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Réblová M, Jaklitsch WM, Réblová K, Štěpánek V. Phylogenetic Reconstruction of the Calosphaeriales and Togniniales Using Five Genes and Predicted RNA Secondary Structures of ITS, and Flabellascus tenuirostris gen. et sp. nov. PLoS One 2015; 10:e0144616. [PMID: 26699541 PMCID: PMC4689446 DOI: 10.1371/journal.pone.0144616] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 09/09/2015] [Accepted: 11/20/2015] [Indexed: 11/18/2022] Open
Abstract
The Calosphaeriales is revisited with new collection data, living cultures, morphological studies of ascoma centrum, secondary structures of the internal transcribed spacer (ITS) rDNA and phylogeny based on novel DNA sequences of five nuclear ribosomal and protein-coding loci. Morphological features, molecular evidence and information from predicted RNA secondary structures of ITS converged upon robust phylogenies of the Calosphaeriales and Togniniales. The current concept of the Calosphaeriales includes the Calosphaeriaceae and Pleurostomataceae encompassing five monophyletic genera, Calosphaeria, Flabellascus gen. nov., Jattaea, Pleurostoma and Togniniella, strongly supported by Bayesian and Maximum Likelihood methods. The structural elements of ITS1 form characteristic patterns that are phylogenetically conserved, corroborate observations based on morphology and have a high predictive value at the generic level. Three major clades containing 44 species of Phaeoacremonium were recovered in the closely related Togniniales based on ITS, actin and β-tubulin sequences. They are newly characterized by sexual and RNA structural characters and ecology. This approach is a first step towards understanding of the molecular systematics of Phaeoacremonium and possibly its new classification. In the Calosphaeriales, Jattaea aphanospora sp. nov. and J. ribicola sp. nov. are introduced, Calosphaeria taediosa is combined in Jattaea and epitypified. The sexual morph of Phaeoacremonium cinereum was encountered for the first time on decaying wood and obtained in vitro. In order to achieve a single nomenclature, the genera of asexual morphs linked with the Calosphaeriales are transferred to synonymy of their sexual morphs following the principle of priority, i.e. Calosphaeriophora to Calosphaeria, Phaeocrella to Togniniella and Pleurostomophora to Pleurostoma. Three new combinations are proposed, i.e. Pleurostoma ochraceum comb. nov., P. repens comb. nov. and P. richardsiae comb. nov. The morphology-based key is provided to facilitate identification of genera accepted in the Calosphaeriales.
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Affiliation(s)
- Martina Réblová
- Department of Taxonomy, Institute of Botany of the Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
- * E-mail:
| | - Walter M. Jaklitsch
- Department of Forest and Soil Sciences, Forest Pathology and Forest Protection, Institute of Forest Entomology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Botany and Biodiversity Research, Division of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | - Kamila Réblová
- Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Václav Štěpánek
- Laboratory of Enzyme Technology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
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202
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Salari S, Khosravi AR, Mousavi SAA, Nikbakht-Brojeni GH. Mechanisms of resistance to fluconazole in Candida albicans clinical isolates from Iranian HIV-infected patients with oropharyngeal candidiasis. J Mycol Med 2015; 26:35-41. [PMID: 26627124 DOI: 10.1016/j.mycmed.2015.10.007] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/27/2015] [Accepted: 10/04/2015] [Indexed: 11/19/2022]
Abstract
OBJECTIVES The opportunistic pathogen Candida albicans is the major agent of oropharyngeal candidiasis (OPC) in HIV/AIDS patients. The increased use of fluconazole can lead to the emergence of azole-resistant strains and treatment failures in PLWH (people living with HIV) receiving long-term therapy for OPC. The purpose of this study was to evaluate CDR1, CDR2, MDR1, and ERG11 gene expression in C. albicans clinically isolated from HIV-infected patients in Iran. PATIENTS AND METHODS In this study, we evaluated the molecular mechanisms of azole resistance in 20 fluconazole-resistant C. albicans isolates obtained from Iranian HIV-infected patients with oropharyngeal candidiasis by Real-Time polymerase chain reaction. RESULTS The overexpression of drug efflux pump CDR1 gene was found to be the major resistance mechanism observed in these isolates. The overexpression of the CDR1 gene correlated strongly with increasing resistance to fluconazole (P<0.05). Additionally, an increased level of mRNA in ERG11 was not observed in any of the tested isolates. CONCLUSIONS Our findings suggested that the CDR1 gene expression to fluconazole resistance in C. albicans is greater than other known genes.
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Affiliation(s)
- S Salari
- Department of Medical Parasitology and Mycology, Kerman University of Medical Sciences, Kerman, Iran; Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Kerman University of Medical Sciences, Kerman, Iran.
| | - A R Khosravi
- Mycology Research Center, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - S A A Mousavi
- Department of Medical Parasitology and Mycology, Kerman University of Medical Sciences, Kerman, Iran
| | - G H Nikbakht-Brojeni
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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203
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Sathishkumar Y, Krishnaraj C, Rajagopal K, Sen D, Lee YS. High throughput de novo RNA sequencing elucidates novel responses in Penicillium chrysogenum under microgravity. Bioprocess Biosyst Eng 2015; 39:223-31. [PMID: 26603994 DOI: 10.1007/s00449-015-1506-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 09/14/2015] [Accepted: 11/10/2015] [Indexed: 12/24/2022]
Abstract
In this study, the transcriptional alterations in Penicillium chrysogenum under simulated microgravity conditions were analyzed for the first time using an RNA-Seq method. The increasing plethora of eukaryotic microbial flora inside the spaceship demands the basic understanding of fungal biology in the absence of gravity vector. Penicillium species are second most dominant fungal contaminant in International Space Station. Penicillium chrysogenum an industrially important organism also has the potential to emerge as an opportunistic pathogen for the astronauts during the long-term space missions. But till date, the cellular mechanisms underlying the survival and adaptation of Penicillium chrysogenum to microgravity conditions are not clearly elucidated. A reference genome for Penicillium chrysogenum is not yet available in the NCBI database. Hence, we performed comparative de novo transcriptome analysis of Penicillium chrysogenum grown under microgravity versus normal gravity. In addition, the changes due to microgravity are documented at the molecular level. Increased response to the environmental stimulus, changes in the cell wall component ABC transporter/MFS transporters are noteworthy. Interestingly, sustained increase in the expression of Acyl-coenzyme A: isopenicillin N acyltransferase (Acyltransferase) under microgravity revealed the significance of gravity in the penicillin production which could be exploited industrially.
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Affiliation(s)
- Yesupatham Sathishkumar
- Department of Forest Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
| | - Chandran Krishnaraj
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, 561-756, Republic of Korea
| | | | - Dwaipayan Sen
- School of Biosciences and Technology, VIT University, Vellore, 632014, India
- Cellular and Molecular Therapeutics Laboratory, Centre for Biomaterials, Cellular and Molecular Theranostics, School of Biosciences and Technology, VIT University, Vellore, 632014, India
| | - Yang Soo Lee
- Department of Forest Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
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Chiba S, Lin YH, Kondo H, Kanematsu S, Suzuki N. A novel betapartitivirus RnPV6 from Rosellinia necatrix tolerates host RNA silencing but is interfered by its defective RNAs. Virus Res 2015; 219:62-72. [PMID: 26494168 DOI: 10.1016/j.virusres.2015.10.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [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: 08/25/2015] [Revised: 10/10/2015] [Accepted: 10/14/2015] [Indexed: 12/17/2022]
Abstract
The family Partitiviridae comprises of five genera with bi-segmented dsRNA genomes that accommodate members infecting plants, fungi or protists. All partitiviruses with only a few exceptions cause asymptomatic infections. We report the characterization of a novel betapartitivirus termed Rosellinia necatrix partitivirus 6 (RnPV6) from a field isolate of a plant pathogenic fungus, white root rot fungus. RnPV6 has typical partitivirus features: dsRNA1 and dsRNA2 are 2462 and 2499bps in length encoding RNA-dependent RNA polymerase and capsid protein. Purified particles are spherical with a diameter of 30nm. Taking advantage of infectivity as virions, RnPV6 was introduced into a model filamentous fungal host, chestnut blight fungus to investigate virus/host interactions. Unlike other partitiviruses tested previously, RnPV6 induced profound phenotypic alterations with symptoms characterized by a reduced growth rate and enhanced pigmentation and was tolerant to host RNA silencing. In addition, a variety of defective RNAs derived from dsRNA1 appear after virion transfection. These sub-viral RNAs were shown to interfere with RnPV6 replication, at least for that of cognate segment dsRNA1. Presence of these sub-viral elements resulted in reduced symptom expression by RnPV6, suggesting their nature as defective-interfering RNAs. The features of RnPV6 are similar to but distinct from those of a previously reported alphapartitivirus, Rosellinia necatrix partitivirus 2 that is susceptible to RNA silencing.
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Affiliation(s)
- Sotaro Chiba
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.
| | - Yu-Hsin Lin
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.
| | - Satoko Kanematsu
- Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Morioka, Iwate 020-0123, Japan.
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.
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205
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Geisberg JV, Moqtaderi Z. Genome-Wide Study of mRNA Isoform Half-Lives. Methods Mol Biol 2015; 1358:317-23. [PMID: 26463393 DOI: 10.1007/978-1-4939-3067-8_20] [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] [Indexed: 02/23/2023]
Abstract
In eukaryotes, RNA polymerase II-driven transcription and processing results in the formation of numerous mRNA 3' isoforms that for any given gene may differ from one another by as little as a single nucleotide. These 3' isoforms can vary in physical properties that may affect their function and stability. Here, we outline a systematic framework to measure individual mRNA 3' isoform half-lives on a genome-wide level in S. cerevisiae. Our approach utilizes the Anchor-Away system to sequester RNA polymerase II (Pol II) in the cytoplasm followed by direct single-molecule RNA sequencing to generate a highly detailed view of 3' isoform stability under most physiological conditions without many of the adverse effects associated with commonly used alternative approaches.
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Affiliation(s)
- Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
| | - Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
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206
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Loureiro A, Azinheira HG, Silva MDC, Talhinhas P. A method for obtaining RNA from Hemileia vastatrix appressoria produced in planta, suitable for transcriptomic analyses. Fungal Biol 2015; 119:1093-1099. [PMID: 26466882 DOI: 10.1016/j.funbio.2015.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 02/11/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 11/20/2022]
Abstract
Appressoria are the first infection structures developed by rust fungi and require specific topographic signals from the host for their differentiation. The ease in obtaining appressoria in vitro for these biotrophic fungi led to studies concerning gene expression and gene discovery at appressorial level, avoiding the need to distinguish plant and fungal transcripts. However, in some pathosystems, it was observed that gene expression in appressoria seems to be influenced by host-derived signals, suggesting that transcriptomic analyses performed from in planta differentiated appressoria would be potentially more informative than those from in vitro differentiated appressoria. Nevertheless analysing appressorial RNA obtained from in planta samples is often hampered by an excessive dilution of fungal RNA within plant RNA, besides uncertainty regarding the fungal or plant origin of RNA from highly conserved genes. To circumvent these difficulties, we have recovered Hemileia vastatrix appressoria from Arabica coffee leaf surface using a film of nitrocellulose dissolved in butyl and ethyl acetates (nail polish), and extracted fungal RNA from the polish peel. RNA thus obtained is of good quality and usable for cDNA synthesis and transcriptomic (quantitative PCR) studies. This method could provide the means to investigate specific host-induced appressoria-related fungal pathogenicity factors.
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Affiliation(s)
- Andreia Loureiro
- (CIFC) Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal; (LEAF) Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Helena Gil Azinheira
- (CIFC) Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal; (LEAF) Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal.
| | - Maria do Céu Silva
- (CIFC) Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal; (LEAF) Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Pedro Talhinhas
- (CIFC) Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal; (LEAF) Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
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207
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Zafrir Z, Tuller T. Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi. RNA 2015; 21:1704-1718. [PMID: 26246046 PMCID: PMC4574748 DOI: 10.1261/rna.051268.115] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/25/2015] [Indexed: 06/04/2023]
Abstract
RNA splicing is the central process of intron removal in eukaryotes known to regulate various cellular functions such as growth, development, and response to external signals. The canonical sequences indicating the splicing sites needed for intronic boundary recognition are well known. However, the roles and evolution of the local folding of intronic and exonic sequence features adjacent to splice sites has yet to be thoroughly studied. Here, focusing on four fungi (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, and Candida albicans), we performed for the first time a comprehensive high-resolution study aimed at characterizing the encoding of intronic splicing efficiency in pre-mRNA transcripts and its effect on intron evolution. Our analysis supports the conjecture that pre-mRNA local folding strength at intronic boundaries is under selective pressure, as it significantly affects splicing efficiency. Specifically, we show that in the immediate region of 12-30 nucleotides (nt) surrounding the intronic donor site there is a preference for weak pre-mRNA folding; similarly, in the region of 15-33 nt surrounding the acceptor and branch sites there is a preference for weak pre-mRNA folding. We also show that in most cases there is a preference for strong pre-mRNA folding further away from intronic splice sites. In addition, we demonstrate that these signals are not associated with gene-specific functions, and they correlate with splicing efficiency measurements (r = 0.77, P = 2.98 × 10(-21)) and with expression levels of the corresponding genes (P = 1.24 × 10(-19)). We suggest that pre-mRNA folding strength in the above-mentioned regions has a direct effect on splicing efficiency by improving the recognition of intronic boundaries. These new discoveries are contributory steps toward a broader understanding of splicing regulation and intronic/transcript evolution.
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Affiliation(s)
- Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 69978, Israel The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
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208
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Martin-Tumasz S, Brow DA. Saccharomyces cerevisiae Sen1 Helicase Domain Exhibits 5'- to 3'-Helicase Activity with a Preference for Translocation on DNA Rather than RNA. J Biol Chem 2015; 290:22880-9. [PMID: 26198638 PMCID: PMC4645616 DOI: 10.1074/jbc.m115.674002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 07/19/2015] [Indexed: 11/06/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, the essential nuclear helicase Sen1 is required for efficient termination of transcription of short noncoding RNA genes by RNA polymerase II. However, the mechanism by which Sen1 promotes transcription termination is not known. Prior biochemical studies on the Sen1 homolog from Schizosaccharomyces pombe showed that it can bind and unwind both DNA and RNA, but the S. pombe protein is not essential and has not been demonstrated to function in transcription. Furthermore, Sen1 from either yeast has not previously been expressed as a recombinant protein, due to its large molecular mass (252 kDa in S. cerevisiae). Here, we report the purification and characterization of the 89-kDa S. cerevisiae Sen1 helicase domain (Sen1-HD) produced in Escherichia coli. Sen1-HD binds single-stranded RNA and DNA with similar affinity in the absence of ATP, but it binds RNA more stably than DNA in the presence of ATP, apparently due to a slower translocation rate on RNA. Translocation occurs in the 5' to 3' direction, as for the S. pombe protein. When purified from E. coli at a moderate salt concentration, Sen1-HD was associated with short RNAs that are enriched for the trinucleotide repeat (CAN)4. We propose that Sen1 binds to RNAs and prevents their stable pairing with DNA, consistent with in vivo studies by others showing increased R-loop (RNA/DNA hybrid) formation when Sen1 activity is impaired by mutations. Our results are consistent with a model in which Sen1 promotes transcription termination by resolving R-loops.
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Affiliation(s)
- Stephen Martin-Tumasz
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - David A Brow
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
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209
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Gritsenko AA, Hulsman M, Reinders MJT, de Ridder D. Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data. PLoS Comput Biol 2015; 11:e1004336. [PMID: 26275099 PMCID: PMC4537299 DOI: 10.1371/journal.pcbi.1004336] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 10/21/2014] [Accepted: 05/10/2015] [Indexed: 11/19/2022] Open
Abstract
Translation of RNA to protein is a core process for any living organism. While for some steps of this process the effect on protein production is understood, a holistic understanding of translation still remains elusive. In silico modelling is a promising approach for elucidating the process of protein synthesis. Although a number of computational models of the process have been proposed, their application is limited by the assumptions they make. Ribosome profiling (RP), a relatively new sequencing-based technique capable of recording snapshots of the locations of actively translating ribosomes, is a promising source of information for deriving unbiased data-driven translation models. However, quantitative analysis of RP data is challenging due to high measurement variance and the inability to discriminate between the number of ribosomes measured on a gene and their speed of translation. We propose a solution in the form of a novel multi-scale interpretation of RP data that allows for deriving models with translation dynamics extracted from the snapshots. We demonstrate the usefulness of this approach by simultaneously determining for the first time per-codon translation elongation and per-gene translation initiation rates of Saccharomyces cerevisiae from RP data for two versions of the Totally Asymmetric Exclusion Process (TASEP) model of translation. We do this in an unbiased fashion, by fitting the models using only RP data with a novel optimization scheme based on Monte Carlo simulation to keep the problem tractable. The fitted models match the data significantly better than existing models and their predictions show better agreement with several independent protein abundance datasets than existing models. Results additionally indicate that the tRNA pool adaptation hypothesis is incomplete, with evidence suggesting that tRNA post-transcriptional modifications and codon context may play a role in determining codon elongation rates. Translation, the process of synthesizing proteins from mRNA templates, is an essential biological process in all living organisms. A better understanding of this process will have ramifications in various fields—from gene regulation, disease understanding and medicine to biotechnology and synthetic biology. Nonetheless, a holistic understanding of the processes remains elusive, making computational modelling a promising approach for studying it. However, accurate modelling of translation is challenging due to many assumptions made by such models and due to the sheer number of parameters that need to be specified. Here, we propose to fit models of translation onto ribosome profiling measurements, which record snapshots of the locations of actively translating ribosomes on mRNAs from millions of cells. We develop statistical and computational methods for fitting the Totally Asymmetric Exclusion Process (TASEP) models of translation on these measurements and verify them by deriving highly accurate translation models for the baker’s yeast Saccharomyces cerevisiae, which outperform existing models on independent datasets. We find that fitted elongation rate parameters from the derived models deviate significantly from the widely accepted tRNA pool adaptation hypothesis.
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Affiliation(s)
- Alexey A. Gritsenko
- The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
- Platform Green Synthetic Biology, Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Marc Hulsman
- The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
| | - Marcel J. T. Reinders
- The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Dick de Ridder
- The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
- Platform Green Synthetic Biology, Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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210
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Choi J, Chung H, Lee GW, Koh SK, Chae SK, Lee YH. Genome-Wide Analysis of Hypoxia-Responsive Genes in the Rice Blast Fungus, Magnaporthe oryzae. PLoS One 2015; 10:e0134939. [PMID: 26241858 PMCID: PMC4524601 DOI: 10.1371/journal.pone.0134939] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 02/17/2015] [Accepted: 07/16/2015] [Indexed: 01/09/2023] Open
Abstract
Rice blast fungus, Magnaporthe oryzae, is the most destructive pathogen in the rice-growing area. This fungus has a biotrophic phase early in infection and later switches to a necrotrophic lifestyle. During the biotrophic phase, the fungus competes with its host for nutrients and oxygen. Continuous uptake of oxygen is essential for successful establishment of blast disease of this pathogen. Here, we report transcriptional responses of the fungus to oxygen limitation. Transcriptome analysis using RNA-Seq identified that 1,047 genes were up-regulated in response to hypoxia. Those genes are involved in mycelial development, sterol biosynthesis, and metal ion transport based on hierarchical GO terms, and are well-conserved among three fungal species. In addition, null mutants of two hypoxia-responsive genes were generated and their roles in fungal development and pathogenicity tested. The mutant for the sterol regulatory element-binding protein gene, MoSRE1, exhibited increased sensitivity to a hypoxia-mimicking agent, increased conidiation, and delayed invasive growth within host cells, which is suggestive of important roles in fungal development. However, such defects did not cause any significant decrease in disease severity. The other null mutant, for the alcohol dehydrogenase gene MoADH1, showed no defect in the hypoxia-mimicking condition (using cobalt chloride) and fungal development. Taken together, this comprehensive transcriptional profiling in response to a hypoxic condition with experimental validations would provide new insights into fungal development and pathogenicity in plant pathogenic fungi.
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Affiliation(s)
- Jaehyuk Choi
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 406–772, Korea
| | - Hyunjung Chung
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea
| | - Gir-Won Lee
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151–921, Korea
| | - Sun-Ki Koh
- Department of Biochemistry, Paichai University, Daejeon 302–735, Korea
| | - Suhn-Kee Chae
- Department of Biochemistry, Paichai University, Daejeon 302–735, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151–921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151–921, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul 151–921, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 151–921, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151–921, Korea
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211
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Handa Y, Nishide H, Takeda N, Suzuki Y, Kawaguchi M, Saito K. RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis. Plant Cell Physiol 2015; 56:1490-511. [PMID: 26009592 DOI: 10.1093/pcp/pcv071] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [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: 12/23/2014] [Accepted: 05/13/2015] [Indexed: 05/03/2023]
Abstract
Gene expression during arbuscular mycorrhizal development is highly orchestrated in both plants and arbuscular mycorrhizal fungi. To elucidate the gene expression profiles of the symbiotic association, we performed a digital gene expression analysis of Lotus japonicus and Rhizophagus irregularis using a HiSeq 2000 next-generation sequencer with a Cufflinks assembly and de novo transcriptome assembly. There were 3,641 genes differentially expressed during arbuscular mycorrhizal development in L. japonicus, approximately 80% of which were up-regulated. The up-regulated genes included secreted proteins, transporters, proteins involved in lipid and amino acid metabolism, ribosomes and histones. We also detected many genes that were differentially expressed in small-secreted peptides and transcription factors, which may be involved in signal transduction or transcription regulation during symbiosis. Co-regulated genes between arbuscular mycorrhizal and root nodule symbiosis were not particularly abundant, but transcripts encoding for membrane traffic-related proteins, transporters and iron transport-related proteins were found to be highly co-up-regulated. In transcripts of arbuscular mycorrhizal fungi, expansion of cytochrome P450 was observed, which may contribute to various metabolic pathways required to accommodate roots and soil. The comprehensive gene expression data of both plants and arbuscular mycorrhizal fungi provide a powerful platform for investigating the functional and molecular mechanisms underlying arbuscular mycorrhizal symbiosis.
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Affiliation(s)
- Yoshihiro Handa
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Hiroyo Nishide
- Data Integration and Analysis Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Naoya Takeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Katsuharu Saito
- Faculty of Agriculture, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
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212
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Chen Y, Gao Q, Huang M, Liu Y, Liu Z, Liu X, Ma Z. Characterization of RNA silencing components in the plant pathogenic fungus Fusarium graminearum. Sci Rep 2015; 5:12500. [PMID: 26212591 PMCID: PMC4515635 DOI: 10.1038/srep12500] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [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: 09/10/2014] [Accepted: 06/26/2015] [Indexed: 02/06/2023] Open
Abstract
The RNA interference (RNAi) plays a critical role in gene regulation in a variety of eukaryotic organisms. However, the role of RNAi remains largely unclear in plant pathogenic fungi. In this study, we explored the roles of core components of the RNAi pathway in Fusarium graminearum, the major causal agent of wheat head blight. Our results demonstrated that the hairpin RNA (hpRNA) can efficiently silence the expression level of target gene, and the argonaute protein FgAgo1 and dicer protein FgDicer2 are important in this silencing process. RNAi machinery was not involved in growth, abiotic stress and pathogenesis in F. graminearum under tested conditions. We firstly applied high-throughput sequencing technology to elucidate small RNA (17-40 nucleotides) (sRNA) transcriptome in F. graminearum, and found that a total of forty-nine micro-like-RNA (milRNA) candidates were identified in the wild-type and ∆FgDICER2, and twenty-four of them were FgDicer2-dependent. Fg-milRNA-4 negatively regulated expression of its target gene. Taken together, our results indicated that the hpRNA-induced gene silencing was a valuable genetic tool for exploring gene function in F. graminearum. FgAgo1 and FgDicer2 proteins played a critical role in the hpRNA mediated gene silencing process. In addition, FgDicer2 was involved in sRNA transcription and milRNA generation in this fungus.
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Affiliation(s)
- Yun Chen
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qixun Gao
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mengmeng Huang
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ye Liu
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zunyong Liu
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xin Liu
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhonghua Ma
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
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213
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Gordon SP, Tseng E, Salamov A, Zhang J, Meng X, Zhao Z, Kang D, Underwood J, Grigoriev IV, Figueroa M, Schilling JS, Chen F, Wang Z. Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing. PLoS One 2015; 10:e0132628. [PMID: 26177194 PMCID: PMC4503453 DOI: 10.1371/journal.pone.0132628] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [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: 03/26/2015] [Accepted: 06/16/2015] [Indexed: 12/27/2022] Open
Abstract
Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a long-read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycistronic transcription is conserved among a wide range of mushroom forming fungi. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identification of mRNA isoforms not recovered via short-read assembly.
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Affiliation(s)
- Sean P. Gordon
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Elizabeth Tseng
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Asaf Salamov
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jiwei Zhang
- Department of Bioproducts & Biosystems Engineering, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Xiandong Meng
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Zhiying Zhao
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Dongwan Kang
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jason Underwood
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jonathan S. Schilling
- Department of Bioproducts & Biosystems Engineering, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Feng Chen
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Zhong Wang
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- School of Natural Sciences, University of California at Merced, Merced, California, United States of America
- * E-mail:
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214
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Kehrein K, Möller-Hergt BV, Ott M. The MIOREX complex--lean management of mitochondrial gene expression. Oncotarget 2015; 6:16806-7. [PMID: 26220710 PMCID: PMC4627264 DOI: 10.18632/oncotarget.4783] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/05/2015] [Indexed: 12/01/2022] Open
MESH Headings
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- Fungal Proteins/biosynthesis
- Fungal Proteins/genetics
- Gene Expression Regulation, Fungal
- Mitochondria/genetics
- Mitochondria/metabolism
- Mitochondrial Proteins/biosynthesis
- Mitochondrial Proteins/genetics
- Mitochondrial Ribosomes/metabolism
- Multiprotein Complexes/biosynthesis
- Multiprotein Complexes/genetics
- RNA Processing, Post-Transcriptional
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic
- Yeasts/genetics
- Yeasts/metabolism
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Affiliation(s)
- Kirsten Kehrein
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
| | - Braulio Vargas Möller-Hergt
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
| | - Martin Ott
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
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215
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Hauk G, Bowman GD. Formation of a Trimeric Xpo1-Ran[GTP]-Ded1 Exportin Complex Modulates ATPase and Helicase Activities of Ded1. PLoS One 2015; 10:e0131690. [PMID: 26120835 PMCID: PMC4484809 DOI: 10.1371/journal.pone.0131690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/05/2015] [Indexed: 11/24/2022] Open
Abstract
The DEAD-box RNA helicase Ded1, which is essential in yeast and known as DDX3 in humans, shuttles between the nucleus and cytoplasm and takes part in several basic processes including RNA processing and translation. A key interacting partner of Ded1 is the exportin Xpo1, which together with the GTP-bound state of the small GTPase Ran, facilitates unidirectional transport of Ded1 out of the nucleus. Here we demonstrate that Xpo1 and Ran[GTP] together reduce the RNA-stimulated ATPase and helicase activities of Ded1. Binding and inhibition of Ded1 by Xpo1 depend on the affinity of the Ded1 nuclear export sequence (NES) for Xpo1 and the presence of Ran[GTP]. Association with Xpo1/Ran[GTP] reduces RNA-stimulated ATPase activity of Ded1 by increasing the apparent KM for the RNA substrate. Despite the increased KM, the Ded1:Xpo1:Ran[GTP] ternary complex retains the ability to bind single stranded RNA, suggesting that Xpo1/Ran[GTP] may modulate the substrate specificity of Ded1. These results demonstrate that, in addition to transport, exportins such as Xpo1 also have the capability to alter enzymatic activities of their cargo.
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Affiliation(s)
- Glenn Hauk
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Gregory D. Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
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216
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Selvi A, Das D, Das N. Potentiality of yeast Candida sp. SMN04 for degradation of cefdinir, a cephalosporin antibiotic: kinetics, enzyme analysis and biodegradation pathway. Environ Technol 2015; 36:3112-3124. [PMID: 26000889 DOI: 10.1080/09593330.2015.1054318] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 12/29/2014] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
A new yeast strain isolated from the pharmaceutical wastewater was capable of utilizing cefdinir as a sole carbon source for their growth in mineral medium. The yeast was identified and named as Candida sp. SMN04 based on morphology and 18S-ITS-D1/D2/D3 rRNA sequence analysis. The interaction between factors pH (3.0-9.0), inoculum dosage (1-7%), time (1-11 day) and cefdinir concentration (50-450 mg/L) was studied using a Box-Behnken design. The factors were studied as a result of their effect on cell dry weight (R1; g/L), extended spectrum β-lactamase (ESBL) assay (R2; mm), P450 activity (R3; U/mL) and degradation (R4; %). Maximum values of R1, R2, R3 and R4 were obtained at central values of all the parameters. The isolated yeast strain efficiently degraded 84% of 250 mg L⁻¹ of cefdinir within 6 days with a half-life of 2.97 days and degradation rate constant of 0.2335 per day. Pseudo-first-order model efficiently described the process. Among the various enzymes tested, the order of activity at the end of Day 4 was noted to be: cytochrome P450 (1.76 ± 0.03) > NADPH reductase (1.51 ± 0.20) > manganese peroxidase and amylase (0.66 ± 0.15; 0.66 ± 0.70). Intermediates were successfully characterized by liquid chromatography-mass spectrometry. The opening of the β-lactam ring involving ESBL activity was considered as one of the major steps in the cefdinir degradation process. Fourier transform-infrared spectroscopy analysis showed the absence of spectral vibrations between 1766 and 1519 cm⁻¹ confirming the complete removal of lactam ring during cefdinir degradation. The results of the present study are promising for the use of isolated yeast Candida sp. SMN04 as a potential bioremediation agent.
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Affiliation(s)
- A Selvi
- a School of Bio Sciences and Technology , VIT University , Vellore 632014 , Tamil Nadu , India
| | - Devlina Das
- a School of Bio Sciences and Technology , VIT University , Vellore 632014 , Tamil Nadu , India
| | - Nilanjana Das
- a School of Bio Sciences and Technology , VIT University , Vellore 632014 , Tamil Nadu , India
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217
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Fu Y, Xu ZZ, Lu ZJ, Zhao S, Mathews DH. Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PLoS One 2015; 10:e0130200. [PMID: 26075601 PMCID: PMC4468099 DOI: 10.1371/journal.pone.0130200] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/17/2015] [Indexed: 01/05/2023] Open
Abstract
Recently, non-coding RNAs (ncRNAs) have been discovered with novel functions, and it has been appreciated that there is pervasive transcription of genomes. Moreover, many novel ncRNAs are not conserved on the primary sequence level. Therefore, de novo computational ncRNA detection that is accurate and efficient is desirable. The purpose of this study is to develop a ncRNA detection method based on conservation of structure in more than two genomes. A new method called Multifind, using Multilign, was developed. Multilign predicts the common secondary structure for multiple input sequences. Multifind then uses measures of structure conservation to estimate the probability that the input sequences are a conserved ncRNA using a classification support vector machine. Multilign is based on Dynalign, which folds and aligns two sequences simultaneously using a scoring scheme that does not include sequence identity; its structure prediction quality is therefore not affected by input sequence diversity. Additionally, ensemble defect was introduced to Multifind as an additional discriminating feature that quantifies the compactness of the folding space for a sequence. Benchmarks showed Multifind performs better than RNAz and LocARNATE+RNAz, a method that uses RNAz on structure alignments generated by LocARNATE, on testing sequences extracted from the Rfam database. For de novo ncRNA discovery in three genomes, Multifind and LocARNATE+RNAz had an advantage over RNAz in low similarity regions of genome alignments. Additionally, Multifind and LocARNATE+RNAz found different subsets of known ncRNA sequences, suggesting the two approaches are complementary.
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Affiliation(s)
- Yinghan Fu
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Zhenjiang Zech Xu
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Zhi J. Lu
- MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shan Zhao
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - David H. Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, United States of America
- Department of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
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218
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Ishida S, Nozaki D, Grossart HP, Kagami M. Novel basal, fungal lineages from freshwater phytoplankton and lake samples. Environ Microbiol Rep 2015; 7:435-441. [PMID: 25625632 DOI: 10.1111/1758-2229.12268] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
Zoosporic fungal parasites are known to control the extent and development of blooms of numerous phytoplankton species. Despite the obvious importance of ecological interactions between parasitic fungi and their phytoplanktonic hosts, their diversity remains largely unknown due to methodological limitations. Here, a method to genetically analyse fungi directly from single, infected colonies of the phytoplanktonic host was applied to field samples of large diatom species from mesotrophic Lake Biwa and eutrophic Lake Inba, Japan. Although previous research on interaction between lacustrine fungi and large phytoplankton has mainly focused on the role of parasitic Chytridiomycota, our results revealed that fungi attached to large diatoms included not only members of Chytridiomycota, but also members of Aphelida, Cryptomycota and yeast. The fungi belonging to Chytridiomycota and Aphelida form novel, basal lineages. Environmental clone libraries also support the occurrence of these lineages in Japanese lakes. The presented method enables us to better characterize individual fungal specimens on phytoplankton, and thus facilitate and improve the investigation of ecological relationships between fungi and phytoplankton in aquatic ecosystems.
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Affiliation(s)
- Seiji Ishida
- Department of Environmental Science, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Daiki Nozaki
- Department of Environmental Science, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Brandenburg, Germany
- Institute for Biochemistry and Biology, Potsdam University, Potsdam, Brandenburg, Germany
| | - Maiko Kagami
- Department of Environmental Science, Faculty of Science, Toho University, Funabashi, Chiba, Japan
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219
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Khan SR, Nirmal JK, Kumar RN, Patel JG. Biodegradation of kerosene: Study of growth optimization and metabolic fate of P. janthinellum SDX7. Braz J Microbiol 2015; 46:397-406. [PMID: 26273254 PMCID: PMC4507531 DOI: 10.1590/s1517-838246220140112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/07/2014] [Indexed: 11/21/2022] Open
Abstract
Penicillum janthinellum SDX7 was isolated from aged petroleum hydrocarbon-affected soil at the site of Anand, Gujarat, India, and was tested for different pH, temperature, agitation and concentrations for optimal growth of the isolate that was capable of degrading upto 95%, 63% and 58% of 1%, 3% and 5% kerosene, respectively, after a period of 16 days, at optimal growth conditions of pH 6.0, 30 °C and 180 rpm agitation. The GC/MS chromatograms revealed that then-alkane fractions are easily degraded; however, the rate might be lower for branched alkanes, n-alkylaromatics, cyclic alkanes and polynuclear aromatics. The test doses caused a concentration-dependent depletion of carbohydrates of P. janthinellum SDX7 by 3% to 80%, proteins by 4% to 81% and amino acids by 8% to 95% upto 16 days of treatment. The optimal concentration of 3% kerosene resulted in the least reduction of the metabolites of P. janthinellum such as carbohydrates, proteins and amino acids with optimal growth compared to 5% and 1% (v/v) kerosene doses on the 12(th) and 16(th) day of exposure. Phenols were found to be mounted by 43% to 66% at lower and higher concentrations during the experimental period. Fungal isolate P. janthinellum SDX7 was also tested for growth on various xenobiotic compounds.
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Affiliation(s)
- Shamiyan R. Khan
- Department of Environmental Science and
Technology, Institute of Science and Technology for Advanced
Studies and Research, Gujarat, India, Department of Environmental Science and
Technology, Institute of Science and Technology for Advanced Studies and
Research, Gujarat, India
| | - J.I. Kumar Nirmal
- Department of Environmental Science and
Technology, Institute of Science and Technology for Advanced
Studies and Research, Gujarat, India, Department of Environmental Science and
Technology, Institute of Science and Technology for Advanced Studies and
Research, Gujarat, India
| | - Rita N. Kumar
- Department of Biological and Environmental
Sciences, Natubhai V Patel College, Gujarat, India, Department of Biological and Environmental
Sciences, Natubhai V Patel College, Gujarat, India
| | - Jignasha G. Patel
- Department of Environmental Science and
Technology, Institute of Science and Technology for Advanced
Studies and Research, Gujarat, India, Department of Environmental Science and
Technology, Institute of Science and Technology for Advanced Studies and
Research, Gujarat, India
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220
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Kast A, Voges R, Schroth M, Schaffrath R, Klassen R, Meinhardt F. Autoselection of cytoplasmic yeast virus like elements encoding toxin/antitoxin systems involves a nuclear barrier for immunity gene expression. PLoS Genet 2015; 11:e1005005. [PMID: 25973601 PMCID: PMC4431711 DOI: 10.1371/journal.pgen.1005005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 11/07/2014] [Accepted: 01/14/2015] [Indexed: 12/13/2022] Open
Abstract
Cytoplasmic virus like elements (VLEs) from Kluyveromyces lactis (Kl), Pichia acaciae (Pa) and Debaryomyces robertsiae (Dr) are extremely A/T-rich (>75%) and encode toxic anticodon nucleases (ACNases) along with specific immunity proteins. Here we show that nuclear, not cytoplasmic expression of either immunity gene (PaORF4, KlORF3 or DrORF5) results in transcript fragmentation and is insufficient to establish immunity to the cognate ACNase. Since rapid amplification of 3' ends (RACE) as well as linker ligation of immunity transcripts expressed in the nucleus revealed polyadenylation to occur along with fragmentation, ORF-internal poly(A) site cleavage due to the high A/T content is likely to prevent functional expression of the immunity genes. Consistently, lowering the A/T content of PaORF4 to 55% and KlORF3 to 46% by gene synthesis entirely prevented transcript cleavage and permitted functional nuclear expression leading to full immunity against the respective ACNase toxin. Consistent with a specific adaptation of the immunity proteins to the cognate ACNases, cross-immunity to non-cognate ACNases is neither conferred by PaOrf4 nor KlOrf3. Thus, the high A/T content of cytoplasmic VLEs minimizes the potential of functional nuclear recruitment of VLE encoded genes, in particular those involved in autoselection of the VLEs via a toxin/antitoxin principle. The rather wide-spread and extremely A/T rich yeast virus like elements (VLEs, also termed linear plasmids) which encode toxic anticodon nucleases (ACNases) ensure autoselection in the cytoplasm by preventing functional nuclear capture of the cognate immunity genes, but how? When expressed in the nucleus, the mRNA of the VLE immunity genes is split into fragments to which poly(A) tails are added. Consistently, lowering the A/T content by gene synthesis prevented transcript cleavage and permitted functional nuclear expression providing full immunity against the respective ACNase toxin. Thus, internal poly(A) cleavage is likely to prevent functional nuclear immunity gene expression.
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Affiliation(s)
- Alene Kast
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Raphael Voges
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Michael Schroth
- Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | | | - Roland Klassen
- Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
- * E-mail: (RK); (FM)
| | - Friedhelm Meinhardt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- * E-mail: (RK); (FM)
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221
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Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR, Coller J. Codon optimality is a major determinant of mRNA stability. Cell 2015; 160:1111-24. [PMID: 25768907 DOI: 10.1016/j.cell.2015.02.029] [Citation(s) in RCA: 588] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/18/2014] [Accepted: 02/11/2015] [Indexed: 11/17/2022]
Abstract
mRNA degradation represents a critical regulated step in gene expression. Although the major pathways in turnover have been identified, accounting for disparate half-lives has been elusive. We show that codon optimality is one feature that contributes greatly to mRNA stability. Genome-wide RNA decay analysis revealed that stable mRNAs are enriched in codons designated optimal, whereas unstable mRNAs contain predominately non-optimal codons. Substitution of optimal codons with synonymous, non-optimal codons results in dramatic mRNA destabilization, whereas the converse substitution significantly increases stability. Further, we demonstrate that codon optimality impacts ribosome translocation, connecting the processes of translation elongation and decay through codon optimality. Finally, we show that optimal codon content accounts for the similar stabilities observed in mRNAs encoding proteins with coordinated physiological function. This work demonstrates that codon optimization exists as a mechanism to finely tune levels of mRNAs and, ultimately, proteins.
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Affiliation(s)
- Vladimir Presnyak
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Najwa Alhusaini
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ying-Hsin Chen
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sophie Martin
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Nathan Morris
- Statistical Science Core in the Center for Clinical Investigation, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Nicholas Kline
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sara Olson
- Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - David Weinberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Kristian E Baker
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Brenton R Graveley
- Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Jeff Coller
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA.
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222
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Dahlmann TA, Kück U. Dicer-Dependent Biogenesis of Small RNAs and Evidence for MicroRNA-Like RNAs in the Penicillin Producing Fungus Penicillium chrysogenum. PLoS One 2015; 10:e0125989. [PMID: 25955857 PMCID: PMC4425646 DOI: 10.1371/journal.pone.0125989] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 12/15/2014] [Accepted: 03/27/2015] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs (sRNAs) that regulate gene expression in a wide range of eukaryotes. In this study, we analyzed regulatory sRNAs in Penicillium chrysogenum, the industrial producer of the β-lactam antibiotic penicillin. To identify sRNAs and microRNA-like RNAs (milRNAs) on a global approach, two sRNA sequencing libraries were constructed. One library was created with pooled total RNA, obtained from twelve differently grown cultures (RNA Mix), and the other with total RNA from a single submerged cultivation (∆ku70FRT2). Illumina sequencing of both RNA libraries produced 84,322,825 mapped reads. To distinguish between Dicer-dependent and independent sRNA formation, we further constructed two single dicer gene mutants (∆dcl2 and ∆dcl1) and a dicer double mutant (∆dcl2∆dcl1) and analyzed an sRNA library from the Dicer-deficient double-mutant. We identified 661 Dicer-dependent loci and in silico prediction revealed 34 milRNAs. Northern blot hybridization of two milRNAs provided evidence for mature milRNAs that are processed either in a complete or partial Dicer-dependent manner from an RNA precursor. Identified milRNAs share typical characteristics of previously discovered fungal milRNAs, like a strong preference for a 5' uracil and the typical length distribution. The detection of potential milRNA target sites in the genome suggests that milRNAs might play a role in posttranscriptional gene regulation. Our data will further increase our knowledge of sRNA dependent gene regulation processes, which is an important prerequisite to develop more effective strategies for improving industrial fermentations with P. chrysogenum.
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Affiliation(s)
- Tim A. Dahlmann
- Christian Doppler Laboratory for “Fungal Biotechnology”, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Ulrich Kück
- Christian Doppler Laboratory for “Fungal Biotechnology”, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
- * E-mail:
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223
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Zhao Q, Huang Y, Zhang P, Sun X, Zhu X. [Interfering effect of an intergenic-derived sRNA of Cryptococcus neoformans]. Wei Sheng Wu Xue Bao 2015; 55:564-569. [PMID: 26259480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
OBJECTIVE We demonstrated the interfering effect of a new intergenic-derived sRNA of Cryptococcus neoformans. METHODS We constructed a library of sRNAs from 20 to 25 nt, and used a reporter gene CLC1 that was fused to the testing sRNAs to show the interference effect, i. e. the degradation of the CLC1 would gene rate an albino phenotype of the transformants. RESULTS Through the CLC-sRNA reporter system, we acquired one sRNA, sRNA-1, located to an intergenic region of the genome of C. neoformans, that displayed interfering effect on CLCl. CONCLUSIONS In C. neoformans, the origination of sRNA may be diverse. The endogenous sRNA should play interfering function via the canonical RNAi pathway.
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224
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Abstract
The cycle of spliceosome assembly, intron excision, and spliceosome disassembly involves large-scale structural rearrangements of U6 snRNA that are functionally important. U6 enters the splicing pathway bound to the Prp24 protein, which chaperones annealing of U6 to U4 RNA to form a U4/U6 di-snRNP. During catalytic activation of the assembled spliceosome, U4 snRNP is released and U6 is paired to U2 snRNA. Here we show that point mutations in U4 and U6 that decrease U4/U6 base-pairing in vivo are lethal in combination. However, this synthetic phenotype is rescued by a mutation in U6 that alters a U6-Prp24 contact and stabilizes U2/U6. Remarkably, the resulting viable triple mutant strain lacks detectable U4/U6 base-pairing and U4/U6 di-snRNP. Instead, this strain accumulates free U4 snRNP, protein-free U6 RNA, and a novel complex containing U2/U6 di-snRNP. Further mutational analysis indicates that disruption of the U6-Prp24 interaction rather than stabilization of U2/U6 renders stable U4/U6 di-snRNP assembly nonessential. We propose that an essential function of U4/U6 pairing is to displace Prp24 from U6 RNA, and thus a destabilized U6-Prp24 complex renders stable U4/U6 pairing nonessential.
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MESH Headings
- Base Pairing
- Base Sequence
- Epistasis, Genetic
- Multiprotein Complexes/genetics
- Multiprotein Complexes/metabolism
- Mutation
- Nucleic Acid Conformation
- Protein Multimerization
- RNA Splicing/genetics
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Spliceosomes/metabolism
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Affiliation(s)
- Jordan E Burke
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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225
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Malabat C, Feuerbach F, Ma L, Saveanu C, Jacquier A. Quality control of transcription start site selection by nonsense-mediated-mRNA decay. eLife 2015; 4:e06722. [PMID: 25905671 PMCID: PMC4434318 DOI: 10.7554/elife.06722] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [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: 01/27/2015] [Accepted: 04/22/2015] [Indexed: 01/01/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficient for RNA degradation pathways revealed that about half of the pervasive transcripts are degraded by NMD, which provides a fail-safe mechanism to remove spurious transcripts that escaped degradation in the nucleus. Moreover, we found that the low specificity of RNA polymerase II TSSs selection generates, for 47% of the expressed genes, NMD-sensitive transcript isoforms carrying uORFs or starting downstream of the ATG START codon. Despite the low abundance of this last category of isoforms, their presence seems to constrain genomic sequences, as suggested by the significant bias against in-frame ATGs specifically found at the beginning of the corresponding genes and reflected by a depletion of methionines in the N-terminus of the encoded proteins.
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Affiliation(s)
- Christophe Malabat
- Institut Pasteur, UMR3525, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Paris, France
| | - Frank Feuerbach
- Institut Pasteur, UMR3525, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Paris, France
| | - Laurence Ma
- Plate-Forme Génomique, Institut Pasteur, Paris, France
| | - Cosmin Saveanu
- Institut Pasteur, UMR3525, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Paris, France
| | - Alain Jacquier
- Institut Pasteur, UMR3525, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Paris, France
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226
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Yang L, Xie L, Xue B, Goodwin PH, Quan X, Zheng C, Liu T, Lei Z, Yang X, Chao Y, Wu C. Comparative transcriptome profiling of the early infection of wheat roots by Gaeumannomyces graminis var. tritici. PLoS One 2015; 10:e0120691. [PMID: 25875107 PMCID: PMC4397062 DOI: 10.1371/journal.pone.0120691] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 09/23/2014] [Accepted: 01/25/2015] [Indexed: 12/15/2022] Open
Abstract
Take-all, which is caused by the fungal pathogen, Gaeumannomyces graminis var. tritici (Ggt), is an important soil-borne root rot disease of wheat occurring worldwide. However, the genetic basis of Ggt pathogenicity remains unclear. In this study, transcriptome sequencing for Ggt in axenic culture and Ggt-infected wheat roots was performed using Illumina paired-end sequencing. Approximately 2.62 and 7.76 Gb of clean reads were obtained, and 87% and 63% of the total reads were mapped to the Ggt genome for RNA extracted from Ggt in culture and infected roots, respectively. A total of 3,258 differentially expressed genes (DEGs) were identified with 2,107 (65%) being 2-fold up-regulated and 1,151 (35%) being 2-fold down-regulated between Ggt in culture and Ggt in infected wheat roots. Annotation of these DEGs revealed that many were associated with possible Ggt pathogenicity factors, such as genes for guanine nucleotide-binding protein alpha-2 subunit, cellulase, pectinase, xylanase, glucosidase, aspartic protease and gentisate 1, 2-dioxygenase. Twelve DEGs were analyzed for expression by qRT-PCR, and could be generally divided into those with high expression only early in infection, only late in infection and those that gradually increasing expression over time as root rot developed. This indicates that these possible pathogenicity factors may play roles during different stages of the interaction, such as signaling, plant cell wall degradation and responses to plant defense compounds. This is the first study to compare the transcriptomes of Ggt growing saprophytically in axenic cultures to it growing parasitically in infected wheat roots. As a result, new candidate pathogenicity factors have been identified, which can be further examined by gene knock-outs and other methods to assess their true role in the ability of Ggt to infect roots.
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Affiliation(s)
- Lirong Yang
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Key Laboratory for Control of Crop Diseases and Insect Pests, IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, P. R. China
| | - Lihua Xie
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Key Laboratory for Control of Crop Diseases and Insect Pests, IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, P. R. China
| | - Baoguo Xue
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Key Laboratory for Control of Crop Diseases and Insect Pests, IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, P. R. China
| | - Paul H. Goodwin
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Xin Quan
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Key Laboratory for Control of Crop Diseases and Insect Pests, IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, P. R. China
| | - Chuanlin Zheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Taiguo Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zhensheng Lei
- Research Centre for Wheat, Henan Academy of Agricultural Science, Zhengzhou, P. R. China
| | - Xiaojie Yang
- Economic Crop Research Institute, Henan Academy of Agricultural Science, Zhengzhou, P. R. China
| | - Yueen Chao
- Research Centre for Wheat, Henan Academy of Agricultural Science, Zhengzhou, P. R. China
| | - Chao Wu
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Key Laboratory for Control of Crop Diseases and Insect Pests, IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, P. R. China
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227
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Lin YL, Ma LT, Lee YR, Lin SS, Wang SY, Chang TT, Shaw JF, Li WH, Chu FH. MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea. PLoS One 2015; 10:e0123245. [PMID: 25860872 PMCID: PMC4393119 DOI: 10.1371/journal.pone.0123245] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 11/12/2014] [Accepted: 03/02/2015] [Indexed: 01/19/2023] Open
Abstract
Antrodia cinnamomea, a precious, host-specific brown-rot fungus that has been used as a folk medicine in Taiwan for centuries is known to have diverse bioactive compounds with potent pharmaceutical activity. In this study, different fermentation states of A. cinnamomea (wild-type fruiting bodies and liquid cultured mycelium) were sequenced using the next-generation sequencing (NGS) technique. A 45.58 Mb genome encoding 6,522 predicted genes was obtained. High quality reads were assembled into a total of 13,109 unigenes. Using a previously constructed pipeline to search for microRNAs (miRNAs), we then identified 4 predicted conserved miRNA and 63 novel predicted miRNA-like small RNA (milRNA) candidates. Target prediction revealed several interesting proteins involved in tri-terpenoid synthesis, mating type recognition, chemical or physical sensory protein and transporters predicted to be regulated by the miRNAs and milRNAs.
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Affiliation(s)
- Yan-Liang Lin
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Li-Ting Ma
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Yi-Ru Lee
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Sheng-Yang Wang
- Department of Forestry, National Chung-Hsing University, Taichun, Taiwan
- Agricultural, Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Agricultural Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
| | - Tun-Tschu Chang
- Division on Forest Protection, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Jei-Fu Shaw
- Department of Biological Science & Technology, I-Shou University, Kaohsiung, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
- Experimental Forest, National Taiwan University, Nan-Tou, Taiwan
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228
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Klassen R, Grunewald P, Thüring KL, Eichler C, Helm M, Schaffrath R. Loss of anticodon wobble uridine modifications affects tRNA(Lys) function and protein levels in Saccharomyces cerevisiae. PLoS One 2015; 10:e0119261. [PMID: 25747122 PMCID: PMC4352028 DOI: 10.1371/journal.pone.0119261] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [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: 05/09/2014] [Accepted: 01/22/2015] [Indexed: 11/22/2022] Open
Abstract
In eukaryotes, wobble uridines in the anticodons of tRNALysUUU, tRNAGluUUC and tRNAGlnUUG are modified to 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm5s2U). While mutations in subunits of the Elongator complex (Elp1-Elp6), which disable mcm5 side chain formation, or removal of components of the thiolation pathway (Ncs2/Ncs6, Urm1, Uba4) are individually tolerated, the combination of both modification defects has been reported to have lethal effects on Saccharomyces cerevisiae. Contrary to such absolute requirement of mcm5s2U for viability, we demonstrate here that in the S. cerevisiae S288C-derived background, both pathways can be simultaneously inactivated, resulting in combined loss of tRNA anticodon modifications (mcm5U and s2U) without a lethal effect. However, an elp3 disruption strain displays synthetic sick interaction and synergistic temperature sensitivity when combined with either uba4 or urm1 mutations, suggesting major translational defects in the absence of mcm5s2U modifications. Consistent with this notion, we find cellular protein levels drastically decreased in an elp3uba4 double mutant and show that this effect as well as growth phenotypes can be partially rescued by excess of tRNALysUUU. These results may indicate a global translational or protein homeostasis defect in cells simultaneously lacking mcm5 and s2 wobble uridine modification that could account for growth impairment and mainly originates from tRNALysUUU hypomodification and malfunction.
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Affiliation(s)
- Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
- * E-mail: (RK); (RS)
| | - Pia Grunewald
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Kathrin L. Thüring
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Christian Eichler
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Mark Helm
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
- * E-mail: (RK); (RS)
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229
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Gautam A, Grainger RJ, Vilardell J, Barrass JD, Beggs JD. Cwc21p promotes the second step conformation of the spliceosome and modulates 3' splice site selection. Nucleic Acids Res 2015; 43:3309-17. [PMID: 25740649 PMCID: PMC4381068 DOI: 10.1093/nar/gkv159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/18/2015] [Indexed: 12/20/2022] Open
Abstract
Pre-mRNA splicing involves two transesterification steps catalyzed by the spliceosome. How RNA substrates are positioned in each step and the molecular rearrangements involved, remain obscure. Here, we show that mutations in PRP16, PRP8, SNU114 and the U5 snRNA that affect this process interact genetically with CWC21, that encodes the yeast orthologue of the human SR protein, SRm300/SRRM2. Our microarray analysis shows changes in 3′ splice site selection at elevated temperature in a subset of introns in cwc21Δ cells. Considering all the available data, we propose a role for Cwc21p positioning the 3′ splice site at the transition to the second step conformation of the spliceosome, mediated through its interactions with the U5 snRNP. This suggests a mechanism whereby SRm300/SRRM2, might influence splice site selection in human cells.
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MESH Headings
- Adenosine Triphosphatases/chemistry
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Alternative Splicing
- Amino Acid Sequence
- Carrier Proteins/chemistry
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Gene Deletion
- Genes, Fungal
- Humans
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Conformation
- RNA Helicases/chemistry
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Splice Sites
- RNA Splicing
- RNA Splicing Factors
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U5 Small Nuclear/chemistry
- Ribonucleoprotein, U5 Small Nuclear/genetics
- Ribonucleoprotein, U5 Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Spliceosomes/chemistry
- Spliceosomes/genetics
- Spliceosomes/metabolism
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Affiliation(s)
- Amit Gautam
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3BF, UK
| | - Richard J Grainger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3BF, UK
| | - J Vilardell
- Department of Molecular Genomics, Institute of Molecular Biology of Barcelona (IBMB), 08028 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - J David Barrass
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3BF, UK
| | - Jean D Beggs
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3BF, UK
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230
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Emerson JB, Keady PB, Brewer TE, Clements N, Morgan EE, Awerbuch J, Miller SL, Fierer N. Impacts of flood damage on airborne bacteria and fungi in homes after the 2013 Colorado Front Range flood. Environ Sci Technol 2015; 49:2675-84. [PMID: 25643125 DOI: 10.1021/es503845j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Flood-damaged homes typically have elevated microbial loads, and their occupants have an increased incidence of allergies, asthma, and other respiratory ailments, yet the microbial communities in these homes remain under-studied. Using culture-independent approaches, we characterized bacterial and fungal communities in homes in Boulder, CO, USA 2-3 months after the historic September, 2013 flooding event. We collected passive air samples from basements in 50 homes (36 flood-damaged, 14 non-flooded), and we sequenced the bacterial 16S rRNA gene (V4-V5 region) and the fungal ITS1 region from these samples for community analyses. Quantitative PCR was used to estimate the abundances of bacteria and fungi in the passive air samples. Results indicate significant differences in bacterial and fungal community composition between flooded and non-flooded homes. Fungal abundances were estimated to be three times higher in flooded, relative to non-flooded homes, but there were no significant differences in bacterial abundances. Penicillium (fungi) and Pseudomonadaceae and Enterobacteriaceae (bacteria) were among the most abundant taxa in flooded homes. Our results suggest that bacterial and fungal communities continue to be affected by flooding, even after relative humidity has returned to baseline levels and remediation has removed any visible evidence of flood damage.
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Affiliation(s)
- Joanne B Emerson
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder , 216 UCB, Boulder, Colorado 80309-0216, United States
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231
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Lovell D, Pawlowsky-Glahn V, Egozcue JJ, Marguerat S, Bähler J. Proportionality: a valid alternative to correlation for relative data. PLoS Comput Biol 2015; 11:e1004075. [PMID: 25775355 PMCID: PMC4361748 DOI: 10.1371/journal.pcbi.1004075] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 12/08/2014] [Indexed: 11/18/2022] Open
Abstract
In the life sciences, many measurement methods yield only the relative abundances of different components in a sample. With such relative-or compositional-data, differential expression needs careful interpretation, and correlation-a statistical workhorse for analyzing pairwise relationships-is an inappropriate measure of association. Using yeast gene expression data we show how correlation can be misleading and present proportionality as a valid alternative for relative data. We show how the strength of proportionality between two variables can be meaningfully and interpretably described by a new statistic ϕ which can be used instead of correlation as the basis of familiar analyses and visualisation methods, including co-expression networks and clustered heatmaps. While the main aim of this study is to present proportionality as a means to analyse relative data, it also raises intriguing questions about the molecular mechanisms underlying the proportional regulation of a range of yeast genes.
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Affiliation(s)
- David Lovell
- Queensland University of Technology, Brisbane, Australia
| | | | - Juan José Egozcue
- Dept. Applied Mathematics III, U. Politécnica de Catalunya, Barcelona, Spain
| | - Samuel Marguerat
- MRC Clinical Sciences Centre, Imperial College London, United Kingdom
| | - Jürg Bähler
- Research Department of Genetics, Evolution and Environment, University College London, United Kingdom
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232
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Rachid CTCC, Balieiro FC, Fonseca ES, Peixoto RS, Chaer GM, Tiedje JM, Rosado AS. Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations. PLoS One 2015; 10:e0118515. [PMID: 25706388 PMCID: PMC4338270 DOI: 10.1371/journal.pone.0118515] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 06/16/2014] [Accepted: 01/19/2015] [Indexed: 11/19/2022] Open
Abstract
Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments: monoculture of Eucalyptus; monoculture of Acacia mangium; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that.
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Affiliation(s)
- Caio T. C. C. Rachid
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Eduardo S. Fonseca
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - Alexandre S. Rosado
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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233
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Gagnon J, Lavoie M, Catala M, Malenfant F, Elela SA. Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals. PLoS Genet 2015; 11:e1005000. [PMID: 25680180 PMCID: PMC4334505 DOI: 10.1371/journal.pgen.1005000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 01/13/2015] [Indexed: 12/11/2022] Open
Abstract
Detection and validation of the RNA degradation signals controlling transcriptome stability are essential steps for understanding how cells regulate gene expression. Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome, and encompass a wide variety of sequences, indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes, and their impact on RNA expression is linked to growth conditions. Together, the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions. RNA degradation is essential for gene regulation. The amount and timing of protein synthesis is determined, at least in part, by messenger RNA stability. Although RNA stability is determined by specific structural and sequence motif, the distribution of the degradation signals in eukaryotic genomes remains unclear. In this study, we describe the genomic distribution of the RNA degradation signals required for selective nuclear degradation in yeast. The results indicate that most RNAs in the yeast transcriptome are predisposed for degradation, but only few are catalytically active. The catalytic reactivity of messenger RNAs were mostly determined by the overall structural context of the degradation signals. Strikingly, most active RNA degradation signals are found in genes associated with respiration and fermentation. Overall, the findings reported here demonstrate how certain RNA are selected for cleavage and illustrated the importance of this selective RNA degradation for fine tuning gene expression in response to changes in growth condition.
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Affiliation(s)
- Jules Gagnon
- Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Mathieu Lavoie
- Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Mathieu Catala
- Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Francis Malenfant
- Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sherif Abou Elela
- Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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234
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Skilandat M, Sigel RKO. The role of Mg(II) in DNA cleavage site recognition in group II intron ribozymes: solution structure and metal ion binding sites of the RNA-DNA complex. J Biol Chem 2015; 289:20650-63. [PMID: 24895129 DOI: 10.1074/jbc.m113.542381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Group II intron ribozymes catalyze the cleavage of (and their reinsertion into) DNA and RNA targets using a Mg2(+)-dependent reaction. The target is cleaved 3' to the last nucleotide of intron binding site 1 (IBS1), one of three regions that form base pairs with the intron's exon binding sites (EBS1 to -3).We solved the NMR solution structure of the d3' hairpin of the Sc.ai5γ intron containing EBS1 in its 11-nucleotide loop in complex with the dIBS1 DNA 7-mer and compare it with the analogous RNA-RNA contact. The EBS1-dIBS1 helix is slightly flexible and non-symmetric. NMR data reveal two major groove binding sites for divalent metal ions at the EBS1-dIBS1 helix, and surface plasmon resonance experiments show that low concentrations of Mg2(+) considerably enhance the affinity of dIBS1 for EBS1. Our results indicate that identification of both RNA and DNA IBS1 targets, presentation of the scissile bond, and stabilization of the structure by metal ions are governed by the overall structure of EBS1-dIBS1 and the surrounding loop nucleotides but are irrespective of different EBS1-(d)IBS1 geometries and interstrand affinities.
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235
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Perez WB, Kinzy TG. Translation elongation factor 1A mutants with altered actin bundling activity show reduced aminoacyl-tRNA binding and alter initiation via eIF2α phosphorylation. J Biol Chem 2015; 289:20928-38. [PMID: 24936063 DOI: 10.1074/jbc.m114.570077] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apart from its canonical function in translation elongation, eukaryotic translation elongation factor 1A (eEF1A) has been shown to interact with the actin cytoskeleton. Amino acid substitutions in eEF1A that reduce its ability to bind and bundle actin in vitro cause improper actin organization in vivo and reduce total translation. Initial in vivo analysis indicated the reduced translation was through initiation. The mutant strains exhibit increased levels of phosphorylated initiation factor 2α (eIF2α) dependent on the presence of the general control non-derepressible 2 (Gcn2p) protein kinase. Gcn2p causes downregulation of total protein synthesis at initiation in response to increases in deacylated tRNA levels in the cell. Increased levels of eIF2α phosphorylation are not due to a general reduction in translation elongation as eEF2 and eEF3 mutants do not exhibit this effect. Deletion of GCN2 from the eEF1A actin bundling mutant strains revealed a second defect in translation. The eEF1A actin-bundling proteins exhibit changes in their elongation activity at the level of aminoacyl-tRNA binding in vitro. These findings implicate eEF1A in a feedback mechanism for regulating translation at initiation.
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236
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Alings F, Sarin LP, Fufezan C, Drexler HCA, Leidel SA. An evolutionary approach uncovers a diverse response of tRNA 2-thiolation to elevated temperatures in yeast. RNA 2015; 21:202-12. [PMID: 25505025 PMCID: PMC4338348 DOI: 10.1261/rna.048199.114] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [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: 05/14/2023]
Abstract
Chemical modifications of transfer RNA (tRNA) molecules are evolutionarily well conserved and critical for translation and tRNA structure. Little is known how these nucleoside modifications respond to physiological stress. Using mass spectrometry and complementary methods, we defined tRNA modification levels in six yeast species in response to elevated temperatures. We show that 2-thiolation of uridine at position 34 (s(2)U34) is impaired at temperatures exceeding 30°C in the commonly used Saccharomyces cerevisiae laboratory strains S288C and W303, and in Saccharomyces bayanus. Upon stress relief, thiolation levels recover and we find no evidence that modified tRNA or s(2)U34 nucleosides are actively removed. Our results suggest that loss of 2-thiolation follows accumulation of newly synthesized tRNA that lack s(2)U34 modification due to temperature sensitivity of the URM1 pathway in S. cerevisiae and S. bayanus. Furthermore, our analysis of the tRNA modification pattern in selected yeast species revealed two alternative phenotypes. Most strains moderately increase their tRNA modification levels in response to heat, possibly constituting a common adaptation to high temperatures. However, an overall reduction of nucleoside modifications was observed exclusively in S288C. This surprising finding emphasizes the importance of studies that utilize the power of evolutionary biology, and highlights the need for future systematic studies on tRNA modifications in additional model organisms.
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Affiliation(s)
- Fiona Alings
- RNA Biology Laboratory, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - L Peter Sarin
- RNA Biology Laboratory, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Christian Fufezan
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Hannes C A Drexler
- Bioanalytical Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Sebastian A Leidel
- RNA Biology Laboratory, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany Faculty of Medicine, University of Münster, 48149 Münster, Germany
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237
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Siozios S, Tosi L, Ferrarini A, Ferrari A, Tononi P, Bellin D, Maurhofer M, Gessler C, Delledonne M, Pertot I. Transcriptional Reprogramming of the Mycoparasitic Fungus Ampelomyces quisqualis During the Powdery Mildew Host-Induced Germination. Phytopathology 2015; 105:199-209. [PMID: 25185010 DOI: 10.1094/phyto-01-14-0013-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Ampelomyces quisqualis is a mycoparasite of a diverse range of phytopathogenic fungi associated with the powdery mildew disease. Among them are several Erysiphaceae species with great economic impact on high-value crops such as grape. Due to its ability to parasitize and prevent the spread of powdery mildews, A. quisqualis has received considerable attention for its biocontrol potential. However, and in sharp contrast to the extensively studied biocontrol species belonging to the genus Trichoderma, little is known about the biology of A. quisqualis at the molecular and genetic levels. We present the first genome-wide transcription profiling in A. quisqualis during host-induced germination. A total of 1,536 putative genes showed significant changes in transcription during the germination of A. quisqualis. This finding denotes an extensive transcriptional reprogramming of A. quisqualis induced by the presence of the host. Several upregulated genes were predicted to encode for putative mycoparasitism-related proteins such as secreted proteases, virulence factors, and proteins related to toxin biosynthesis. Our data provide the most comprehensive sequence resource currently available for A. quisqualis in addition to offering valuable insights into the biology of A. quisqualis and its mycoparasitic lifestyle. Eventually, this may improve the biocontrol capacity of this mycoparasite.
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238
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Ment D, Alkan N, Luria N, Bi FC, Reuveni E, Fluhr R, Prusky D. A Role of AREB in the Regulation of PACC-Dependent Acid-Expressed-Genes and Pathogenicity of Colletotrichum gloeosporioides. Mol Plant Microbe Interact 2015; 28:154-66. [PMID: 25317668 DOI: 10.1094/mpmi-09-14-0252-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Gene expression regulation by pH in filamentous fungi and yeasts is controlled by the PACC/RIM101 transcription factor. In Colletotrichum gloeosporioides, PACC is known to act as positive regulator of alkaline-expressed genes, and this regulation was shown to contribute to fungal pathogenicity. PACC is also a negative regulator of acid-expressed genes, however; the mechanism of downregulation of acid-expressed genes by PACC and their contribution to C. gloeosporioides pathogenicity is not well understood. RNA sequencing data analysis was employed to demonstrate that PACC transcription factor binding sites (TFBS) are significantly overrepresented in the promoter of PACC-upregulated, alkaline-expressed genes. In contrast, they are not overrepresented in the PACC-downregulated, acid-expressed genes. Instead, acid-expressed genes showed overrepresentation of AREB GATA TFBS in C. gloeosporioides and in homologs of five other ascomycetes genomes. The areB promoter contains PACC TFBS; its transcript was upregulated at pH 7 and repressed in ΔpacC. Furthermore, acid-expressed genes were found to be constitutively upregulated in ΔareB during alkalizing conditions. The areB mutants showed significantly reduced ammonia secretion and pathogenicity on tomato fruit. Present results indicate that PACC activates areB expression, thereby conditionally repressing acid-expressed genes and contributing critically to C. gloeosporioides pathogenicity.
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239
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Han L, Kon Y, Phizicky EM. Functional importance of Ψ38 and Ψ39 in distinct tRNAs, amplified for tRNAGln(UUG) by unexpected temperature sensitivity of the s2U modification in yeast. RNA 2015; 21:188-201. [PMID: 25505024 PMCID: PMC4338347 DOI: 10.1261/rna.048173.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The numerous modifications of tRNA play central roles in controlling tRNA structure and translation. Modifications in and around the anticodon loop often have critical roles in decoding mRNA and in maintaining its reading frame. Residues U38 and U39 in the anticodon stem-loop are frequently modified to pseudouridine (Ψ) by members of the widely conserved TruA/Pus3 family of pseudouridylases. We investigate here the cause of the temperature sensitivity of pus3Δ mutants of the yeast Saccharomyces cerevisiae and find that, although Ψ38 or Ψ39 is found on at least 19 characterized cytoplasmic tRNA species, the temperature sensitivity is primarily due to poor function of tRNA(Gln(UUG)), which normally has Ψ38. Further investigation reveals that at elevated temperatures there are substantially reduced levels of the s(2)U moiety of mcm(5)s(2)U34 of tRNA(Gln(UUG)) and the other two cytoplasmic species with mcm(5)s(2)U34, that the reduced s(2)U levels occur in the parent strain BY4741 and in the widely used strain W303, and that reduced levels of the s(2)U moiety are detectable in BY4741 at temperatures as low as 33°C. Additional examination of the role of Ψ38,39 provides evidence that Ψ38 is important for function of tRNA(Gln(UUG)) at permissive temperature, and indicates that Ψ39 is important for the function of tRNA(Trp(CCA)) in trm10Δ pus3Δ mutants and of tRNA(Leu(CAA)) as a UAG nonsense suppressor. These results provide evidence for important roles of both Ψ38 and Ψ39 in specific tRNAs, and establish that modification of the wobble position is subject to change under relatively mild growth conditions.
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Affiliation(s)
- Lu Han
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Yoshiko Kon
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
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240
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Niederer RO, Zappulla DC. Refined secondary-structure models of the core of yeast and human telomerase RNAs directed by SHAPE. RNA 2015; 21:254-261. [PMID: 25512567 PMCID: PMC4338352 DOI: 10.1261/rna.048959.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 10/31/2014] [Accepted: 11/14/2014] [Indexed: 06/04/2023]
Abstract
Telomerase catalyzes the addition of nucleotides to the ends of chromosomes to complete genomic DNA replication in eukaryotes and is implicated in multiple diseases, including most cancers. The core enzyme is composed of a reverse transcriptase and an RNA subunit, which provides the template for DNA synthesis. Despite extensive divergence at the sequence level, telomerase RNAs share several structural features within the catalytic core, suggesting a conserved enzyme mechanism. We have investigated the structure of the core of the human and yeast telomerase RNAs using SHAPE, which interrogates flexibility of each nucleotide. We present improved secondary-structure models, refined by addition of five base triples within the yeast pseudoknot and an alternate pairing within the human-specific element J2a.1 in the human pseudoknot, both of which have implications for thermodynamic stability. We also identified a potentially structured CCC region within the template that may facilitate substrate binding and enzyme mechanism. Overall, the SHAPE findings reveal multiple similarities between the Saccharomyces cerevisiae and Homo sapiens telomerase RNA cores.
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Affiliation(s)
- Rachel O Niederer
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - David C Zappulla
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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241
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Roque S, Cerciat M, Gaugué I, Mora L, Floch AG, de Zamaroczy M, Heurgué-Hamard V, Kervestin S. Interaction between the poly(A)-binding protein Pab1 and the eukaryotic release factor eRF3 regulates translation termination but not mRNA decay in Saccharomyces cerevisiae. RNA 2015; 21:124-134. [PMID: 25411355 PMCID: PMC4274632 DOI: 10.1261/rna.047282.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/26/2014] [Indexed: 06/04/2023]
Abstract
Eukaryotic release factor 3 (eRF3) is implicated in translation termination and also interacts with the poly(A)-binding protein (PABP, Pab1 in yeast), a major player in mRNA metabolism. Despite conservation of this interaction, its precise function remains elusive. First, we showed experimentally that yeast eRF3 does not contain any obvious consensus PAM2 (PABP-interacting motif 2). Thus, in yeast this association is different from the well described interaction between the metazoan factors. To gain insight into the exact function of this interaction, we then analyzed the phenotypes resulting from deleting the respective binding domains. Deletion of the Pab1 interaction domain on eRF3 did not affect general mRNA stability or nonsense-mediated mRNA decay (NMD) pathway and induced a decrease in translational readthrough. Furthermore, combined deletions of the respective interacting domains on eRF3 and on Pab1 were viable, did not affect Pab1 function in mRNA stability and harbored an antisuppression phenotype. Our results show that in Saccharomyces cerevisiae the role of the Pab1 C-terminal domain in mRNA stability is independent of eRF3 and the association of these two factors negatively regulates translation termination.
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Affiliation(s)
- Sylvain Roque
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Marie Cerciat
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Isabelle Gaugué
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Liliana Mora
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Aurélie G Floch
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Miklos de Zamaroczy
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Valérie Heurgué-Hamard
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Stephanie Kervestin
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France Metabolism and function of RNA in the nucleus, Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris 75013, France
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242
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Abstract
mRNA steady state levels vary depending on environmental conditions. Regulation of the steady state accumulation levels of an mRNA ensures that the correct amount of protein is synthesized for the cell's specific growth conditions. One approach for measuring mRNA decay rates is inhibiting transcription and subsequently monitoring the disappearance of the already present mRNA. The rate of mRNA decay can then be quantified, and an accurate half-life can be determined utilizing several techniques. In S. cerevisiae, protocols that measure mRNA half-lives have been developed and include inhibiting transcription of mRNA using strains that harbor a temperature sensitive allele of RNA polymerase II, rpb1-1. Other techniques for measuring mRNA half-lives include inhibiting transcription with transcriptional inhibitors such as thiolutin or 1,10-phenanthroline, or alternatively, by utilizing mRNAs that are under the control of a regulatable promoter such as the galactose inducible promoter and the TET-off system. Here, we describe measurement of S. cerevisiae mRNA decay rates using the temperature sensitive allele of RNA polymerase II. This technique can be used to measure mRNA decay rates of individual mRNAs or genome-wide.
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243
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Sollier J, Stork CT, García-Rubio ML, Paulsen RD, Aguilera A, Cimprich KA. Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability. Mol Cell 2014; 56:777-85. [PMID: 25435140 DOI: 10.1016/j.molcel.2014.10.020] [Citation(s) in RCA: 379] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 10/07/2014] [Accepted: 10/22/2014] [Indexed: 11/19/2022]
Abstract
R-loops, consisting of an RNA-DNA hybrid and displaced single-stranded DNA, are physiological structures that regulate various cellular processes occurring on chromatin. Intriguingly, changes in R-loop dynamics have also been associated with DNA damage accumulation and genome instability; however, the mechanisms underlying R-loop-induced DNA damage remain unknown. Here we demonstrate in human cells that R-loops induced by the absence of diverse RNA processing factors, including the RNA/DNA helicases Aquarius (AQR) and Senataxin (SETX), or by the inhibition of topoisomerase I, are actively processed into DNA double-strand breaks (DSBs) by the nucleotide excision repair endonucleases XPF and XPG. Surprisingly, DSB formation requires the transcription-coupled nucleotide excision repair (TC-NER) factor Cockayne syndrome group B (CSB), but not the global genome repair protein XPC. These findings reveal an unexpected and potentially deleterious role for TC-NER factors in driving R-loop-induced DNA damage and genome instability.
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Affiliation(s)
- Julie Sollier
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caroline Townsend Stork
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Avenida Américo Vespucio, 41092 Seville, Spain
| | - Renee D Paulsen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Avenida Américo Vespucio, 41092 Seville, Spain
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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244
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Kikuchi Y, Hijikata N, Yokoyama K, Ohtomo R, Handa Y, Kawaguchi M, Saito K, Ezawa T. Polyphosphate accumulation is driven by transcriptome alterations that lead to near-synchronous and near-equivalent uptake of inorganic cations in an arbuscular mycorrhizal fungus. New Phytol 2014; 204:638-649. [PMID: 25039900 DOI: 10.1111/nph.12937] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 04/30/2014] [Accepted: 06/11/2014] [Indexed: 05/09/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi accumulate a massive amount of phosphate as polyphosphate to deliver to the host, but the underlying physiological and molecular mechanisms have yet to be elucidated. In the present study, the dynamics of cationic components during polyphosphate accumulation were investigated in conjunction with transcriptome analysis. Rhizophagus sp. HR1 was grown with Lotus japonicus under phosphorus-deficient conditions, and extraradical mycelia were harvested after phosphate application at prescribed intervals. Levels of polyphosphate, inorganic cations and amino acids were measured, and RNA-Seq was performed on the Illumina platform. Phosphate application triggered not only polyphosphate accumulation but also near-synchronous and near-equivalent uptake of Na(+) , K(+) , Ca(2+) and Mg(2+) , whereas no distinct changes in the levels of amino acids were observed. During polyphosphate accumulation, the genes responsible for mineral uptake, phosphate and nitrogen metabolism and the maintenance of cellular homeostasis were up-regulated. The results suggest that inorganic cations play a major role in neutralizing the negative charge of polyphosphate, and these processes are achieved by the orchestrated regulation of gene expression. Our findings provide, for the first time, a global picture of the cellular response to increased phosphate availability, which is the initial process of nutrient delivery in the associations.
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Affiliation(s)
- Yusuke Kikuchi
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Nowaki Hijikata
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Kaede Yokoyama
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Ryo Ohtomo
- National Agriculture and Food Research Organization, Hokkaido Agricultural Research Center, Sapporo, 062-8555, Japan
| | - Yoshihiro Handa
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Katsuharu Saito
- Faculty of Agriculture, Shinshu University, Minamiminowa, 399-4598, Japan
| | - Tatsuhiro Ezawa
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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245
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Abstract
Application of the CRISPR-Cas9 genome editing system in the model organism Schizosaccharomyces pombe has been hampered by the lack of constructs to express RNA of arbitrary sequence. Here we present expression constructs that use the promoter/leader RNA of K RNA (rrk1) and a ribozyme to produce the targeting guide RNA. Together with constitutive expression of Cas9, this system achieves selection-free specific mutagenesis with efficiencies approaching 100%. The rrk1 CRISPR-Cas9 method enables rapid and efficient genome manipulation and unlocks the CRISPR toolset for use in fission yeast.
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Affiliation(s)
- Jake Z Jacobs
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Keith M Ciccaglione
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Vincent Tournier
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Mikel Zaratiegui
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
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246
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Zid BM, O'Shea EK. Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. Nature 2014; 514:117-21. [PMID: 25119046 PMCID: PMC4184922 DOI: 10.1038/nature13578] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 06/11/2014] [Indexed: 01/22/2023]
Abstract
A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes that encode proteins important for survival. Under many such conditions, the overall protein synthesis level is reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in Saccharomyces cerevisiae (yeast), translation is rapidly repressed, yet the transcription of many stress- and glucose-repressed genes is increased. Here we show, using ribosomal profiling and microscopy, that this transcriptionally upregulated gene set consists of two classes: one class produces messenger RNAs that are translated during glucose starvation and are diffusely localized in the cytoplasm, including many heat-shock protein mRNAs; and the other class produces mRNAs that are not efficiently translated during glucose starvation and are concentrated in foci that co-localize with P bodies and stress granules, a class that is enriched for mRNAs involved in glucose metabolism. Surprisingly, the information specifying the differential localization and protein production of these two classes of mRNA is encoded in the promoter sequence: promoter responsiveness to heat-shock factor 1 (Hsf1) specifies diffuse cytoplasmic localization and higher protein production on glucose starvation. Thus, promoter sequences can influence not only the levels of mRNAs but also the subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to the environmental conditions.
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Affiliation(s)
- Brian M Zid
- 1] Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Erin K O'Shea
- 1] Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA [3] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA [4] Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
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247
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Abstract
The abundance of a transcript is determined by its rate of synthesis and its rate of degradation; however, global methods for quantifying RNA abundance cannot distinguish variation in these two processes. Here, we introduce RNA approach to equilibrium sequencing (RATE-seq), which uses in vivo metabolic labeling of RNA and approach to equilibrium kinetics, to determine absolute RNA degradation and synthesis rates. RATE-seq does not disturb cellular physiology, uses straightforward normalization with exogenous spike-ins, and can be readily adapted for studies in most organisms. We demonstrate the use of RATE-seq to estimate genome-wide kinetic parameters for coding and noncoding transcripts in Saccharomyces cerevisiae.
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Affiliation(s)
- Benjamin Neymotin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
| | - Rodoniki Athanasiadou
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
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248
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Abstract
In all three domains of life ribosomal RNAs are extensively modified at functionally important sites of the ribosome. These modifications are believed to fine-tune the ribosome structure for optimal translation. However, the precise mechanistic effect of modifications on ribosome function remains largely unknown. Here we show that a cluster of methylated nucleotides in domain IV of 25S rRNA is critical for integrity of the large ribosomal subunit. We identified the elusive cytosine-5 methyltransferase for C2278 in yeast as Rcm1 and found that a combined loss of cytosine-5 methylation at C2278 and ribose methylation at G2288 caused dramatic ribosome instability, resulting in loss of 60S ribosomal subunits. Structural and biochemical analyses revealed that this instability was caused by changes in the structure of 25S rRNA and a consequent loss of multiple ribosomal proteins from the large ribosomal subunit. Our data demonstrate that individual RNA modifications can strongly affect structure of large ribonucleoprotein complexes.
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Affiliation(s)
- Andriana Gigova
- Biochemistry Center and Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
| | - Sujitha Duggimpudi
- Biochemistry Center and Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
| | - Tim Pollex
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Matthias Schaefer
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Martin Koš
- Biochemistry Center and Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
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249
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Makange M, Kulaya N, Biseko E, Kalenga P, Mutagwaba S, Misinzo G. Batrachochytrium dendrobatidis detected in Kihansi spray toads at a captive breeding facility (Kihansi, Tanzania). Dis Aquat Organ 2014; 111:159-164. [PMID: 25266903 DOI: 10.3354/dao02775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The chytrid fungus Batrachochytrium dendrobatidis (Bd) is the aetiological agent of amphibian chytridiomycosis, a disease associated with global amphibian population declines. In November 2012, mass mortalities of Kihansi spray toads Nectophrynoides asperginis were observed at the Kihansi captive breeding facility, located in the Udzungwa Mountains, Tanzania. Mortalities increased rapidly, and dead toads showed typical clinical signs of chytridiomycosis, including reddening of the skin that was especially evident on the toe pads. Treatment of toads with itraconazole rapidly reduced mortalities. Dead toads (n = 49) were collected and used to perform Bd-specific polymerase chain reaction and subsequent nucleotide sequencing. All toads collected at the facility were positive for Bd. The obtained Bd 5.8S rRNA gene and flanking internal transcribed spacer regions (ITS1 and ITS2) were not 100% identical to any other Bd sequences in GenBank, but closely resembled isolates from Ecuador, Japan, USA, Brazil, Korea, and South Africa. To our knowledge, this is the first study reporting molecular characteristics of Bd isolated from the Udzungwa Mountains. Strict biosecurity measures at the breeding facility and in Kihansi spray wetlands where toads have been reintroduced have been implemented. Further studies on Bd epidemiology in the Udzungwa Mountains are recommended in order to understand its origin, prevalence, and molecular characteristics in wild amphibian populations. This will be important for conservation of several endemic amphibian species in the Udzungwa Mountains, which are part of the Eastern Arc Mountains, a global biodiversity hotspot.
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Affiliation(s)
- Mariam Makange
- Department of Veterinary Microbiology and Parasitology, Faculty of Veterinary Medicine, Sokoine University of Agriculture, Morogoro, Tanzania
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250
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Roy K, Chanfreau G. Stress-induced nuclear RNA degradation pathways regulate yeast bromodomain factor 2 to promote cell survival. PLoS Genet 2014; 10:e1004661. [PMID: 25232960 PMCID: PMC4169253 DOI: 10.1371/journal.pgen.1004661] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/11/2014] [Indexed: 11/23/2022] Open
Abstract
Bromodomain proteins are key regulators of gene expression. How the levels of these factors are regulated in specific environmental conditions is unknown. Previous work has established that expression of yeast Bromodomain factor 2 (BDF2) is limited by spliceosome-mediated decay (SMD). Here we show that BDF2 is subject to an additional layer of post-transcriptional control through RNase III-mediated decay (RMD). We found that the yeast RNase III Rnt1p cleaves a stem-loop structure within the BDF2 mRNA to down-regulate its expression. However, these two nuclear RNA degradation pathways play distinct roles in the regulation of BDF2 expression, as we show that the RMD and SMD pathways of the BDF2 mRNA are differentially activated or repressed in specific environmental conditions. RMD is hyper-activated by salt stress and repressed by hydroxyurea-induced DNA damage while SMD is inactivated by salt stress and predominates during DNA damage. Mutations of cis-acting signals that control SMD and RMD rescue numerous growth defects of cells lacking Bdf1p, and show that SMD plays an important role in the DNA damage response. These results demonstrate that specific environmental conditions modulate nuclear RNA degradation pathways to control BDF2 expression and Bdf2p-mediated gene regulation. Moreover, these results show that precise dosage of Bromodomain factors is essential for cell survival in specific environmental conditions, emphasizing their importance for controlling chromatin structure and gene expression in response to environmental stress. Cells adapt to changes in the environment through modulating gene expression at both the RNA and protein levels. RNA degradation plays a central role in this adaption response, by controlling the stability of specific mRNAs to optimize protein production in different conditions. In this study, we show that the gene encoding Bromodomain Factor 2 (BDF2) is tightly regulated according to environmental conditions by two distinct RNA degradation mechanisms. We show that these RNA degradation pathways are critical for cell growth in specific conditions. Our study suggests that environmental modulation of nuclear RNA degradation pathways is a previously unappreciated aspect of gene expression control.
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Affiliation(s)
- Kevin Roy
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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