifet-1 is a broad-scale translational repressor required for normal P granule formation in C. elegans. J Cell Sci 2012; 126:850-9. [PMID: 23264733 DOI: 10.1242/jcs.119834] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Large cytoplasmic ribonucleoprotein germ granule complexes are a common feature in germ cells. In C. elegans these are called P granules and for much of the life-cycle they associate with nuclear pore complexes in germ cells. P granules are rich in proteins that function in diverse RNA pathways. Here we report that the C. elegans homolog of the eIF4E-transporter IFET-1 is required for oogenesis but not spermatogenesis. We show that IFET-1 is required for translational repression of several maternal mRNAs in the distal gonad and functions in conjunction with the broad-scale translational regulators CGH-1, CAR-1 and PATR-1 to regulate germ cell sex determination. Furthermore we have found that IFET-1 localizes to P granules throughout the gonad and in the germ cell lineage in the embryo. Interestingly, IFET-1 is required for the normal ultrastructure of P granules and for the localization of CGH-1 and CAR-1 to P granules. Our findings suggest that IFET-1 is a key translational regulator and is required for normal P granule formation.
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Affiliation(s)
- Madhu S Sengupta
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
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30
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Traven A, Jänicke A, Harrison P, Swaminathan A, Seemann T, Beilharz TH. Transcriptional profiling of a yeast colony provides new insight into the heterogeneity of multicellular fungal communities. PLoS One 2012; 7:e46243. [PMID: 23029448 PMCID: PMC3460911 DOI: 10.1371/journal.pone.0046243] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 08/28/2012] [Indexed: 11/22/2022] Open
Abstract
Understanding multicellular fungal structures is important for designing better strategies against human fungal pathogens. For example, the ability to form multicellular biofilms is a key virulence property of the yeast Candida albicans. C. albicans biofilms form on indwelling medical devices and are drug resistant, causing serious infections in hospital settings. Multicellular fungal communities are heterogeneous, consisting of cells experiencing different environments. Heterogeneity is likely important for the phenotypic characteristics of communities, yet it is poorly understood. Here we used colonies of the yeast Saccharomyces cerevisiae as a model fungal multicellular structure. We fractionated the outside colony layers from the cells in the center by FACS, using a Cit1-GFP marker expressed exclusively on the outside. Transcriptomics analysis of the two subpopulations revealed that the outside colony layers are actively growing by fermentative metabolism, while the cells residing on the inside are in a resting state and experience changes to mitochondrial activity. Our data shows several parallels with C. albicans biofilms providing insight into the contributions of heterogeneity to biofilm phenotypes. Hallmarks of C. albicans biofilms – the expression of ribosome and translation functions and activation of glycolysis and ergosterol biosynthesis occur on the outside of colonies, while expression of genes associates with sulfur assimilation is observed in the colony center. Cell wall restructuring occurs in biofilms, and cell wall functions are enriched in both fractions: the outside cells display enrichment of cell wall biosynthesis enzymes and cell wall proteins, while the inside cells express cell wall degrading enzymes. Our study also suggests that noncoding transcription and posttranscriptional mRNA regulation play important roles during growth of yeast in colonies, setting the scene for investigating these pathways in the development of multicellular fungal communities.
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Affiliation(s)
- Ana Traven
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail: (THB); (AT)
| | - Amrei Jänicke
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Paul Harrison
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
| | - Angavai Swaminathan
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
| | - Traude H. Beilharz
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail: (THB); (AT)
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Jänicke A, Vancuylenberg J, Boag PR, Traven A, Beilharz TH. ePAT: a simple method to tag adenylated RNA to measure poly(A)-tail length and other 3' RACE applications. RNA 2012; 18:1289-95. [PMID: 22543866 PMCID: PMC3358650 DOI: 10.1261/rna.031898.111] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The addition of a poly(A)-tail to the 3' termini of RNA molecules influences stability, nuclear export, and efficiency of translation. In the cytoplasm, dynamic changes in the length of the poly(A)-tail have long been recognized as reflective of the switch between translational silence and activation. Thus, measurement of the poly(A)-tail associated with any given mRNA at steady-state can serve as a surrogate readout of its translation-state. Here, we describe a simple new method to 3'-tag adenylated RNA in total RNA samples using the intrinsic property of Escherichia coli DNA polymerase I to extend an RNA primer using a DNA template. This tag can serve as an anchor for cDNA synthesis and subsequent gene-specific PCR to assess poly(A)-tail length. We call this method extension Poly(A) Test (ePAT). The ePAT approach is as efficient as traditional Ligation-Mediated Poly(A) Test (LM-PAT) assays, avoids problems of internal priming associated with oligo-dT-based methods, and allows for the accurate analysis of both the poly(A)-tail length and alternate 3' UTR usage in 3' RACE applications.
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Affiliation(s)
- Amrei Jänicke
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - John Vancuylenberg
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Peter R. Boag
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Ana Traven
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Traude H. Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Corresponding author.E-mail .
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32
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Uwamahoro N, Qu Y, Jelicic B, Lo TL, Beaurepaire C, Bantun F, Quenault T, Boag PR, Ramm G, Callaghan J, Beilharz TH, Nantel A, Peleg AY, Traven A. The functions of Mediator in Candida albicans support a role in shaping species-specific gene expression. PLoS Genet 2012; 8:e1002613. [PMID: 22496666 PMCID: PMC3320594 DOI: 10.1371/journal.pgen.1002613] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 02/07/2012] [Indexed: 01/01/2023] Open
Abstract
The Mediator complex is an essential co-regulator of RNA polymerase II that is conserved throughout eukaryotes. Here we present the first study of Mediator in the pathogenic fungus Candida albicans. We focused on the Middle domain subunit Med31, the Head domain subunit Med20, and Srb9/Med13 from the Kinase domain. The C. albicans Mediator shares some roles with model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, such as functions in the response to certain stresses and the role of Med31 in the expression of genes regulated by the activator Ace2. The C. albicans Mediator also has additional roles in the transcription of genes associated with virulence, for example genes related to morphogenesis and gene families enriched in pathogens, such as the ALS adhesins. Consistently, Med31, Med20, and Srb9/Med13 contribute to key virulence attributes of C. albicans, filamentation, and biofilm formation; and ALS1 is a biologically relevant target of Med31 for development of biofilms. Furthermore, Med31 affects virulence of C. albicans in the worm infection model. We present evidence that the roles of Med31 and Srb9/Med13 in the expression of the genes encoding cell wall adhesins are different between S. cerevisiae and C. albicans: they are repressors of the FLO genes in S. cerevisiae and are activators of the ALS genes in C. albicans. This suggests that Mediator subunits regulate adhesion in a distinct manner between these two distantly related fungal species.
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Affiliation(s)
- Nathalie Uwamahoro
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Yue Qu
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Branka Jelicic
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Tricia L. Lo
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Cecile Beaurepaire
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada
| | - Farkad Bantun
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Tara Quenault
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Peter R. Boag
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Georg Ramm
- Monash Micro Imaging, Monash University, Clayton, Australia
| | - Judy Callaghan
- Monash Micro Imaging, Monash University, Clayton, Australia
| | - Traude H. Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - André Nantel
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada
- * E-mail: (AT); (AN)
| | - Anton Y. Peleg
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Ana Traven
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail: (AT); (AN)
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Clancy JL, Wei GH, Echner N, Humphreys DT, Beilharz TH, Preiss T. mRNA isoform diversity can obscure detection of miRNA-mediated control of translation. RNA 2011; 17:1025-1031. [PMID: 21467217 PMCID: PMC3096034 DOI: 10.1261/rna.2567611] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 03/03/2011] [Indexed: 05/30/2023]
Abstract
Reporter-based studies support inhibition of translation at the level of initiation as a substantial component of the miRNA mechanism, yet recent global analyses have suggested that they predominantly act through decreasing target mRNA stability. Cells commonly coexpress several processing isoforms of an mRNA, which may also differ in their regulatory untranslated regions (UTR). In particular, cancer cells are known to express high levels of short 3' UTR isoforms that evade miRNA-mediated regulation, whereas longer 3' UTRs predominate in nontransformed cells. To test whether mRNA isoform diversity can obscure detection of miRNA-mediated control at the level of translation, we assayed the responses of 11 endogenous let-7 targets to inactivation of this miRNA in HeLa cells, an intensively studied model system. We show that translational regulation in many cases appears to be modest when measuring the composite polysome profile of all extant isoforms of a given mRNA by density ultracentrifugation. In contrast, we saw clear effects at the level of translation initiation for multiple examples when selectively profiling mRNA isoforms carrying the 5' or 3' untranslated regions that were actually permissive to let-7 action, or when let-7 and a second targeting miRNA were jointly manipulated. Altogether, these results highlight a caveat to the mechanistic interpretation of data from global miRNA target analyses in transformed cells. Importantly, they reaffirm the importance of translational control as part of the miRNA mechanism in animal cells.
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Affiliation(s)
- Jennifer L Clancy
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
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34
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Abstract
Nearly all eukaryotic mRNAs terminate in a poly(A) tail that serves important roles in mRNA utilization. In the cytoplasm, the poly(A) tail promotes both mRNA stability and translation, and these functions are frequently regulated through changes in tail length. To identify the scope of poly(A) tail length control in a transcriptome, we developed the polyadenylation state microarray (PASTA) method. It involves the purification of mRNA based on poly(A) tail length using thermal elution from poly(U) sepharose, followed by microarray analysis of the resulting fractions. In this chapter we detail our PASTA approach and describe some methods for bulk and mRNA-specific poly(A) tail length measurements of use to monitor the procedure and independently verify the microarray data.
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Affiliation(s)
- Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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35
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Dagley MJ, Gentle IE, Beilharz TH, Pettolino FA, Djordjevic JT, Lo TL, Uwamahoro N, Rupasinghe T, Tull DL, McConville M, Beaurepaire C, Nantel A, Lithgow T, Mitchell AP, Traven A. Cell wall integrity is linked to mitochondria and phospholipid homeostasis in Candida albicans through the activity of the post-transcriptional regulator Ccr4-Pop2. Mol Microbiol 2010; 79:968-89. [PMID: 21299651 DOI: 10.1111/j.1365-2958.2010.07503.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cell wall is essential for viability of fungi and is an effective drug target in pathogens such as Candida albicans. The contribution of post-transcriptional gene regulators to cell wall integrity in C. albicans is unknown. We show that the C. albicans Ccr4-Pop2 mRNA deadenylase, a regulator of mRNA stability and translation, is required for cell wall integrity. The ccr4/pop2 mutants display reduced wall β-glucans and sensitivity to the echinocandin caspofungin. Moreover, the deadenylase mutants are compromised for filamentation and virulence. We demonstrate that defective cell walls in the ccr4/pop2 mutants are linked to dysfunctional mitochondria and phospholipid imbalance. To further understand mitochondrial function in cell wall integrity, we screened a Saccharomyces cerevisiae collection of mitochondrial mutants. We identify several mitochondrial proteins required for caspofungin tolerance and find a connection between mitochondrial phospholipid homeostasis and caspofungin sensitivity. We focus on the mitochondrial outer membrane SAM complex subunit Sam37, demonstrating that it is required for both trafficking of phospholipids between the ER and mitochondria and cell wall integrity. Moreover, in C. albicans also Sam37 is essential for caspofungin tolerance. Our study provides the basis for an integrative view of mitochondrial function in fungal cell wall biogenesis and resistance to echinocandin antifungal drugs.
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Affiliation(s)
- Michael J Dagley
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
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36
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Abstract
A flurry of recent studies, carried out primarily in transfected cells or in vitro translation systems, have attempted to reveal the molecular means by which animal microRNAs (miRNAs) attenuate mRNA translation. Despite these intense efforts it has not yet been possible to derive a consensus model for such a mechanism. Here we summarise our own experimental contributions to this topic, which led us to propose that miRNAs control early translation initiation by affecting eukaryotic initiation factor 4E/cap structure and poly(A) tail function, and place them in a current context of this rapidly moving and challenging field.
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Affiliation(s)
- Traude H Beilharz
- Molecular Genetics Division, Victor Chang Cardiac Research Institute (VCCRI), Darlinghurst, Sydney, NSW, 2010, Australia
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37
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Beilharz TH, Humphreys DT, Clancy JL, Thermann R, Martin DIK, Hentze MW, Preiss T. microRNA-mediated messenger RNA deadenylation contributes to translational repression in mammalian cells. PLoS One 2009; 4:e6783. [PMID: 19710908 PMCID: PMC2728509 DOI: 10.1371/journal.pone.0006783] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 07/24/2009] [Indexed: 12/11/2022] Open
Abstract
Animal microRNAs (miRNAs) typically regulate gene expression by binding to partially complementary target sites in the 3' untranslated region (UTR) of messenger RNA (mRNA) reducing its translation and stability. They also commonly induce shortening of the mRNA 3' poly(A) tail, which contributes to their mRNA decay promoting function. The relationship between miRNA-mediated deadenylation and translational repression has been less clear. Using transfection of reporter constructs carrying three imperfectly matching let-7 target sites in the 3' UTR into mammalian cells we observe rapid target mRNA deadenylation that precedes measureable translational repression by endogenous let-7 miRNA. Depleting cells of the argonaute co-factors RCK or TNRC6A can impair let-7-mediated repression despite ongoing mRNA deadenylation, indicating that deadenylation alone is not sufficient to effect full repression. Nevertheless, the magnitude of translational repression by let-7 is diminished when the target reporter lacks a poly(A) tail. Employing an antisense strategy to block deadenylation of target mRNA with poly(A) tail also partially impairs translational repression. On the one hand, these experiments confirm that tail removal by deadenylation is not strictly required for translational repression. On the other hand they show directly that deadenylation can augment miRNA-mediated translational repression in mammalian cells beyond stimulating mRNA decay. Taken together with published work, these results suggest a dual role of deadenylation in miRNA function: it contributes to translational repression as well as mRNA decay and is thus critically involved in establishing the quantitatively appropriate physiological response to miRNAs.
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Affiliation(s)
- Traude H. Beilharz
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- School of Biotechnology & Biomolecular Sciences and St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - David T. Humphreys
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Jennifer L. Clancy
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Rolf Thermann
- European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, Germany
| | - David I. K. Martin
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Matthias W. Hentze
- European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, Germany
| | - Thomas Preiss
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- School of Biotechnology & Biomolecular Sciences and St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail:
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Beilharz TH, Preiss T. Transcriptome-wide measurement of mRNA polyadenylation state. Methods 2009; 48:294-300. [PMID: 19233282 DOI: 10.1016/j.ymeth.2009.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 02/09/2009] [Accepted: 02/09/2009] [Indexed: 10/21/2022] Open
Abstract
The 3' poly(A) tail has important roles throughout the eukaryotic mRNA life cycle. A characteristic aspect of poly(A) tail function is furthermore that it can be modulated by changes in its length. This is in turn a well-recognised cellular means to regulate both, mRNA translation and stability, and a positive correlation has often been found between the efficiency of mRNA translation and the length of its poly(A) tail. Here we describe methodology to measure mRNA polyadenylation state in a transcriptome-wide manner, using separation of cellular mRNA populations on poly(U) sepharose in combination with microarray analysis of the resulting fractions. We further detail methods for bulk and mRNA-specific poly(A) tail length measurements to monitor the efficiency of initial mRNA separation and to verify candidates selected from the microarray data. Although detailed here for the study of yeast mRNAs, these methods are adaptable to the investigation of any cellular context in which poly(A) tail length control is known or suspected to operate.
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Affiliation(s)
- Traude H Beilharz
- Molecular Genetics Division, Victor Chang Cardiac Research Institute (VCCRI), Lowy Packer Building, 405 Liverpool Street, Darlinghurst (Sydney), NSW 2010, Australia.
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Abstract
Control of poly(A) tail length can affect translation and stability of eukaryotic mRNAs. Although well established for individual cases, it was not known to what extent this type of adjustable gene control is used to shape expression of eukaryotic transcriptomes. Here we report on microarray-based measurements of mRNA poly(A) tail lengths and association with the poly(A)-binding protein Pab1 in S. cerevisiae, revealing extensive correlation between tail length and other physical and functional mRNA characteristics. Gene ontology analyses and further directed experiments indicate coregulation of tail length on functionally and cytotopically related mRNAs to coordinate cell-cycle progression, ribosome biogenesis, and retrotransposon expression. We show that the 3'-untranslated region drives transcript-specific adenylation control and translational efficiency of multiple mRNAs. Our findings suggest a wide-spread interdependence between 3'-untranslated region-mediated poly(A) tail length control, Pab1 binding, and mRNA translation in budding yeast. They further provide a molecular explanation for deadenylase function in the cell cycle and suggest additional cellular processes that depend on control of mRNA polyadenylation.
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Affiliation(s)
- Traude H Beilharz
- Molecular Genetics Program, Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW, Australia
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Lackner DH, Beilharz TH, Marguerat S, Mata J, Watt S, Schubert F, Preiss T, Bähler J. A network of multiple regulatory layers shapes gene expression in fission yeast. Mol Cell 2007; 26:145-55. [PMID: 17434133 PMCID: PMC1885965 DOI: 10.1016/j.molcel.2007.03.002] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 02/12/2007] [Accepted: 03/01/2007] [Indexed: 01/26/2023]
Abstract
Gene expression is controlled at multiple layers, and cells may integrate different regulatory steps for coherent production of proper protein levels. We applied various microarray-based approaches to determine key gene-expression intermediates in exponentially growing fission yeast, providing genome-wide data for translational profiles, mRNA steady-state levels, polyadenylation profiles, start-codon sequence context, mRNA half-lives, and RNA polymerase II occupancy. We uncovered widespread and unexpected relationships between distinct aspects of gene expression. Translation and polyadenylation are aligned on a global scale with both the lengths and levels of mRNAs: efficiently translated mRNAs have longer poly(A) tails and are shorter, more stable, and more efficiently transcribed on average. Transcription and translation may be independently but congruently optimized to streamline protein production. These rich data sets, all acquired under a standardized condition, reveal a substantial coordination between regulatory layers and provide a basis for a systems-level understanding of multilayered gene-expression programs.
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Affiliation(s)
- Daniel H. Lackner
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Traude H. Beilharz
- Molecular Genetics Program, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Samuel Marguerat
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Juan Mata
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Stephen Watt
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Falk Schubert
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Thomas Preiss
- Molecular Genetics Program, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jürg Bähler
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
- Corresponding author
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Woolstencroft RN, Beilharz TH, Cook MA, Preiss T, Durocher D, Tyers M. Ccr4 contributes to tolerance of replication stress through control of CRT1 mRNA poly(A) tail length. J Cell Sci 2007; 119:5178-92. [PMID: 17158920 DOI: 10.1242/jcs.03221] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Saccharomyces cerevisiae, DNA replication stress activates the replication checkpoint, which slows S-phase progression, stabilizes slowed or stalled replication forks, and relieves inhibition of the ribonucleotide reductase (RNR) complex. To identify novel genes that promote cellular viability after replication stress, the S. cerevisiae non-essential haploid gene deletion set (4812 strains) was screened for sensitivity to the RNR inhibitor hydroxyurea (HU). Strains bearing deletions in either CCR4 or CAF1/POP2, which encode components of the cytoplasmic mRNA deadenylase complex, were particularly sensitive to HU. We found that Ccr4 cooperated with the Dun1 branch of the replication checkpoint, such that ccr4Delta dun1Delta strains exhibited irreversible hypersensitivity to HU and persistent activation of Rad53. Moreover, because ccr4Delta and chk1Delta exhibited epistasis in several genetic contexts, we infer that Ccr4 and Chk1 act in the same pathway to overcome replication stress. A counterscreen for suppressors of ccr4Delta HU sensitivity uncovered mutations in CRT1, which encodes the transcriptional repressor of the DNA-damage-induced gene regulon. Whereas Dun1 is known to inhibit Crt1 repressor activity, we found that Ccr4 regulates CRT1 mRNA poly(A) tail length and may subtly influence Crt1 protein abundance. Simultaneous overexpression of RNR2, RNR3 and RNR4 partially rescued the HU hypersensitivity of a ccr4Delta dun1Delta strain, consistent with the notion that the RNR genes are key targets of Crt1. These results implicate the coordinated regulation of Crt1 via Ccr4 and Dun1 as a crucial nodal point in the response to DNA replication stress.
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H Beilharz T, Preiss T. ?Cradle?to?grave? regulation of mRNA fate. Microbiol Aust 2007. [DOI: 10.1071/ma07085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Microarray studies in Saccharomyces cerevisiae have set the benchmark for genome-wide analyses, available data-sets covering practically every stage of gene expression from DNA-binding by transcription factors to mRNA export, sub-cellular localisation, translation and decay. A theme to emerge from such data has been the prevalence of coordinate gene regulation. Thus, gene modules or ?regulons? are well recognised at the level of gene transcription and the activity of transcription factors provides an obvious molecular explanation for such coordination. More surprising was the organisation of mRNAs into co-regulated ?post-transcriptional operons?. RNA-binding proteins (RBPs), but also ribonucleoprotein (RNP) complexes involving noncoding RNA, have been proposed as the conceptual equivalent of transcription factors at this level.
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Clancy JL, Nousch M, Humphreys DT, Westman BJ, Beilharz TH, Preiss T. Methods to Analyze MicroRNA‐Mediated Control of mRNA Translation. Methods Enzymol 2007; 431:83-111. [DOI: 10.1016/s0076-6879(07)31006-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Beilharz TH, Preiss T. Translational profiling: The genome-wide measure of the nascent proteome. Briefings in Functional Genomics and Proteomics 2004; 3:103-11. [PMID: 15355593 DOI: 10.1093/bfgp/3.2.103] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Translation in eukaryotic cells is both physically and temporally separated from transcription. This provides cells with extended options to alter their proteome: (1) directly, by synchronizing translation with an altering transcriptional profile; (2) by imposing a changed translational control over transcripts already present in the transcriptome; or (3) by a combination of (1) and (2). In this paper, recent findings in the controlled translation of the transcriptome using microarray analyses are reviewed. A guide to the current technologies and data analysis is also provided, and future directions in the study of translational control as the interface between the transcriptome and the proteome are outlined. This survey is focused on the yeast Saccharomyces cerevisiae, but the topics covered have universal relevance to the control of translation in eukaryotic cells.
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Affiliation(s)
- Traude H Beilharz
- Molecular Genetics Program, Victor Chrang Cardiac Research Institute and St Vincent's Clinical School, University of New South Wales, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
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Miller EA, Beilharz TH, Malkus PN, Lee MCS, Hamamoto S, Orci L, Schekman R. Multiple cargo binding sites on the COPII subunit Sec24p ensure capture of diverse membrane proteins into transport vesicles. Cell 2003; 114:497-509. [PMID: 12941277 DOI: 10.1016/s0092-8674(03)00609-3] [Citation(s) in RCA: 398] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have characterized the mechanisms of cargo selection into ER-derived vesicles by the COPII subunit Sec24p. We identified a site on Sec24p that recognizes the v-SNARE Bet1p and show that packaging of a number of cargo molecules is disrupted when mutations are introduced at this site. Surprisingly, cargo proteins affected by these mutations did not share a single common sorting signal, nor were proteins sharing a putative class of signal affected to the same degree. We show that the same site is conserved as a cargo-interaction domain on the Sec24p homolog Lst1p, which only packages a subset of the cargoes recognized by Sec24p. Finally, we identified an additional mutation that defines another cargo binding domain on Sec24p, which specifically interacts with the SNARE Sec22p. Together, our data support a model whereby Sec24p proteins contain multiple independent cargo binding domains that allow for recognition of a diverse set of sorting signals.
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Affiliation(s)
- Elizabeth A Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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