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Sun W, Zhang X, Chen D, Murchie AIH. Interactions between the 5' UTR mRNA of the spe2 gene and spermidine regulate translation in S. pombe. RNA 2020; 26:137-149. [PMID: 31826924 PMCID: PMC6961545 DOI: 10.1261/rna.072975.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/10/2019] [Indexed: 05/20/2023]
Abstract
The 5' untranslated regions (5' UTR) of mRNAs play an important role in the eukaryotic translation initiation process. Additional levels of translational regulation may be mediated through interactions between structured mRNAs that can adopt interchangeable secondary or tertiary structures and the regulatory protein/RNA factors or components of the translational apparatus. Here we report a regulatory function of the 5' UTR mRNA of the spe2 gene (SAM decarboxylase) in polyamine metabolism of the fission yeast Schizosaccharomyces pombe Reporter assays, biochemical experiments, and mutational analysis demonstrate that this 5' UTR mRNA of spe2 can bind to spermidine to regulate translation. A tertiary structure transition in the 5' UTR RNA upon spermidine binding is essential for translation regulation. This study provides biochemical evidence for spermidine binding to regulate translation of the spe2 gene through interactions with the 5' UTR mRNA. The identification of such a regulatory RNA that is directly associated with an essential eukaryotic metabolic process suggests that other ligand-binding RNAs may also contribute to eukaryotic gene regulation.
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Affiliation(s)
- Wenxia Sun
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xuhui Zhang
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Dongrong Chen
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Alastair I H Murchie
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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Brady JR, Whittaker CA, Tan MC, Kristensen DL, Ma D, Dalvie NC, Love KR, Love JC. Comparative genome-scale analysis of Pichia pastoris variants informs selection of an optimal base strain. Biotechnol Bioeng 2020; 117:543-555. [PMID: 31654411 PMCID: PMC7003935 DOI: 10.1002/bit.27209] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/04/2019] [Accepted: 10/22/2019] [Indexed: 01/08/2023]
Abstract
Komagataella phaffii, also known as Pichia pastoris, is a common host for the production of biologics and enzymes, due to fast growth, high productivity, and advancements in host engineering. Several K. phaffii variants are commonly used as interchangeable base strains, which confounds efforts to improve this host. In this study, genomic and transcriptomic analyses of Y-11430 (CBS7435), GS115, X-33, and eight other variants enabled a comparative assessment of the relative fitness of these hosts for recombinant protein expression. Cell wall integrity explained the majority of the variation among strains, impacting transformation efficiency, growth, methanol metabolism, and secretion of heterologous proteins. Y-11430 exhibited the highest activity of genes involved in methanol utilization, up to two-fold higher transcription of heterologous genes, and robust growth. With a more permeable cell wall, X-33 displayed a six-fold higher transformation efficiency and up to 1.2-fold higher titers than Y-11430. X-33 also shared nearly all mutations, and a defective variant of HIS4, with GS115, precluding robust growth. Transferring two beneficial mutations identified in X-33 into Y-11430 resulted in an optimized base strain that provided up to four-fold higher transformation efficiency and three-fold higher protein titers, while retaining robust growth. The approach employed here to assess unique banked variants in a species and then transfer key beneficial variants into a base strain should also facilitate rational assessment of a broad set of other recombinant hosts.
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Affiliation(s)
- Joseph R. Brady
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Charles A. Whittaker
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Melody C. Tan
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - D. Lee Kristensen
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Duanduan Ma
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Neil C. Dalvie
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Kerry Routenberg Love
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - J. Christopher Love
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
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Zhang X, Sun W, Chen D, Murchie AIH. Interactions between SAM and the 5' UTR mRNA of the sam1 gene regulate translation in S. pombe. RNA 2020; 26:150-161. [PMID: 31767786 PMCID: PMC6961541 DOI: 10.1261/rna.072983.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/14/2019] [Indexed: 05/03/2023]
Abstract
The 5' untranslated region (5' UTR) of eukaryotic mRNA plays an important role in translation. Here we report the function of the 5' UTR mRNA of S-adenosylmethionine synthetase (sam1) in translational modulation in the presence of SAM in fission yeast Schizosaccharomyces pombe Reporter assays, binding and chemical probing experiments, and mutational analysis show that the 5' UTR mRNA of sam1 binds to SAM to effect translation. Translational modulation is dependent on a tertiary structure transition in the RNA upon SAM binding. The characterization of such an RNA that is directly associated with an essential metabolic process in eukaryotes provides additional evidence that ligand binding by RNAs plays an important role in eukaryotic gene regulation.
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Affiliation(s)
- Xuhui Zhang
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wenxia Sun
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Dongrong Chen
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Alastair I H Murchie
- Fudan University Pudong Medical Center, Pudong and Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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Navickas A, Chamois S, Saint-Fort R, Henri J, Torchet C, Benard L. No-Go Decay mRNA cleavage in the ribosome exit tunnel produces 5'-OH ends phosphorylated by Trl1. Nat Commun 2020; 11:122. [PMID: 31913314 PMCID: PMC6949252 DOI: 10.1038/s41467-019-13991-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/11/2019] [Indexed: 11/24/2022] Open
Abstract
The No-Go Decay (NGD) mRNA surveillance pathway degrades mRNAs containing stacks of stalled ribosomes. Although an endoribonuclease has been proposed to initiate cleavages upstream of the stall sequence, the production of two RNA fragments resulting from a unique cleavage has never been demonstrated. Here we use mRNAs expressing a 3'-ribozyme to produce truncated transcripts in vivo to mimic naturally occurring truncated mRNAs known to trigger NGD. This technique allows us to analyse endonucleolytic cleavage events at single-nucleotide resolution starting at the third collided ribosome, which we show to be Hel2-dependent. These cleavages map precisely in the mRNA exit tunnel of the ribosome, 8 nucleotides upstream of the first P-site residue and release 5'-hydroxylated RNA fragments requiring 5'-phosphorylation prior to digestion by the exoribonuclease Xrn1, or alternatively by Dxo1. Finally, we identify the RNA kinase Trl1, alias Rlg1, as an essential player in the degradation of NGD RNAs.
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Affiliation(s)
- Albertas Navickas
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Sébastien Chamois
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Rénette Saint-Fort
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Julien Henri
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Claire Torchet
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Lionel Benard
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France.
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Porrua O. Purification and In Vitro Analysis of the Exosome Cofactors Nrd1-Nab3 and Trf4-Air2. Methods Mol Biol 2020; 2062:277-289. [PMID: 31768982 DOI: 10.1007/978-1-4939-9822-7_14] [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: 06/10/2023]
Abstract
In many eukaryotic organisms from yeast to human, the exosome plays an important role in the control of pervasive transcription and in non-coding RNA (ncRNA) processing and quality control by trimming precursor RNAs and degrading aberrant transcripts. In Saccharomyces cerevisiae this function is enabled by the interaction of the exosome with several cofactors: the Nrd1-Nab3 heterodimer and the Trf4-Air2-Mtr4 (TRAMP4) complex. Nrd1 and Nab3 are RNA binding proteins that recognize specific motifs enriched in the target ncRNAs, whereas TRAMP4 adds polyA tails at the 3' end of transcripts and stimulates RNA degradation by the exosome. This chapter provides protocols for the purification of recombinant forms of these exosome cofactors and for the in vitro assessment of their activity.
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Affiliation(s)
- Odil Porrua
- Institut Jacques Monod-UMR7592, CNRS, Université de Paris, Paris, France.
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Li ZH, Meng H, Ma B, Tao X, Liu M, Wang FQ, Wei DZ. Immediate, multiplexed and sequential genome engineering facilitated by CRISPR/Cas9 in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2020; 47:83-96. [PMID: 31768773 DOI: 10.1007/s10295-019-02251-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 09/14/2019] [Accepted: 11/11/2019] [Indexed: 01/22/2023]
Abstract
A method called Cas-3P allowing for immediate, multiplexed and sequential genome engineering was developed using one plasmid expressing Cas9 and three marked plasmid backbones (P1, P2 and P3) for guide RNA (gRNA) expression. The three marked gRNA plasmid backbones were recurred in a P1-P2-P3 order for sequential gene targeting, without construction of any additional plasmid and elimination of gRNA plasmid by induction in each round. The efficiency of direct gRNA plasmid curing mediated by Cas-3P was more than 40% in sequential gene targeting. Besides, Cas-3P allowed single-, double- and triple-loci gene targeting with an efficiency of 75%, 36.8% and 8.2% within 3-4 days, respectively. Through three sequential rounds of gene targeting within 10 days, S. cerevisiae was optimized for the production of patchoulol by replacing one promoter, overexpressing three genes and disrupting four genes. The work is important for practical application in the cell factory engineering of S. cerevisiae.
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Affiliation(s)
- Zhen-Hai Li
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Hao Meng
- Hunan Norchem Pharmaceutical Co Ltd, ChangSha, China
| | - Bin Ma
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Xinyi Tao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Min Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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Achar YJ, Adhil M, Choudhary R, Gilbert N, Foiani M. Negative supercoil at gene boundaries modulates gene topology. Nature 2020; 577:701-705. [PMID: 31969709 DOI: 10.1038/s41586-020-1934-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [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: 04/30/2019] [Accepted: 11/25/2019] [Indexed: 11/08/2022]
Abstract
Transcription challenges the integrity of replicating chromosomes by generating topological stress and conflicts with forks1,2. The DNA topoisomerases Top1 and Top2 and the HMGB family protein Hmo1 assist DNA replication and transcription3-6. Here we describe the topological architecture of genes in Saccharomyces cerevisiae during the G1 and S phases of the cell cycle. We found under-wound DNA at gene boundaries and over-wound DNA within coding regions. This arrangement does not depend on Pol II or S phase. Top2 and Hmo1 preserve negative supercoil at gene boundaries, while Top1 acts at coding regions. Transcription generates RNA-DNA hybrids within coding regions, independently of fork orientation. During S phase, Hmo1 protects under-wound DNA from Top2, while Top2 confines Pol II and Top1 at coding units, counteracting transcription leakage and aberrant hybrids at gene boundaries. Negative supercoil at gene boundaries prevents supercoil diffusion and nucleosome repositioning at coding regions. DNA looping occurs at Top2 clusters. We propose that Hmo1 locks gene boundaries in a cruciform conformation and, with Top2, modulates the architecture of genes that retain the memory of the topological arrangements even when transcription is repressed.
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MESH Headings
- Chromatin Assembly and Disassembly
- DNA Replication
- DNA Topoisomerases, Type I/metabolism
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA, Cruciform/chemistry
- DNA, Cruciform/genetics
- DNA, Cruciform/metabolism
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- G1 Phase
- Gene Expression Regulation, Fungal
- Genes, Fungal
- High Mobility Group Proteins/metabolism
- Mutation
- Nucleic Acid Hybridization
- Nucleosomes/chemistry
- Nucleosomes/genetics
- Nucleosomes/metabolism
- Open Reading Frames/genetics
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- S Phase
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Transcription, Genetic
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Affiliation(s)
| | - Mohamood Adhil
- IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy
| | - Ramveer Choudhary
- IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Marco Foiani
- IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy.
- Università degli Studi di Milano, Milan, Italy.
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Wang Y, Shao Y, Zhu Y, Wang K, Ma B, Zhou Q, Chen A, Chen H. XRN1-associated long non-coding RNAs may contribute to fungal virulence and sexual development in entomopathogenic fungus Cordyceps militaris. Pest Manag Sci 2019; 75:3302-3311. [PMID: 31025499 DOI: 10.1002/ps.5453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 01/01/2019] [Revised: 04/11/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Numerous long non-coding RNAs (lncRNAs) identified and characterized in mammals, plants, and fungi have been found to play critical regulatory roles in biological processes. However, little is known about the role of lncRNAs in insect pathogenic fungi. RESULTS By profiling the transcriptomes of sexual and asexual development in the insect-pathogenic fungus Cordyceps militaris, 4140 lncRNAs were identified and found to be dynamically expressed during fungal development. The lncRNAs had shorter transcript lengths and lower numbers of exons compared to protein-coding genes. The expressed target genes (neighboring and cis-regulated) of various expressed lncRNAs were predicted, and these genes showed significant enrichment in energy metabolism and signaling pathways, such as 'Glycolysis/Gluconeogenesis' and "MAPK signaling pathway". To better understand how lncRNAs function in the fungus, xrn1, the final gene of the NMD pathway, which determines the fate of lncRNAs, was disrupted. The Δxrn1 deletion mutant displayed significant (P < 0.05) attenuation of virulence and a lower growth rate in C. militaris. Quantitative RT-PCR results revealed 10 lncRNAs with significantly higher expression, while 8 of these 10 lncRNA target genes (virulence- and sexual development-related) showed significantly lower expression in Δxrn1 compared to in the wild-type, suggesting that lncRNA expression regulates fungal virulence and sexual development by affecting gene expression. CONCLUSION These findings suggest that lncRNAs in C. militaris play important roles in the fungal infection progress and fruiting body production, providing a broad repertoire and resource for further studies of lncRNAs. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Yulong Wang
- Jiangsu Key Construction Laboratory of Food Resource Development and Quality Safe, Xuzhou University of Technology, Xuzhou, China
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Quality Improvement of Anhui Province/Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ying Shao
- Jiangsu Key Construction Laboratory of Food Resource Development and Quality Safe, Xuzhou University of Technology, Xuzhou, China
| | - Yunlan Zhu
- Jiangsu Key Construction Laboratory of Food Resource Development and Quality Safe, Xuzhou University of Technology, Xuzhou, China
| | - Kun Wang
- Jiangsu KONEN Biological Engineering Co., Ltd, Nanjing, China
| | - Bin Ma
- Jiangsu KONEN Biological Engineering Co., Ltd, Nanjing, China
| | - Qiumei Zhou
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Anhui Chen
- Jiangsu Key Construction Laboratory of Food Resource Development and Quality Safe, Xuzhou University of Technology, Xuzhou, China
| | - Hongwei Chen
- Jiangsu Key Construction Laboratory of Food Resource Development and Quality Safe, Xuzhou University of Technology, Xuzhou, China
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Chutrakul C, Panchanawaporn S, Jeennor S, Anantayanon J, Vorapreeda T, Vichai V, Laoteng K. Functional Characterization of Novel U6 RNA Polymerase III Promoters: Their Implication for CRISPR-Cas9-Mediated Gene Editing in Aspergillus oryzae. Curr Microbiol 2019; 76:1443-1451. [PMID: 31541261 DOI: 10.1007/s00284-019-01770-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 11/21/2018] [Accepted: 09/09/2019] [Indexed: 01/04/2023]
Abstract
U6 RNA polymerase III promoter (PU6), which is a key element in controlling the generation of single-guide RNA (sgRNA) for gene editing through CRISPR-Cas9 system, was investigated in this work. Using bioinformatics approach, two novel U6 ribonucleic acid (U6 RNA) sequences of Aspergillus niger were identified, showing that they had conserved motifs similar to other U6 RNAs. The putative PU6 located at the upstream sequence of A. niger U6 RNA exhibited the consensus motif, CCAATYA, and the TATA box which shared highly conserved characteristics across Aspergilli, whereas the A- and B-boxes were found at the intragenic and downstream of the structural genes, respectively. Using Aspergillus oryzae as a workhorse system, the function of A. niger PU6s for controlling the transcripts of sgRNA was verified, in which the orotidine-5'-phosphate decarboxylase (pyrG) sequence was used as a target for gene disruption through CRISPR-Cas9 system. Quantitative reverse transcription-polymerase chain reaction (RT-qPCR) analysis of the selected pyrG auxotrophic strains showed the expression of sgRNA, indicating that the non-native promoters could efficiently drive sgRNA expression in A. oryzae. These identified promoters are useful genetic tools for precise engineering of metabolic pathways in the industrially important fungus through the empowered CRISPR-Cas9-associated gene-editing system.
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Affiliation(s)
- Chanikul Chutrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand.
| | - Sarocha Panchanawaporn
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Sukanya Jeennor
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Jutamas Anantayanon
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Tayvich Vorapreeda
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC) At King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, 10150, Thailand
| | - Vanicha Vichai
- Biosensing and Bioprospecting Technology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Kobkul Laoteng
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
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Chen C, Li Q, Fu R, Wang J, Xiong C, Fan Z, Hu R, Zhang H, Lu D. Characterization of the mitochondrial genome of the pathogenic fungus Scytalidium auriculariicola (Leotiomycetes) and insights into its phylogenetics. Sci Rep 2019; 9:17447. [PMID: 31768013 PMCID: PMC6877775 DOI: 10.1038/s41598-019-53941-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 07/19/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022] Open
Abstract
Scytalidium auriculariicola is the causative pathogen of slippery scar disease in the cultivated cloud ear fungus, Auricularia polytricha. In the present study, the mitogenome of S. auriculariicola was sequenced and assembled by next-generation sequencing technology. The circular mitogenome is 96,857 bp long and contains 56 protein-coding genes, 2 ribosomal RNA genes, and 30 transfer RNA genes (tRNAs). The high frequency of A and T used in codons contributed to the high AT content (73.70%) of the S. auriculariicola mitogenome. Comparative analysis indicated that the base composition and the number of introns and protein-coding genes in the S. auriculariicola mitogenome varied from that of other Leotiomycetes mitogenomes, including a uniquely positive AT skew. Five distinct groups were found in the gene arrangements of Leotiomycetes. Phylogenetic analyses based on combined gene datasets (15 protein-coding genes) yielded well-supported (BPP = 1) topologies. A single-gene phylogenetic tree indicated that the nad4 gene may be useful as a molecular marker to analyze the phylogenetic relationships of Leotiomycetes species. This study is the first report on the mitochondrial genome of the genus Scytalidium, and it will contribute to our understanding of the population genetics and evolution of S. auriculariicola and related species.
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Affiliation(s)
- Cheng Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, 610066, Sichuan, P.R. China
| | - Qiang Li
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, P.R. China
| | - Rongtao Fu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Jian Wang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Zhonghan Fan
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Rongping Hu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Hong Zhang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Daihua Lu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China.
- Sichuan Academy of Agricultural Sciences, 20 # Jingjusi Rd, Chengdu, 610066, Sichuan, P.R. China.
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Branco P, Candeias A, Caldeira AT, González‐Pérez M. An important step forward for the future development of an easy and fast procedure for identifying the most dangerous wine spoilage yeast, Dekkera bruxellensis, in wine environment. Microb Biotechnol 2019; 12:1237-1248. [PMID: 31197952 PMCID: PMC6801150 DOI: 10.1111/1751-7915.13422] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 04/04/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
Dekkera bruxellensis is the main reason for spoilage in the wine industry. It renders the products unacceptable leading to large economic losses. Fluorescence In Situ Hybridization (FISH) technique has the potential for allowing its specific detection. Nevertheless, some experimental difficulties can be encountered when FISH technique is applied in the wine environment (e.g. matrix and cells' autofluorescence, fluorophore inadequate selection and probes' low specificity to the target organisms). An easy and fast in-suspension RNA-FISH procedure was applied for the first time for identifying D. bruxellensis in wine. A previously designed RNA-FISH probe to detect D. bruxellensis (26S D. brux.5.1) was used, and the matrix and cells' fluorescence interferences, the influence of three fluorophores in FISH performance and the probe specificity were evaluated. The results revealed that to apply RNA-FISH technique in the wine environment, a red-emitting fluorophore should be used. Good probe performance and specificity were achieved with 25% of formamide. The resulting RNA-FISH protocol was applied in wine samples artificially inoculated with D. bruxellensis. This spoilage microorganism was detected in wine at cell densities lower than those associated with phenolic off-flavours. Thus, the RNA-FISH procedure described in this work represents an advancement to facilitate early detection of the most dangerous wine spoilage yeast and, consequently, to reduce the economic losses caused by this yeast to the wine industry.
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Affiliation(s)
- Patrícia Branco
- HERCULES LaboratoryÉvora UniversityLargo Marquês de Marialva 87000‐809ÉvoraPortugal
| | - António Candeias
- HERCULES LaboratoryÉvora UniversityLargo Marquês de Marialva 87000‐809ÉvoraPortugal
- Chemistry DepartmentSchool of Sciences and TechnologyÉvora UniversityRua Romão Ramalho 597000‐671ÉvoraPortugal
| | - Ana Teresa Caldeira
- HERCULES LaboratoryÉvora UniversityLargo Marquês de Marialva 87000‐809ÉvoraPortugal
- Chemistry DepartmentSchool of Sciences and TechnologyÉvora UniversityRua Romão Ramalho 597000‐671ÉvoraPortugal
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Hu Y, Bennett HW, Liu N, Moravec M, Williams JF, Azzalin CM, King MC. RNA-DNA Hybrids Support Recombination-Based Telomere Maintenance in Fission Yeast. Genetics 2019; 213:431-447. [PMID: 31405990 PMCID: PMC6781888 DOI: 10.1534/genetics.119.302606] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/09/2019] [Indexed: 11/18/2022] Open
Abstract
A subset of cancers rely on telomerase-independent mechanisms to maintain their chromosome ends. The predominant "alternative lengthening of telomeres" pathway appears dependent on homology-directed repair (HDR) to maintain telomeric DNA. However, the molecular changes needed for cells to productively engage in telomeric HDR are poorly understood. To gain new insights into this transition, we monitored the state of telomeres during serial culture of fission yeast (Schizosaccharomyces pombe) lacking the telomerase recruitment factor Ccq1. Rad52 is loaded onto critically short telomeres shortly after germination despite continued telomere erosion, suggesting that recruitment of recombination factors is not sufficient to maintain telomeres in the absence of telomerase function. Instead, survivor formation coincides with the derepression of telomeric repeat-containing RNA (TERRA). In this context, degradation of TERRA associated with the telomere in the form of R-loops drives a severe growth crisis, ultimately leading to a novel type of survivor with linear chromosomes and altered cytological telomere characteristics, including the loss of the shelterin component Rap1 (but not the TRF1/TRF2 ortholog, Taz1) from the telomere. We demonstrate that deletion of Rap1 is protective in this context, preventing the growth crisis that is otherwise triggered by degradation of telomeric R-loops in survivors with linear chromosomes. These findings suggest that upregulation of telomere-engaged TERRA, or altered recruitment of shelterin components, can support telomerase-independent telomere maintenance.
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Affiliation(s)
- Yan Hu
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Henrietta W Bennett
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Na Liu
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Martin Moravec
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), 8093, Switzerland
| | - Jessica F Williams
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Claus M Azzalin
- Instituto de Medicina Molecular João Lobo Antunes (iMM), Faculdade de Medicina da Universidade de Lisboa, 1649-028, Portugal
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
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Chen CF, Pohl TJ, Chan A, Slocum JS, Zakian VA. Saccharomyces cerevisiae Centromere RNA Is Negatively Regulated by Cbf1 and Its Unscheduled Synthesis Impacts CenH3 Binding. Genetics 2019; 213:465-479. [PMID: 31391265 PMCID: PMC6781895 DOI: 10.1534/genetics.119.302528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 06/20/2019] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
Two common features of centromeres are their transcription into noncoding centromere RNAs (cen-RNAs) and their assembly into nucleosomes that contain a centromere-specific histone H3 (cenH3). Here, we show that Saccharomyces cerevisiae cen-RNA was present in low amounts in wild-type (WT) cells, and that its appearance was tightly cell cycle-regulated, appearing and disappearing in a narrow window in S phase after centromere replication. In cells lacking Cbf1, a centromere-binding protein, cen-RNA was 5-12 times more abundant throughout the cell cycle. In WT cells, cen-RNA appearance occurred at the same time as loss of Cbf1's centromere binding, arguing that the physical presence of Cbf1 inhibits cen-RNA production. Binding of the Pif1 DNA helicase, which happens in mid-late S phase, occurred at about the same time as Cbf1 loss from the centromere, suggesting that Pif1 may facilitate this loss by its known ability to displace proteins from DNA. Cen-RNAs were more abundant in rnh1Δ cells but only in mid-late S phase. However, fork pausing at centromeres was not elevated in rnh1Δ cells but rather was due to centromere-binding proteins, including Cbf1 Strains with increased cen-RNA lost centromere plasmids at elevated rates. In cbf1Δ cells, where both the levels and the cell cycle-regulated appearance of cen-RNA were disrupted, the timing and levels of cenH3 centromere binding were perturbed. Thus, cen-RNAs are highly regulated, and disruption of this regulation correlates with changes in centromere structure and function.
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Affiliation(s)
- Chi-Fu Chen
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Thomas J Pohl
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Angela Chan
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Joshua S Slocum
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Virginia A Zakian
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
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Khoshnevis S, Liu X, Dattolo MD, Karbstein K. Rrp5 establishes a checkpoint for 60S assembly during 40S maturation. RNA 2019; 25:1164-1176. [PMID: 31217256 PMCID: PMC6800521 DOI: 10.1261/rna.071225.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 03/14/2019] [Accepted: 06/16/2019] [Indexed: 06/09/2023]
Abstract
Even though the RNAs contained in the small (40S) and large (60S) ribosomal subunits are cotranscribed, their assembly proceeds largely separately, involving entirely distinct machineries. Nevertheless, separation of the two subunits, an event that is critical for assembly of the small subunit, is delayed until domain I of the large subunit is transcribed, indicating crosstalk between the two assembly pathways. Here we show that this crosstalk is mediated by the assembly factor Rrp5, one of only three proteins required for assembly of both ribosomal subunits. Quantitative RNA binding and cleavage data demonstrate that early on, Rrp5 blocks separation of the two subunits, and thus 40S maturation by inhibiting the access of Rcl1 to promote cleavage of the nascent rRNA. Upon transcription of domain I of 25S rRNA, the 60S assembly factors Noc1/Noc2 bind both this RNA and Rrp5 to change the Rrp5 RNA binding mode to enable pre-40S rRNA processing. Mutants in the HEAT-repeat domain of Noc1 are deficient in the separation of the subunits, which is rescued by overexpression of wild-type but not inactive Rcl1 in vivo. Thus, Rrp5 establishes a checkpoint for 60S assembly during 40S maturation to ensure balanced levels of the two subunits.
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Affiliation(s)
- Sohail Khoshnevis
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Xin Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Maria D Dattolo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- HHMI Faculty Scholar
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65
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Trotta E. RNA polymerase II (RNAP II)-associated factors are recruited to tRNA loci, revealing that RNAP II- and RNAP III-mediated transcriptions overlap in yeast. J Biol Chem 2019; 294:12349-12358. [PMID: 31235518 PMCID: PMC6699833 DOI: 10.1074/jbc.ra119.008529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 03/22/2019] [Revised: 06/19/2019] [Indexed: 07/24/2023] Open
Abstract
In yeast (Saccharomyces cerevisiae), the synthesis of tRNAs by RNA polymerase III (RNAP III) down-regulates the transcription of the nearby RNAP II-transcribed genes by a mechanism that is poorly understood. To clarify the basis of this tRNA gene-mediated (TGM) silencing, here, conducting a bioinformatics analysis of available ChIP-chip and ChIP-sequencing genomic data from yeast, we investigated whether the RNAP III transcriptional machinery can recruit protein factors required for RNAP II transcription. An analysis of 46 genome-wide protein-density profiles revealed that 12 factors normally implicated in RNAP II-mediated gene transcription are more enriched at tRNA than at mRNA loci. These 12 factors typically have RNA-binding properties, participate in the termination stage of the RNAP II transcription, and preferentially localize to the tRNA loci by a mechanism that apparently is based on the RNAP III transcription level. The factors included two kinases of RNAP II (Bur1 and Ctk1), a histone demethylase (Jhd2), and a mutated form of a nucleosome-remodeling factor (Spt6) that have never been reported to be recruited to tRNA loci. Moreover, we show that the expression levels of RNAP II-transcribed genes downstream of tRNA loci correlate with the distance from the tRNA gene by a mechanism that depends on their orientation. These results are consistent with the notion that pre-tRNAs recruit RNAP II-associated factors, thereby reducing the availability of these factors for RNAP II transcription and contributing, at least in part, to the TGM-silencing mechanism.
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Affiliation(s)
- Edoardo Trotta
- Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche (CNR), Roma 00133, Italy.
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66
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D'Orazio KN, Wu CCC, Sinha N, Loll-Krippleber R, Brown GW, Green R. The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay. eLife 2019; 8:e49117. [PMID: 31219035 PMCID: PMC6598757 DOI: 10.7554/elife.49117] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 06/19/2019] [Indexed: 01/04/2023] Open
Abstract
Translation of problematic sequences in mRNAs leads to ribosome collisions that trigger a series of quality control events including ribosome rescue, degradation of the stalled nascent polypeptide, and targeting of the mRNA for decay (No Go Decay or NGD). Using a reverse genetic screen in yeast, we identify Cue2 as the conserved endonuclease that is recruited to stalled ribosomes to promote NGD. Ribosome profiling and biochemistry provide strong evidence that Cue2 cleaves mRNA within the A site of the colliding ribosome. We demonstrate that NGD primarily proceeds via Xrn1-mediated exonucleolytic decay and Cue2-mediated endonucleolytic decay normally constitutes a secondary decay pathway. Finally, we show that the Cue2-dependent pathway becomes a major contributor to NGD in cells depleted of factors required for the resolution of stalled ribosome complexes. Together these results provide insights into how multiple decay processes converge to process problematic mRNAs in eukaryotic cells..
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Affiliation(s)
- Karole N D'Orazio
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Colin Chih-Chien Wu
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Niladri Sinha
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Raphael Loll-Krippleber
- Donnelly Centre for Cellular and Biomolecular Research, Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Grant W Brown
- Donnelly Centre for Cellular and Biomolecular Research, Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Rachel Green
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
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67
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Jeseničnik T, Štajner N, Radišek S, Jakše J. RNA interference core components identified and characterised in Verticillium nonalfalfae, a vascular wilt pathogenic plant fungi of hops. Sci Rep 2019; 9:8651. [PMID: 31209232 PMCID: PMC6572790 DOI: 10.1038/s41598-019-44494-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/17/2019] [Indexed: 12/31/2022] Open
Abstract
The conserved RNA interference mechanism (RNAi) in the fungal kingdom has become a focus of intense scientific investigation. The three catalytic core components, Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RdRP), and their associated small interfering RNA molecules (siRNAs) have been identified and characterised in several fungal species. Recent studies have proposed that RNAi is a major contributor to the virulence of fungal pathogens as a result of so-called trans-kingdom RNA silencing. In the present study, we report on the existence of three core RNAi proteins in the pathogenic plant fungus Verticillium nonalfalfae, which is a soilborne plant pathogen that causes severe wilting disease in hops (Humulus lupulus L.). Two DCL proteins, two AGO proteins, and two RdRP proteins were identified, and their conserved RNAi domains were characterised. Our phylogeny results confirm the existing taxonomic relationships in the Ascomycete fungal phylum and show that the fungi of the Hypocreomycetidae subclass of the Sordariomycetes class have high amino acid sequence similarity. The expression analysis revealed a potential role of RNAi in the pathogenicity of the fungi, since all the RNAi genes were highly upregulated in the highly virulent isolate T2 and were also differentially expressed in the V. nonalfalfae-susceptible Celeia and V. nonalfalfae-resistant Wye Target cultivars.
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Affiliation(s)
- Taja Jeseničnik
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Ljubljana, 1000, Slovenia
| | - Nataša Štajner
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Ljubljana, 1000, Slovenia
| | - Sebastjan Radišek
- Slovenian Institute of Hop Research and Brewing, Žalec, 3310, Slovenia
| | - Jernej Jakše
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Ljubljana, 1000, Slovenia.
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68
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Abstract
Transcript levels powerfully influence cell behavior and phenotype and are carefully regulated at several steps. Recently developed single cell approaches such as RNA single molecule fluorescence in-situ hybridization (smFISH) have produced advances in our understanding of how these steps work within the cell. In comparison to single-cell sequencing, smFISH provides more accurate quantification of RNA levels. Additionally, transcript subcellular localization is directly visualized, enabling the analysis of transcription (initiation and elongation), RNA export and degradation. As part of our efforts to investigate how this type of analysis can generate improved models of gene expression, we used smFISH to quantify the kinetic expression of STL1 and CTT1 mRNAs in single Saccharomyces cerevisiae cells upon 0.2 and 0.4 M NaCl osmotic stress. In this Data Descriptor, we outline our procedure along with our data in the form of raw images and processed mRNA counts. We discuss how these data can be used to develop single cell modelling approaches, to study fundamental processes in transcription regulation and develop single cell image processing approaches.
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Affiliation(s)
- Guoliang Li
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
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69
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Polonio Á, Pineda M, Bautista R, Martínez-Cruz J, Pérez-Bueno ML, Barón M, Pérez-García A. RNA-seq analysis and fluorescence imaging of melon powdery mildew disease reveal an orchestrated reprogramming of host physiology. Sci Rep 2019; 9:7978. [PMID: 31138852 PMCID: PMC6538759 DOI: 10.1038/s41598-019-44443-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 11/13/2018] [Accepted: 05/16/2019] [Indexed: 02/04/2023] Open
Abstract
The cucurbit powdery mildew elicited by Podosphaera xanthii is one of the most important limiting factors in cucurbit production. Our knowledge of the genetic and molecular bases underlying the physiological processes governing this disease is very limited. We used RNA-sequencing to identify differentially expressed genes in leaves of Cucumis melo upon inoculation with P. xanthii, using RNA samples obtained at different time points during the early stages of infection and their corresponding uninfected controls. In parallel, melon plants were phenotypically characterized using imaging techniques. We found a high number of differentially expressed genes (DEGs) in infected plants, which allowed for the identification of many plant processes that were dysregulated by the infection. Among those, genes involved in photosynthesis and related processes were found to be upregulated, whereas genes involved in secondary metabolism pathways, such as phenylpropanoid biosynthesis, were downregulated. These changes in gene expression could be functionally validated by chlorophyll fluorescence imaging and blue-green fluorescence imaging analyses, which corroborated the alterations in photosynthetic activity and the suppression of phenolic compound biosynthesis. The powdery mildew disease in melon is a consequence of a complex and multifaceted process that involves the dysregulation of many plant pathways such as primary and secondary metabolism.
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Affiliation(s)
- Álvaro Polonio
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur 31, 29071, Málaga, Spain
| | - Mónica Pineda
- Departamento de Bioquímica y Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008, Granada, Spain
| | - Rocío Bautista
- Plataforma Andaluza de Bioinformática, Edificio de Bioinnovación, Severo Ochoa 34, Parque Tecnológico de Andalucía, 29590, Málaga, Spain
| | - Jesús Martínez-Cruz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur 31, 29071, Málaga, Spain
| | - María Luisa Pérez-Bueno
- Departamento de Bioquímica y Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008, Granada, Spain
| | - Matilde Barón
- Departamento de Bioquímica y Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008, Granada, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain.
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur 31, 29071, Málaga, Spain.
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70
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Sharma AK, Sormanni P, Ahmed N, Ciryam P, Friedrich UA, Kramer G, O’Brien EP. A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data. PLoS Comput Biol 2019; 15:e1007070. [PMID: 31120880 PMCID: PMC6559674 DOI: 10.1371/journal.pcbi.1007070] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 10/15/2018] [Revised: 06/11/2019] [Accepted: 05/06/2019] [Indexed: 01/23/2023] Open
Abstract
Analysis methods based on simulations and optimization have been previously developed to estimate relative translation rates from next-generation sequencing data. Translation involves molecules and chemical reactions, hence bioinformatics methods consistent with the laws of chemistry and physics are more likely to produce accurate results. Here, we derive simple equations based on chemical kinetic principles to measure the translation-initiation rate, transcriptome-wide elongation rate, and individual codon translation rates from ribosome profiling experiments. Our methods reproduce the known rates from ribosome profiles generated from detailed simulations of translation. By applying our methods to data from S. cerevisiae and mouse embryonic stem cells, we find that the extracted rates reproduce expected correlations with various molecular properties, and we also find that mouse embryonic stem cells have a global translation speed of 5.2 AA/s, in agreement with previous reports that used other approaches. Our analysis further reveals that a codon can exhibit up to 26-fold variability in its translation rate depending upon its context within a transcript. This broad distribution means that the average translation rate of a codon is not representative of the rate at which most instances of that codon are translated, and it suggests that translational regulation might be used by cells to a greater degree than previously thought.
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Affiliation(s)
- Ajeet K. Sharma
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Nabeel Ahmed
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Prajwal Ciryam
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ulrike A. Friedrich
- Center for Molecular Biology of the Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of the Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Edward P. O’Brien
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Institute for CyberScience, Pennsylvania State University, University Park, Pennsylvania, United States of America
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71
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Bhattacharya S, Jhunjhunwala A, Halder A, Bhattacharyya D, Mitra A. Going beyond base-pairs: topology-based characterization of base-multiplets in RNA. RNA 2019; 25:573-589. [PMID: 30792229 PMCID: PMC6467009 DOI: 10.1261/rna.068551.118] [Citation(s) in RCA: 7] [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: 08/31/2018] [Accepted: 02/18/2019] [Indexed: 05/17/2023]
Abstract
Identification and characterization of base-multiplets, which are essentially mediated by base-pairing interactions, can provide insights into the diversity in the structure and dynamics of complex functional RNAs, and thus facilitate hypothesis driven biological research. The necessary nomenclature scheme, an extension of the geometric classification scheme for base-pairs by Leontis and Westhof, is however available only for base-triplets. In the absence of information on topology, this scheme is not applicable to quartets and higher order multiplets. Here we propose a topology-based classification scheme which, in conjunction with a graph-based algorithm, can be used for the automated identification and characterization of higher order base-multiplets in RNA structures. Here, the RNA structure is represented as a graph, where nodes represent nucleotides and edges represent base-pairing connectivity. Sets of connected components (of n nodes) within these graphs constitute subgraphs representing multiplets of "n" nucleotides. The different topological variants of the RNA multiplets thus correspond to different nonisomorphic forms of these subgraphs. To annotate RNA base-multiplets unambiguously, we propose a set of topology-based nomenclature rules for quartets, which are extendable to higher multiplets. We also demonstrate the utility of our approach toward the identification and annotation of higher order RNA multiplets, by investigating the occurrence contexts of selected examples in order to gain insights regarding their probable functional roles.
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Affiliation(s)
- Sohini Bhattacharya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF, Bidhannagar, Kolkata 700064, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
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Scull CE, Ingram ZM, Lucius AL, Schneider DA. A Novel Assay for RNA Polymerase I Transcription Elongation Sheds Light on the Evolutionary Divergence of Eukaryotic RNA Polymerases. Biochemistry 2019; 58:2116-2124. [PMID: 30912638 PMCID: PMC6600827 DOI: 10.1021/acs.biochem.8b01256] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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] [Indexed: 11/29/2022]
Abstract
Eukaryotic cells express at least three nuclear RNA polymerases (Pols), each with a unique set of gene targets. Though these enzymes are homologous, there are many differences among the Pols. In this study, a novel assay for Pol I transcription elongation was developed to probe enzymatic differences among the Pols. In Saccharomyces cerevisiae, a mutation in the universally conserved hinge region of the trigger loop, E1103G, induces a gain of function in the Pol II elongation rate, whereas the corresponding mutation in Pol I, E1224G, results in a loss of function. The E1103G Pol II mutation stabilizes the closed conformation of the trigger loop, promoting the catalytic step, the putative rate-limiting step for Pol II. In single-nucleotide and multinucleotide addition assays, we observe a decrease in the rate of nucleotide addition and dinucleotide cleavage activity by E1224G Pol I and an increase in the rate of misincorporation. Collectively, these data suggest that Pol I is at least in part rate-limited by the same step as Pol II, the catalytic step.
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Affiliation(s)
- Catherine E. Scull
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Zachariah M. Ingram
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Aaron L. Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
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Ghosh A, Gangadharan A, Verma M, Das S, Matai L, Dash DP, Dash D, Mapa K, Chakraborty K. Cellular responses to proteostasis perturbations reveal non-optimal feedback in chaperone networks. Cell Mol Life Sci 2019; 76:1605-1621. [PMID: 30683983 PMCID: PMC11105298 DOI: 10.1007/s00018-019-03013-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 09/14/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 11/30/2022]
Abstract
The proteostasis network (PN) comprises a plethora of proteins that are dedicated to aid in protein folding and maintenance; some with overlapping functions. Despite this, there are multiple pathophysiological states associated with depletion of chaperones. This is counter-intuitive, assuming cells have the ability to re-program transcriptional outputs in accordance with its proteostasic limitations. Here, we have used S. cerevisiae to understand how cells respond to different types of proteostasis impairments. We monitored the proteostasis status and transcriptome of single deletions of fourteen different Protein Quality Control (PQC) genes. In most cases, cellular response did not activate proteostasis components or pathways that could either complement the function of the missing PQC gene or restore proteostasis. Over-expression of alternate machineries could restore part of the proteostasis defect in two representative PQC gene deletion strains. We posit that S. cerevisiae inherently lacks the ability to sense and respond optimally to defects in proteostasis caused due to deletion of specific PQC components.
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Affiliation(s)
- Asmita Ghosh
- CSIR-Institute of Genomics and Integrative Biology, Delhi, 110025, India
- Academy of Scientific and Innovative Research, Coordination Office, CSIR-Human Resource Development Centre Campus, Ghaziabad, 201002, India
| | - Abhilash Gangadharan
- CSIR-Institute of Genomics and Integrative Biology, Delhi, 110025, India
- Academy of Scientific and Innovative Research, Coordination Office, CSIR-Human Resource Development Centre Campus, Ghaziabad, 201002, India
| | - Monika Verma
- CSIR-Institute of Genomics and Integrative Biology, Delhi, 110025, India
- Academy of Scientific and Innovative Research, Coordination Office, CSIR-Human Resource Development Centre Campus, Ghaziabad, 201002, India
| | - Sarada Das
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, 201314, India
| | - Latika Matai
- CSIR-Institute of Genomics and Integrative Biology, Delhi, 110025, India
- Academy of Scientific and Innovative Research, Coordination Office, CSIR-Human Resource Development Centre Campus, Ghaziabad, 201002, India
| | - Devi Prasanna Dash
- CSIR-Institute of Genomics and Integrative Biology, Delhi, 110025, India
- Academy of Scientific and Innovative Research, Coordination Office, CSIR-Human Resource Development Centre Campus, Ghaziabad, 201002, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, Delhi, 110025, India
- Academy of Scientific and Innovative Research, Coordination Office, CSIR-Human Resource Development Centre Campus, Ghaziabad, 201002, India
| | - Koyeli Mapa
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, 201314, India
| | - Kausik Chakraborty
- CSIR-Institute of Genomics and Integrative Biology, Delhi, 110025, India.
- Academy of Scientific and Innovative Research, Coordination Office, CSIR-Human Resource Development Centre Campus, Ghaziabad, 201002, India.
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Alves LR, Peres da Silva R, Sanchez DA, Zamith-Miranda D, Rodrigues ML, Goldenberg S, Puccia R, Nosanchuk JD. Extracellular Vesicle-Mediated RNA Release in Histoplasma capsulatum. mSphere 2019; 4:e00176-19. [PMID: 30918062 PMCID: PMC6437275 DOI: 10.1128/msphere.00176-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/03/2023] Open
Abstract
Eukaryotic cells, including fungi, release extracellular vesicles (EVs). These lipid bilayered compartments play essential roles in cellular communication and pathogenesis. EV composition is complex and includes proteins, glycans, pigments, and RNA. RNAs with putative roles in pathogenesis have been described in EVs produced by fungi. Here we describe the RNA content in EVs produced by the G186AR and G217B strains of Histoplasma capsulatum, an important human-pathogenic fungal pathogen. A total of 124 mRNAs were identified in both strains. In this set of RNA classes, 93 transcripts were enriched in EVs from the G217B strain, whereas 31 were enriched in EVs produced by the G186AR strain. This result suggests that there are important strain-specific properties in the mRNA composition of fungal EVs. We also identified short fragments (25 to 40 nucleotides in length) that were strain specific, with a greater number identified in EVs produced by the G217B strain. Remarkably, the most highly enriched processes were stress responses and translation. Half of these fragments aligned to the reverse strand of the transcript, suggesting the occurrence of microRNA (miRNA)-like molecules in fungal EVs. We also compared the transcriptome profiles of H. capsulatum with the RNA composition of EVs, and no correlation was observed. Taking the results together, our study provided information about the RNA molecules present in H. capsulatum EVs and about the differences in composition between the strains. In addition, we found no correlation between the most highly expressed transcripts in the cell and their presence in the EVs, reinforcing the idea that the RNAs were directed to the EVs by a regulated mechanism.IMPORTANCE Extracellular vesicles (EVs) play important roles in cellular communication and pathogenesis. The RNA molecules in EVs have been implicated in a variety of processes. EV-associated RNA classes have recently been described in pathogenic fungi; however, only a few reports of studies describing the RNAs in fungal EVs are available. Improved knowledge of EV-associated RNA will contribute to the understanding of their role during infection. In this study, we described the RNA content in EVs produced by two isolates of Histoplasma capsulatum Our results add this important pathogen to the current short list of fungal species with the ability to use EVs for the extracellular release of RNA.
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Affiliation(s)
- Lysangela R Alves
- Instituto Carlos Chagas, Fiocruz, Curitiba, Cidade Industrial de Curitiba, Brazil
| | - Roberta Peres da Silva
- Departamento de Microbiologia, Imunologia e Parasitologia da Escola Paulista de Medicina, Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - David A Sanchez
- Departments of Medicine (Division of Infectious Diseases) and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Daniel Zamith-Miranda
- Departments of Medicine (Division of Infectious Diseases) and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Marcio L Rodrigues
- Instituto Carlos Chagas, Fiocruz, Curitiba, Cidade Industrial de Curitiba, Brazil
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Samuel Goldenberg
- Instituto Carlos Chagas, Fiocruz, Curitiba, Cidade Industrial de Curitiba, Brazil
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia da Escola Paulista de Medicina, Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Joshua D Nosanchuk
- Departments of Medicine (Division of Infectious Diseases) and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
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Silvestri A, Fiorilli V, Miozzi L, Accotto GP, Turina M, Lanfranco L. In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant. BMC Genomics 2019; 20:169. [PMID: 30832582 PMCID: PMC6399891 DOI: 10.1186/s12864-019-5561-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 10/29/2018] [Accepted: 02/22/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are short non-coding RNA molecules (20-30 nt) that regulate gene expression at transcriptional or post-transcriptional levels in many eukaryotic organisms, through a mechanism known as RNA interference (RNAi). Recent studies have highlighted that they are also involved in cross-kingdom communication: sRNAs can move across the contact surfaces from "donor" to "receiver" organisms and, once in the host cells of the receiver, they can target specific mRNAs, leading to a modulation of host metabolic pathways and defense responses. Very little is known about RNAi mechanism and sRNAs occurrence in Arbuscular Mycorrhizal Fungi (AMF), an important component of the plant root microbiota that provide several benefits to host plants, such as improved mineral uptake and tolerance to biotic and abiotic stress. RESULTS Taking advantage of the available genomic resources for the AMF Rhizophagus irregularis we described its putative RNAi machinery, which is characterized by a single Dicer-like (DCL) gene and an unusual expansion of Argonaute-like (AGO-like) and RNA-dependent RNA polymerase (RdRp) gene families. In silico investigations of previously published transcriptomic data and experimental assays carried out in this work provided evidence of gene expression for most of the identified sequences. Focusing on the symbiosis between R. irregularis and the model plant Medicago truncatula, we characterized the fungal sRNA population, highlighting the occurrence of an active sRNA-generating pathway and the presence of microRNA-like sequences. In silico analyses, supported by host plant degradome data, revealed that several fungal sRNAs have the potential to target M. truncatula transcripts, including some specific mRNA already shown to be modulated in roots upon AMF colonization. CONCLUSIONS The identification of RNAi-related genes, together with the characterization of the sRNAs population, suggest that R. irregularis is equipped with a functional sRNA-generating pathway. Moreover, the in silico analysis predicted 237 plant transcripts as putative targets of specific fungal sRNAs suggesting that cross-kingdom post-transcriptional gene silencing may occur during AMF colonization.
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Affiliation(s)
- Alessandro Silvestri
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
| | - Laura Miozzi
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 73, 10131 Torino, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 73, 10131 Torino, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 73, 10131 Torino, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
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76
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Athanasiadou R, Neymotin B, Brandt N, Wang W, Christiaen L, Gresham D, Tranchina D. A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory. PLoS Comput Biol 2019; 15:e1006794. [PMID: 30856174 PMCID: PMC6428340 DOI: 10.1371/journal.pcbi.1006794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 08/07/2018] [Revised: 03/21/2019] [Accepted: 01/16/2019] [Indexed: 01/09/2023] Open
Abstract
A fundamental assumption, common to the vast majority of high-throughput transcriptome analyses, is that the expression of most genes is unchanged among samples and that total cellular RNA remains constant. As the number of analyzed experimental systems increases however, different independent studies demonstrate that this assumption is often violated. We present a calibration method using RNA spike-ins that allows for the measurement of absolute cellular abundance of RNA molecules. We apply the method to pooled RNA from cell populations of known sizes. For each transcript, we compute a nominal abundance that can be converted to absolute by dividing by a scale factor determined in separate experiments: the yield coefficient of the transcript relative to that of a reference spike-in measured with the same protocol. The method is derived by maximum likelihood theory in the context of a complete statistical model for sequencing counts contributed by cellular RNA and spike-ins. The counts are based on a sample from a fixed number of cells to which a fixed population of spike-in molecules has been added. We illustrate and evaluate the method with applications to two global expression data sets, one from the model eukaryote Saccharomyces cerevisiae, proliferating at different growth rates, and differentiating cardiopharyngeal cell lineages in the chordate Ciona robusta. We tested the method in a technical replicate dilution study, and in a k-fold validation study.
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Affiliation(s)
- Rodoniki Athanasiadou
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Benjamin Neymotin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Nathan Brandt
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Wei Wang
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York, United States of America
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Daniel Tranchina
- Department of Biology, New York University, New York, New York, United States of America
- Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
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77
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Chang Z, Billmyre RB, Lee SC, Heitman J. Broad antifungal resistance mediated by RNAi-dependent epimutation in the basal human fungal pathogen Mucor circinelloides. PLoS Genet 2019; 15:e1007957. [PMID: 30742617 PMCID: PMC6386414 DOI: 10.1371/journal.pgen.1007957] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 10/01/2018] [Revised: 02/22/2019] [Accepted: 01/11/2019] [Indexed: 12/03/2022] Open
Abstract
Mucormycosis—an emergent, deadly fungal infection—is difficult to treat, in part because the causative species demonstrate broad clinical antifungal resistance. However, the mechanisms underlying drug resistance in these infections remain poorly understood. Our previous work demonstrated that one major agent of mucormycosis, Mucor circinelloides, can develop resistance to the antifungal agents FK506 and rapamycin through a novel, transient RNA interference-dependent mechanism known as epimutation. Epimutations silence the drug target gene and are selected by drug exposure; the target gene is re-expressed and sensitivity is restored following passage without drug. This silencing process involves generation of small RNA (sRNA) against the target gene via core RNAi pathway proteins. To further elucidate the role of epimutation in the broad antifungal resistance of Mucor, epimutants were isolated that confer resistance to another antifungal agent, 5-fluoroorotic acid (5-FOA). We identified epimutant strains that exhibit resistance to 5-FOA without mutations in PyrF or PyrG, enzymes which convert 5-FOA into the active toxic form. Using sRNA hybridization as well as sRNA library analysis, we demonstrate that these epimutants harbor sRNA against either pyrF or pyrG, and further show that this sRNA is lost after reversion to drug sensitivity. We conclude that epimutation is a mechanism capable of targeting multiple genes, enabling Mucor to develop resistance to a variety of antifungal agents. Elucidation of the role of RNAi in epimutation affords a fuller understanding of mucormycosis. Furthermore, it improves our understanding of fungal pathogenesis and adaptation to stresses, including the evolution of drug resistance. The emerging infection mucormycosis causes high mortality in part because the major causative fungi, including Mucor circinelloides, are resistant to most clinically available antifungal drugs. We previously discovered an RNA interference-based resistance mechanism, epimutation, through which M. circinelloides develops transient resistance to the antifungal agent FK506 by altering endogenous RNA expression. We further characterize this novel mechanism by isolating epimutations in two genes that confer resistance to another antifungal agent, 5-fluoroorotic acid. Thus, we demonstrate epimutation can induce resistance to multiple antifungals by targeting a variety of genes. These results reveal epimutation plays a broad role enabling rapid and reversible fungal responses to environmental stresses, including drug exposure, and controlling antifungal drug resistance and RNA expression. As resistance to antifungals emerges, a deeper understanding of the causative mechanisms is crucial for improving treatment.
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Affiliation(s)
- Zanetta Chang
- Department of Molecular Genetics and Microbiology, Duke University, Duke University Medical Center, Durham, North Carolina, United States of America
| | - R. Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University, Duke University Medical Center, Durham, North Carolina, United States of America
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University, Duke University Medical Center, Durham, North Carolina, United States of America
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, University of Texas, San Antonio, San Antonio, Texas, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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Wada M, Ito K. Misdecoding of rare CGA codon by translation termination factors, eRF1/eRF3, suggests novel class of ribosome rescue pathway in S. cerevisiae. FEBS J 2019; 286:788-802. [PMID: 30471181 PMCID: PMC7379694 DOI: 10.1111/febs.14709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 05/07/2018] [Revised: 10/24/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022]
Abstract
The CGA arginine codon is a rare codon in Saccharomyces cerevisiae. Thus, full-length mature protein synthesis from reporter genes with internal CGA codon repeats are markedly reduced, and the reporters, instead, produce short-sized polypeptides via an unknown mechanism. Considering the product size and similar properties between CGA sense and UGA stop codons, we hypothesized that eukaryote polypeptide-chain release factor complex eRF1/eRF3 catalyses polypeptide release at CGA repeats. Herein, we performed a series of analyses and report that the CGA codon can be, to a certain extent, decoded as a stop codon in yeast. This also raises an intriguing possibility that translation termination factors eRF1/eRF3 rescue ribosomes stalled at CGA codons, releasing premature polypeptides, and competing with canonical tRNAICG to the CGA codon. Our results suggest an alternative ribosomal rescue pathway in eukaryotes. The present results suggest that misdecoding of low efficient codons may play a novel role in global translation regulation in S. cerevisiae.
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Affiliation(s)
- Miki Wada
- Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoKashiwa‐cityJapan
- Technical officeThe Institute of Medical ScienceThe University of TokyoMinato‐kuJapan
| | - Koichi Ito
- Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoKashiwa‐cityJapan
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Linnemann J, Pöll G, Jakob S, Ferreira-Cerca S, Griesenbeck J, Tschochner H, Milkereit P. Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors. PLoS One 2019; 14:e0203415. [PMID: 30653518 PMCID: PMC6336269 DOI: 10.1371/journal.pone.0203415] [Citation(s) in RCA: 7] [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: 08/17/2018] [Accepted: 01/01/2019] [Indexed: 11/25/2022] Open
Abstract
Many of the small ribosomal subunit proteins are required for the stabilisation of late small ribosomal subunit (SSU) precursors and for final SSU rRNA processing in S. cerevisiae. Among them are ribosomal proteins (r-proteins) which form a protein cluster around rpS0 (uS2) at the "neck" of the SSU (S0-cluster) and others forming a nearby protein cluster around rpS3 (uS3) at the SSU "beak". Here we applied semi-quantitative proteomics together with complementary biochemical approaches to study how incomplete assembly of these two r-protein clusters affects binding and release of SSU maturation factors and assembly of other r-proteins in late SSU precursors in S. cerevisiae. For each of the two clusters specific impairment of the local r-protein assembly state was observed in Rio2 associated SSU precursors. Besides, cluster-specific effects on the association of biogenesis factors were detected. These suggested a role of S0-cluster formation for the efficient release of the two nuclear export factors Rrp12 and Slx9 from SSU precursors and for the correct incorporation of the late acting biogenesis factor Rio2. Based on our and on previous results we propose the existence of at least two different r-protein assembly checkpoints during late SSU maturation in S. cerevisiae. We discuss in the light of recent SSU precursor structure models how r-protein assembly states might be sensed by biogenesis factors at the S0-cluster checkpoint.
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Affiliation(s)
- Jan Linnemann
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Gisela Pöll
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Steffen Jakob
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | | | - Joachim Griesenbeck
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
| | - Herbert Tschochner
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
| | - Philipp Milkereit
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
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80
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Shinde S, Zerbs S, Collart FR, Cumming JR, Noirot P, Larsen PE. Pseudomonas fluorescens increases mycorrhization and modulates expression of antifungal defense response genes in roots of aspen seedlings. BMC Plant Biol 2019; 19:4. [PMID: 30606121 PMCID: PMC6318872 DOI: 10.1186/s12870-018-1610-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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] [Received: 06/19/2018] [Accepted: 12/20/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Plants, fungi, and bacteria form complex, mutually-beneficial communities within the soil environment. In return for photosynthetically derived sugars in the form of exudates from plant roots, the microbial symbionts in these rhizosphere communities provide their host plants access to otherwise inaccessible nutrients in soils and help defend the plant against biotic and abiotic stresses. One role that bacteria may play in these communities is that of Mycorrhizal Helper Bacteria (MHB). MHB are bacteria that facilitate the interactions between plant roots and symbiotic mycorrhizal fungi and, while the effects of MHB on the formation of plant-fungal symbiosis and on plant health have been well documented, the specific molecular mechanisms by which MHB drive gene regulation in plant roots leading to these benefits remain largely uncharacterized. RESULTS Here, we investigate the effects of the bacterium Pseudomonas fluorescens SBW25 (SBW25) on aspen root transcriptome using a tripartite laboratory community comprised of Populus tremuloides (aspen) seedlings and the ectomycorrhizal fungus Laccaria bicolor (Laccaria). We show that SBW25 has MHB activity and promotes mycorrhization of aspen roots by Laccaria. Using transcriptomic analysis of aspen roots under multiple community compositions, we identify clusters of co-regulated genes associated with mycorrhization, the presence of SBW25, and MHB-associated functions, and we generate a combinatorial logic network that links causal relationships in observed patterns of gene expression in aspen seedling roots in a single Boolean circuit diagram. The predicted regulatory circuit is used to infer regulatory mechanisms associated with MHB activity. CONCLUSIONS In our laboratory conditions, SBW25 increases the ability of Laccaria to form ectomycorrhizal interactions with aspen seedling roots through the suppression of aspen root antifungal defense responses. Analysis of transcriptomic data identifies that potential molecular mechanisms in aspen roots that respond to MHB activity are proteins with homology to pollen recognition sensors. Pollen recognition sensors integrate multiple environmental signals to down-regulate pollenization-associated gene clusters, making proteins with homology to this system an excellent fit for a predicted mechanism that integrates information from the rhizosphere to down-regulate antifungal defense response genes in the root. These results provide a deeper understanding of aspen gene regulation in response to MHB and suggest additional, hypothesis-driven biological experiments to validate putative molecular mechanisms of MHB activity in the aspen-Laccaria ectomycorrhizal symbiosis.
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Affiliation(s)
- Shalaka Shinde
- Argonne National Laboratory, Biosciences Division, 9700 S. Cass Ave., Argonne, IL 60439 USA
- Present address: Oil-Dri Innovation Center, 777 Forest Edge Rd., Vernon Hills, IL 60061 USA
| | - Sarah Zerbs
- Argonne National Laboratory, Biosciences Division, 9700 S. Cass Ave., Argonne, IL 60439 USA
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, 9700 S. Cass Ave., Argonne, IL 60439 USA
| | - Jonathan R. Cumming
- Department of Biology, West Virginia University, 53 Campus Dr, Morgantown, WV 26506 USA
| | - Philippe Noirot
- Argonne National Laboratory, Biosciences Division, 9700 S. Cass Ave., Argonne, IL 60439 USA
| | - Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, 9700 S. Cass Ave., Argonne, IL 60439 USA
- Department of Bioengineering, University of Illinois at Chicago, 851 South Morgan St., Chicago, IL 60612 USA
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81
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Kovalchuk A, Zeng Z, Ghimire RP, Kivimäenpää M, Raffaello T, Liu M, Mukrimin M, Kasanen R, Sun H, Julkunen-Tiitto R, Holopainen JK, Asiegbu FO. Dual RNA-seq analysis provides new insights into interactions between Norway spruce and necrotrophic pathogen Heterobasidion annosum s.l. BMC Plant Biol 2019; 19:2. [PMID: 30606115 PMCID: PMC6318961 DOI: 10.1186/s12870-018-1602-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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] [Received: 07/12/2018] [Accepted: 12/12/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Root and butt rot of conifer trees caused by fungi belonging to the Heterobasidion annosum species complex is one of the most economically important fungal diseases in commercial conifer plantations throughout the Northern hemisphere. We investigated the interactions between Heterobasidion fungi and their host by conducting dual RNA-seq and chemical analysis on Norway spruce trees naturally infected by Heterobasidion spp. We analyzed host and pathogen transcriptome and phenolic and terpenoid contents of the spruce trees. RESULTS Presented results emphasize the role of the phenylpropanoid and flavonoid pathways in the chemical defense of Norway spruce trees. Accumulation of lignans was observed in trees displaying symptoms of wood decay. A number of candidate genes with a predicted role in the higher level regulation of spruce defense responses were identified. Our data indicate a possible role of abscisic acid (ABA) signaling in the spruce defense against Heterobasidion infection. Fungal transcripts corresponding to genes encoding carbohydrate- and lignin-degrading enzymes, secondary metabolism genes and effector-like genes were expressed during the host colonization. CONCLUSIONS Our results provide additional insight into defense strategies employed by Norway spruce trees against Heterobasidion infection. The potential applications of the identified candidate genes as markers for higher resistance against root and butt rot deserve further evaluation.
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Affiliation(s)
- Andriy Kovalchuk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, FIN-00014 Helsinki, Finland
| | - Zhen Zeng
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, FIN-00014 Helsinki, Finland
| | - Rajendra P. Ghimire
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland (UEF), P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Minna Kivimäenpää
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland (UEF), P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Tommaso Raffaello
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, FIN-00014 Helsinki, Finland
| | - Mengxia Liu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, FIN-00014 Helsinki, Finland
| | - Mukrimin Mukrimin
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, FIN-00014 Helsinki, Finland
- Department of Forestry, Universitas Hasanuddin, Jln. Perintis Kemerdekaan Km. 10, Makassar, 90245 Indonesia
| | - Risto Kasanen
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, FIN-00014 Helsinki, Finland
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Riitta Julkunen-Tiitto
- Department of Environmental and Biological Sciences, Joensuu Campus, University of Eastern Finland (UEF), P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Jarmo K. Holopainen
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland (UEF), P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Fred O. Asiegbu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, FIN-00014 Helsinki, Finland
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82
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Hu J, Xia Y. Increased virulence in the locust-specific fungal pathogen Metarhizium acridum expressing dsRNAs targeting the host F 1 F 0 -ATPase subunit genes. Pest Manag Sci 2019; 75:180-186. [PMID: 29797423 DOI: 10.1002/ps.5085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 12/20/2017] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Metarhizium acridum is a host-specific fungal pathogen with great potential for locust control. However, the slow killing action of M. acridum has impeded its widespread application. To enhance fungal virulence, we constructed transgenic M. acridum strains that express double-stranded (ds)RNAs targeting the genes of the F1 F0 -ATP synthase α and β subunits in Locusta migratoria. RESULTS The two host genes were transcriptionally suppressed in L. migratoria nymphs (instar V) infected by RNA interference (RNAi) strains targeting one or two subunit genes of the host ATP synthase, followed by reduced ATPase activity and ATP synthesis. Consequently, the RNAi strain targeting both subunit genes displayed high virulence that was 3.7-fold that in the wild-type strain. CONCLUSION Our results demonstrate that dsRNA expression in M. acridum can cause host RNA silencing during infection and greatly enhances the fungal virulence through interference with critical host genes, highlighting a new strategy for augmentation of fungal virulence against insect pests. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Jun Hu
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, China
| | - Yuxian Xia
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, China
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83
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Gu KX, Song XS, Xiao XM, Duan XX, Wang JX, Duan YB, Hou YP, Zhou MG. A β 2-tubulin dsRNA derived from Fusarium asiaticum confers plant resistance to multiple phytopathogens and reduces fungicide resistance. Pestic Biochem Physiol 2019; 153:36-46. [PMID: 30744895 DOI: 10.1016/j.pestbp.2018.10.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [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: 07/12/2018] [Revised: 09/28/2018] [Accepted: 10/29/2018] [Indexed: 05/20/2023]
Abstract
Crops are attacked by a large number of pathogens which are responsible for an approximately 30% loss in global crop production at pre- and post-harvest levels. In light of the continuing emergence of fungicide resistance, the needs for new agricultural drugs turn out to be much more critical. Here we demonstrated a Faβ2Tub-3 dsRNA derived from Fusarium asiaticum had broad-spectrum antifungal activity against Fusarium spp., Botrytis cinerea, Magnaporthe oryzae and Colletotrichum truncatum, with an additional function of reducing the dosage of carbendazim (MBC) fungicide. RNAi molecules derived from different regions of β2-tubulin gene had different effects on mycelial growth, asexual reproduction and virulence. Faβ2Tub-3 (one of β2-tubulin segments) exhibited a strong silencing efficacy both on β1-tubulin and β2-tubulin genes in F. asiaticum. Faβ2Tub-3 sequence was found to be highly conserved among Fusarium spp., Botrytis cinerea, Magnaporthe oryzae and Colletotrichum truncatum. The Faβ2Tub-3 dsRNA demonstrated a broad-spectrum antifungal activity against these fungi in vitro and on living plant. More importantly, Faβ2Tub-3 dsRNA increased the fungal sensitivity to MBC, while MBC increased the duration of Faβ2Tub-3 dsRNA. Our findings suggest a new anti-fungal agent (Faβ2Tub-3 dsRNA) for plant protection against diverse pathogens and for fungicide reduction.
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Affiliation(s)
- Kai-Xin Gu
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Xiu-Shi Song
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Xue-Mei Xiao
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Xiao-Xin Duan
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Jian-Xin Wang
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Ya-Bing Duan
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Yi-Ping Hou
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China
| | - Ming-Guo Zhou
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Jiangsu Province, Nanjing 210095, China.
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84
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Wu ACK, Patel H, Chia M, Moretto F, Frith D, Snijders AP, van Werven FJ. Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor. Mol Cell 2018; 72:942-954.e7. [PMID: 30576656 PMCID: PMC6310685 DOI: 10.1016/j.molcel.2018.10.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/06/2018] [Accepted: 10/10/2018] [Indexed: 12/17/2022]
Abstract
Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here, we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1-regulated gene promoters. Specifically, Rap1 prevents transcription initiation at cryptic promoters near its binding sites, which is uncoupled from transcription regulation in the protein-coding direction. We further provide evidence that Rap1 acts independently of previously described chromatin-based mechanisms to repress cryptic or divergent transcription. Finally, we show that divergent transcription in the absence of Rap1 is elicited by the RSC chromatin remodeler. We propose that a sequence-specific transcription factor limits access of basal transcription machinery to regulatory elements and adjacent sequences that act as divergent cryptic promoters, thereby providing directionality toward productive transcription.
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Affiliation(s)
- Andrew C K Wu
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Minghao Chia
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Frith
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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85
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Peña-Moreno IC, Castro Parente D, da Silva JM, Andrade Mendonça A, Rojas LAV, de Morais Junior MA, de Barros Pita W. Nitrate boosts anaerobic ethanol production in an acetate-dependent manner in the yeast Dekkera bruxellensis. J Ind Microbiol Biotechnol 2018; 46:209-220. [PMID: 30539327 DOI: 10.1007/s10295-018-2118-1] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/05/2018] [Indexed: 12/29/2022]
Abstract
In the past few years, the yeast Dekkera bruxellensis has gained much of attention among the so-called non-conventional yeasts for its potential in the biotechnological scenario, especially in fermentative processes. This yeast has been regarded as an important competitor to Saccharomyces cerevisiae in bioethanol production plants in Brazil and several studies have reported its capacity to produce ethanol. However, our current knowledge concerning D. bruxellensis is restricted to its aerobic metabolism, most likely because wine and beer strains cannot grow in full anaerobiosis. Hence, the present work aimed to fulfil a gap regarding the lack of information on the physiology of Dekkera bruxellensis growing in the complete absence of oxygen and the relationship with assimilation of nitrate as nitrogen source. The ethanol strain GDB 248 was fully capable of growing anaerobically and produces ethanol at the same level of S. cerevisiae. The presence of nitrate in the medium increased this capacity. Moreover, nitrate is consumed faster than ammonium and this increased rate coincided with a higher speed of glucose consumption. The profile of gene expression helped us to figure out that even in anaerobiosis, the presence of nitrate drives the yeast cells to an oxidative metabolism that ultimately incremented both biomass and ethanol production. These results finally provide the clues to explain most of the success of this yeast in industrial processes of ethanol production.
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Affiliation(s)
| | - Denise Castro Parente
- Department of Genetics, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil
| | | | | | | | | | - Will de Barros Pita
- Department of Antibiotics, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil.
- Departamento de Antibióticos, Universidade Federal de Pernambuco, Avenida Professor Artur de Sá, Cidade Universitária, 50740520, Recife, PE, Brazil.
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86
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Lao JP, Ulrich KM, Johnson JR, Newton BW, Vashisht AA, Wohlschlegel JA, Krogan NJ, Toczyski DP. The Yeast DNA Damage Checkpoint Kinase Rad53 Targets the Exoribonuclease, Xrn1. G3 (Bethesda) 2018; 8:3931-3944. [PMID: 30377154 PMCID: PMC6288840 DOI: 10.1534/g3.118.200767] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 06/22/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022]
Abstract
The highly conserved DNA damage response (DDR) pathway monitors the genomic integrity of the cell and protects against genotoxic stresses. The apical kinases, Mec1 and Tel1 (ATR and ATM in human, respectively), initiate the DNA damage signaling cascade through the effector kinases, Rad53 and Chk1, to regulate a variety of cellular processes including cell cycle progression, DNA damage repair, chromatin remodeling, and transcription. The DDR also regulates other cellular pathways, but direct substrates and mechanisms are still lacking. Using a mass spectrometry-based phosphoproteomic screen in Saccharomyces cerevisiae, we identified novel targets of Rad53, many of which are proteins that are involved in RNA metabolism. Of the 33 novel substrates identified, we verified that 12 are directly phosphorylated by Rad53 in vitro: Xrn1, Gcd11, Rps7b, Ded1, Cho2, Pus1, Hst1, Srv2, Set3, Snu23, Alb1, and Scp160. We further characterized Xrn1, a highly conserved 5' exoribonuclease that functions in RNA degradation and the most enriched in our phosphoproteomics screen. Phosphorylation of Xrn1 by Rad53 does not appear to affect Xrn1's intrinsic nuclease activity in vitro, but may affect its activity or specificity in vivo.
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Affiliation(s)
- Jessica P Lao
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Katie M Ulrich
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Ajay A Vashisht
- Department of Biological Chemistry, School of Medicine, University of California, Los Angeles, CA 90095
| | - James A Wohlschlegel
- Department of Biological Chemistry, School of Medicine, University of California, Los Angeles, CA 90095
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - David P Toczyski
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
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87
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Moqtaderi Z, Geisberg JV, Struhl K. Extensive Structural Differences of Closely Related 3' mRNA Isoforms: Links to Pab1 Binding and mRNA Stability. Mol Cell 2018; 72:849-861.e6. [PMID: 30318446 PMCID: PMC6289678 DOI: 10.1016/j.molcel.2018.08.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/05/2018] [Accepted: 08/29/2018] [Indexed: 12/24/2022]
Abstract
Alternative polyadenylation generates numerous 3' mRNA isoforms that can vary in biological properties, such as stability and localization. We developed methods to obtain transcriptome-scale structural information and protein binding on individual 3' mRNA isoforms in vivo. Strikingly, near-identical mRNA isoforms can possess dramatically different structures throughout the 3' UTR. Analyses of identical mRNAs in different species or refolded in vitro indicate that structural differences in vivo are often due to trans-acting factors. The level of Pab1 binding to poly(A)-containing isoforms is surprisingly variable, and differences in Pab1 binding correlate with the extent of structural variation for closely spaced isoforms. A pattern encompassing single-strandedness near the 3' terminus, double-strandedness of the poly(A) tail, and low Pab1 binding is associated with mRNA stability. Thus, individual 3' mRNA isoforms can be remarkably different physical entities in vivo. Sequences responsible for isoform-specific structures, differential Pab1 binding, and mRNA stability are evolutionarily conserved, indicating biological function.
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Affiliation(s)
- Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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88
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Zeidan Q, He F, Zhang F, Zhang H, Jacobson A, Hinnebusch AG. Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo. PLoS Genet 2018; 14:e1007806. [PMID: 30532217 PMCID: PMC6307823 DOI: 10.1371/journal.pgen.1007806] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 06/01/2018] [Revised: 12/27/2018] [Accepted: 11/02/2018] [Indexed: 12/21/2022] Open
Abstract
Scd6 protein family members are evolutionarily conserved components of translationally silent mRNA granules. Yeast Scd6 interacts with Dcp2 and Dhh1, respectively a subunit and a regulator of the mRNA decapping enzyme, and also associates with translation initiation factor eIF4G to inhibit translation in cell extracts. However, the role of Scd6 in mRNA turnover and translational repression in vivo is unclear. We demonstrate that tethering Scd6 to a GFP reporter mRNA reduces mRNA abundance via Dcp2 and suppresses reporter mRNA translation via Dhh1. Thus, in a dcp2Δ mutant, tethered Scd6 reduces GFP protein expression with little effect on mRNA abundance, whereas tethered Scd6 has no impact on GFP protein or mRNA expression in a dcp2Δ dhh1Δ double mutant. The conserved LSm domain of Scd6 is required for translational repression and mRNA turnover by tethered Scd6. Both functions are enhanced in a ccr4Δ mutant, suggesting that the deadenylase function of Ccr4-Not complex interferes with a more efficient repression pathway enlisted by Scd6. Ribosome profiling and RNA-Seq analysis of scd6Δ and dhh1Δ mutants suggests that Scd6 cooperates with Dhh1 in translational repression and turnover of particular native mRNAs, with both processes dependent on Dcp2. Our results suggest that Scd6 can (i) recruit Dhh1 to confer translational repression and (ii) activate mRNA decapping by Dcp2 with attendant degradation of specific mRNAs in vivo, in a manner dependent on the Scd6 LSm domain and modulated by Ccr4.
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Affiliation(s)
- Quira Zeidan
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Fan Zhang
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Hongen Zhang
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Alan G. Hinnebusch
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
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89
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Cheng Z, Mugler CF, Keskin A, Hodapp S, Chan LYL, Weis K, Mertins P, Regev A, Jovanovic M, Brar GA. Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate. Mol Cell 2018; 73:36-47.e10. [PMID: 30503772 DOI: 10.1016/j.molcel.2018.10.032] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [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: 05/10/2018] [Revised: 09/04/2018] [Accepted: 10/18/2018] [Indexed: 01/13/2023]
Abstract
Levels of the ribosome, the conserved molecular machine that mediates translation, are tightly linked to cellular growth rate. In humans, ribosomopathies are diseases associated with cell-type-specific pathologies and reduced ribosomal protein (RP) levels. Because gene expression defects resulting from ribosome deficiency have not yet been experimentally defined, we systematically probed mRNA, translation, and protein signatures that were either unlinked from or linked to cellular growth rate in RP-deficient yeast cells. Ribosome deficiency was associated with altered translation of gene subclasses, and profound general secondary effects of RP loss on the spectrum of cellular mRNAs were seen. Among these effects, growth-defective 60S mutants increased synthesis of proteins involved in proteasome-mediated degradation, whereas 40S mutants accumulated mature 60S subunits and increased translation of ribosome biogenesis genes. These distinct signatures of protein synthesis suggest intriguing and currently mysterious differences in the cellular consequences of deficiency for small and large ribosomal subunits.
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MESH Headings
- Cell Proliferation
- Gene Expression Regulation, Fungal
- Mutation
- Protein Processing, Post-Translational
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Time Factors
- Transcriptome
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Affiliation(s)
- Ze Cheng
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher Frederick Mugler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, Institute of Biochemistry, ETH, 8093 Zurich, Switzerland
| | - Abdurrahman Keskin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Stefanie Hodapp
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Leon Yen-Lee Chan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, Institute of Biochemistry, ETH, 8093 Zurich, Switzerland
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, ETH, 8093 Zurich, Switzerland
| | - Philipp Mertins
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Aviv Regev
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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90
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Simms CL, Kim KQ, Yan LL, Qiu J, Zaher HS. Interactions between the mRNA and Rps3/uS3 at the entry tunnel of the ribosomal small subunit are important for no-go decay. PLoS Genet 2018; 14:e1007818. [PMID: 30475795 PMCID: PMC6283612 DOI: 10.1371/journal.pgen.1007818] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 07/26/2018] [Revised: 12/06/2018] [Accepted: 11/07/2018] [Indexed: 11/25/2022] Open
Abstract
No-go Decay (NGD) is a process that has evolved to deal with stalled ribosomes resulting from structural blocks or aberrant mRNAs. The process is distinguished by an endonucleolytic cleavage prior to degradation of the transcript. While many of the details of the pathway have been described, the identity of the endonuclease remains unknown. Here we identify residues of the small subunit ribosomal protein Rps3 that are important for NGD by affecting the cleavage reaction. Mutation of residues within the ribosomal entry tunnel that contact the incoming mRNA leads to significantly reduced accumulation of cleavage products, independent of the type of stall sequence, and renders cells sensitive to damaging agents thought to trigger NGD. These phenotypes are distinct from those seen in combination with other NGD factors, suggesting a separate role for Rps3 in NGD. Conversely, ribosomal proteins ubiquitination is not affected by rps3 mutations, indicating that upstream ribosome quality control (RQC) events are not dependent on these residues. Together, these results suggest that Rps3 is important for quality control on the ribosome and strongly supports the notion that the ribosome itself plays a central role in the endonucleolytic cleavage reaction during NGD. In all organisms, optimum cellular fitness depends on the ability of cells to recognize and degrade aberrant molecules. Messenger RNA is subject to alterations and, as a result, often presents roadblocks for the translating ribosomes. It is not surprising, then, that organisms evolved pathways to resolve these valuable stuck ribosomes. In eukaryotes, this process is called no-go decay (NGD) because it is coupled with decay of mRNAs that are associated with ribosomes that do not ‘go’. This decay process initiates with cleavage of the mRNA near the stall site, but some important details about this reaction are lacking. Here, we show that the ribosome itself is very central to the cleavage reaction. In particular, we identified a pair of residues of a ribosomal protein to be important for cleavage efficiency. These observations are consistent with prior structural studies showing that the residues make intimate contacts with the incoming mRNA in the entry tunnel. Altogether our data provide important clues about this quality-control pathway and suggest that the endonuclease not only recognizes stalled ribosomes but may have coevolved with the translation machinery to take advantage of certain residues of the ribosome to fulfill its function.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Amino Acid Substitution
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- GTP-Binding Proteins/genetics
- GTP-Binding Proteins/metabolism
- Genes, Fungal
- Models, Molecular
- Mutagenesis, Site-Directed
- Mutation
- Peptide Chain Elongation, Translational
- Protein Conformation
- RNA Stability
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Small/genetics
- Ribosome Subunits, Small/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Homology, Amino Acid
- Ubiquitination
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Affiliation(s)
- Carrie L. Simms
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Kyusik Q. Kim
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Liewei L. Yan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jessica Qiu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
- * E-mail:
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91
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Affiliation(s)
- Ines Teichert
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universitaet Bochum, Germany
- * E-mail:
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92
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Kusch S, Frantzeskakis L, Thieron H, Panstruga R. Small RNAs from cereal powdery mildew pathogens may target host plant genes. Fungal Biol 2018; 122:1050-1063. [PMID: 30342621 DOI: 10.1016/j.funbio.2018.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 05/31/2018] [Revised: 08/25/2018] [Accepted: 08/28/2018] [Indexed: 12/24/2022]
Abstract
Small RNAs (sRNAs) play a key role in eukaryotic gene regulation, for example by gene silencing via RNA interference (RNAi). The biogenesis of sRNAs depends on proteins that are generally conserved in all eukaryotic lineages, yet some species that lack part or all the components of the mechanism exist. Here we explored the presence of the RNAi machinery and its expression as well as the occurrence of sRNA candidates and their putative endogenous as well as host targets in phytopathogenic powdery mildew fungi. We focused on the species Blumeria graminis, which occurs in various specialized forms (formae speciales) that each have a strictly limited host range. B. graminis f. sp. hordei and B. graminis f. sp. tritici, colonizing barley and wheat, respectively, have genomes that are characterized by extensive gene loss. Nonetheless, we find that the RNAi machinery appears to be largely complete and expressed during infection. sRNA sequencing data enabled the identification of putative sRNAs in both pathogens. While a considerable part of the sRNA candidates have predicted target sites in endogenous genes and transposable elements, a small proportion appears to have targets in planta, suggesting potential cross-kingdom RNA transfer between powdery mildew fungi and their respective plant hosts.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Lamprinos Frantzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Hannah Thieron
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
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93
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Atkinson SR, Marguerat S, Bitton DA, Rodríguez-López M, Rallis C, Lemay JF, Cotobal C, Malecki M, Smialowski P, Mata J, Korber P, Bachand F, Bähler J. Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast. RNA 2018; 24:1195-1213. [PMID: 29914874 PMCID: PMC6097657 DOI: 10.1261/rna.065524.118] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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] [Received: 01/02/2018] [Accepted: 06/14/2018] [Indexed: 05/31/2023]
Abstract
Long noncoding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to pervasive noncoding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play important roles in gene regulation and diseases. Here we systematically uncover and analyze lncRNAs in Schizosaccharomyces pombe. Based on RNA-seq data from twelve RNA-processing mutants and nine physiological conditions, we identify 5775 novel lncRNAs, nearly 4× the previously annotated lncRNAs. The expression of most lncRNAs becomes strongly induced under the genetic and physiological perturbations, most notably during late meiosis. Most lncRNAs are cryptic and suppressed by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease, and RNAi. Double-mutant analyses reveal substantial coordination and redundancy among these pathways. We classify lncRNAs by their dominant pathway into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease, along with RNAi, dampens the expression of thousands of lncRNAs and mRNAs that become induced during meiosis. Antisense lncRNA expression mostly negatively correlates with sense mRNA expression in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. Our results highlight both similarities and differences to lncRNA regulation in budding yeast. This broad survey of the lncRNA repertoire and characteristics in S. pombe, and the interwoven regulatory pathways that target lncRNAs, provides a rich framework for their further functional analyses.
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Affiliation(s)
- Sophie R Atkinson
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Samuel Marguerat
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Danny A Bitton
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Maria Rodríguez-López
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Charalampos Rallis
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Jean-François Lemay
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Cristina Cotobal
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Michal Malecki
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Pawel Smialowski
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Philipp Korber
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - François Bachand
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Jürg Bähler
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
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94
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Grahl N, Dolben EL, Filkins LM, Crocker AW, Willger SD, Morrison HG, Sogin ML, Ashare A, Gifford AH, Jacobs NJ, Schwartzman JD, Hogan DA. Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA. mSphere 2018; 3:e00292-18. [PMID: 30089648 PMCID: PMC6083091 DOI: 10.1128/msphere.00292-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/10/2018] [Indexed: 12/26/2022] Open
Abstract
Here, we report an approach to detect diverse bacterial and fungal taxa in complex samples by direct analysis of community RNA in one step using NanoString probe sets. We designed rRNA-targeting probe sets to detect 42 bacterial and fungal genera or species common in cystic fibrosis (CF) sputum and demonstrated the taxon specificity of these probes, as well as a linear response over more than 3 logs of input RNA. Culture-based analyses correlated qualitatively with relative abundance data on bacterial and fungal taxa obtained by NanoString, and the analysis of serial samples demonstrated the use of this method to simultaneously detect bacteria and fungi and to detect microbes at low abundance without an amplification step. Compared at the genus level, the relative abundances of bacterial taxa detected by analysis of RNA correlated with the relative abundances of the same taxa as measured by sequencing of the V4V5 region of the 16S rRNA gene amplified from community DNA from the same sample. We propose that this method may complement other methods designed to understand dynamic microbial communities, may provide information on bacteria and fungi in the same sample with a single assay, and with further development, may provide quick and easily interpreted diagnostic information on diverse bacteria and fungi at the genus or species level.IMPORTANCE Here we demonstrate the use of an RNA-based analysis of specific taxa of interest, including bacteria and fungi, within microbial communities. This multiplex method may be useful as a means to identify samples with specific combinations of taxa and to gain information on how specific populations vary over time and space or in response to perturbation. A rapid means to measure bacterial and fungal populations may aid in the study of host response to changes in microbial communities.
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Affiliation(s)
- Nora Grahl
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Emily L Dolben
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Laura M Filkins
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Alex W Crocker
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Sven D Willger
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Mitchell L Sogin
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Alix Ashare
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Alex H Gifford
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Nicholas J Jacobs
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Joseph D Schwartzman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Deborah A Hogan
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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95
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Roy KR, Smith JD, Vonesch SC, Lin G, Tu CS, Lederer AR, Chu A, Suresh S, Nguyen M, Horecka J, Tripathi A, Burnett WT, Morgan MA, Schulz J, Orsley KM, Wei W, Aiyar RS, Davis RW, Bankaitis VA, Haber JE, Salit ML, St Onge RP, Steinmetz LM. Multiplexed precision genome editing with trackable genomic barcodes in yeast. Nat Biotechnol 2018; 36:512-520. [PMID: 29734294 PMCID: PMC5990450 DOI: 10.1038/nbt.4137] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [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: 11/19/2017] [Accepted: 03/12/2018] [Indexed: 12/26/2022]
Abstract
Our understanding of how genotype controls phenotype is limited by the scale at which we can precisely alter the genome and assess the phenotypic consequences of each perturbation. Here we describe a CRISPR-Cas9-based method for multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) in Saccharomyces cerevisiae. MAGESTIC uses array-synthesized guide-donor oligos for plasmid-based high-throughput editing and features genomic barcode integration to prevent plasmid barcode loss and to enable robust phenotyping. We demonstrate that editing efficiency can be increased more than fivefold by recruiting donor DNA to the site of breaks using the LexA-Fkh1p fusion protein. We performed saturation editing of the essential gene SEC14 and identified amino acids critical for chemical inhibition of lipid signaling. We also constructed thousands of natural genetic variants, characterized guide mismatch tolerance at the genome scale, and ascertained that cryptic Pol III termination elements substantially reduce guide efficacy. MAGESTIC will be broadly useful to uncover the genetic basis of phenotypes in yeast.
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Affiliation(s)
- Kevin R. Roy
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Genome-Scale Measurements Group, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
- Joint Initiative for Metrology in Biology, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Justin D. Smith
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Sibylle C. Vonesch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Gen Lin
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Chelsea Szu Tu
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Alex R. Lederer
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Angela Chu
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Sundari Suresh
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Michelle Nguyen
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Joe Horecka
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Ashutosh Tripathi
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, USA
| | - Wallace T. Burnett
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Maddison A. Morgan
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Julia Schulz
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Kevin M. Orsley
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Wu Wei
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Raeka S. Aiyar
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Ronald W. Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Vytas A. Bankaitis
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - James E. Haber
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Marc L. Salit
- Genome-Scale Measurements Group, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
- Joint Initiative for Metrology in Biology, Stanford, California, USA
| | - Robert P. St Onge
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Lars M. Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Joint Initiative for Metrology in Biology, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
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96
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O’Brien CE, McCarthy CGP, Walshe AE, Shaw DR, Sumski DA, Krassowski T, Fitzpatrick DA, Butler G. Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade. PLoS One 2018; 13:e0198957. [PMID: 29944657 PMCID: PMC6019693 DOI: 10.1371/journal.pone.0198957] [Citation(s) in RCA: 10] [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: 12/12/2017] [Accepted: 05/28/2018] [Indexed: 11/18/2022] Open
Abstract
Diutina catenulata (Candida catenulata) is an ascomycetous yeast that has been isolated from humans, animals and environmental sources. The species is a contaminant of dairy products, and has been linked to superficial and invasive infections in both humans and animals. Previous phylogenetic analyses have assigned the species to the Saccharomycetales, but failed to identify its specific clade. Here, we report the genome sequence of an environmental isolate of D. catenulata. Examination of the tRNA repertoire and coding potential of this species shows that it translates the CUG codon as serine and not leucine. In addition, two phylogenetic analyses using 204 ubiquitous gene family alignments and 3,826 single-copy genes both confirm the placement of the species in the Debaryomycetaceae/Metschnikowiaceae, or CTG-Ser clade. The sequenced isolate contains an MTLα idiomorph. However, unlike most MTL loci in related species, poly (A) polymerase (PAP) is not adjacent to MTLα1.
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Affiliation(s)
- Caoimhe E. O’Brien
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Charley G. P. McCarthy
- Department of Biology, Genome Evolution Laboratory, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Annie E. Walshe
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Dennis R. Shaw
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Deirdre A. Sumski
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Tadeusz Krassowski
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David A. Fitzpatrick
- Department of Biology, Genome Evolution Laboratory, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
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97
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Martinson SA, Greenwood SJ, Wadowska D, Martin K. Histopathological, ultrastructural and molecular phylogenetic analysis of a novel microsporidium in a loggerhead sea turtle Caretta caretta. Dis Aquat Organ 2018; 129:31-39. [PMID: 29916390 DOI: 10.3354/dao03234] [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] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Microsporidial spores were identified in the musculature of a loggerhead sea turtle Caretta caretta found dead on the shore in New Brunswick, Canada. Gastroenteritis was diagnosed on gross postmortem examination, with no gross abnormalities detected in the skeletal muscle. Histologically, the microsporidial spores were associated with inflammation and muscular necrosis and measured 1.1-1.7 × 2.2-3.4 µm. Spores were typically identified within sporophorous vesicles and, less often, in sporophorocysts and were weakly Gram positive, had punctate PAS staining, and were occasionally strongly acid-fast. Ultrastructural characteristics included 7-10 polar filament coils and other standard features of microsporidial spores. PCR for the microsporidial small subunit rRNA gene sequence was performed on DNA extracted from the muscle and small intestine, and the resulting amplicon was sequenced and queried against published microsporidial genomes. DNA sequences shared 98.2-99.8% sequence identity to Clade III of the Marinosporidia. This is the first report of a microsporidial infection contributing to the mortality of a sea turtle.
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Affiliation(s)
- S A Martinson
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
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98
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Guo R, Chen D, Xiong C, Hou C, Zheng Y, Fu Z, Diao Q, Zhang L, Wang H, Hou Z, Li W, Kumar D, Liang Q. Identification of long non-coding RNAs in the chalkbrood disease pathogen Ascospheara apis. J Invertebr Pathol 2018; 156:1-5. [PMID: 29894727 DOI: 10.1016/j.jip.2018.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 01/14/2023]
Abstract
Ascospheara apis is a widespread fungal pathogen that exclusively invades honeybee larvae. Thus far, non-coding RNA in A. apis has not yet been documented. In this study, we sequenced A. apis using strand specific cDNA library construction and Illumina RNA sequencing methods, and identified 379 lncRNAs, including antisense lncRNAs, lincRNAs, intronic lncRNAs and sense lncRNAs. Additionally, these lncRNAs were found to be shorter in length and have fewer exons and transcript isoforms than protein-coding genes, similar to those identified in mammals and plants. Furthermore, the existence of 15 predicted lncRNAs of A. apis was confirmed using RT-PCR and expression levels of 11 were lower than those of adjacent protein-coding genes. Our findings not only enlarge the lncRNA database for fungi, but also lay a foundation for further investigation of potential lncRNA-mediated regulation of genes in A. apis.
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Affiliation(s)
- Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Cuiling Xiong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Yanzhen Zheng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongmin Fu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Lu Zhang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongquan Wang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhixian Hou
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wendong Li
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dhiraj Kumar
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Qin Liang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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99
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Roth AJ, Shuman S, Schwer B. Defining essential elements and genetic interactions of the yeast Lsm2-8 ring and demonstration that essentiality of Lsm2-8 is bypassed via overexpression of U6 snRNA or the U6 snRNP subunit Prp24. RNA 2018; 24:853-864. [PMID: 29615482 PMCID: PMC5959253 DOI: 10.1261/rna.066175.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/30/2018] [Indexed: 06/08/2023]
Abstract
A seven-subunit Lsm2-8 protein ring assembles on the U-rich 3' end of the U6 snRNA. A structure-guided mutational analysis of the Saccharomyces cerevisiae Lsm2-8 ring affords new insights to structure-function relations and genetic interactions of the Lsm subunits. Alanine scanning of 39 amino acids comprising the RNA-binding sites or intersubunit interfaces of Lsm2, Lsm3, Lsm4, Lsm5, and Lsm8 identified only one instance of lethality (Lsm3-R69A) and one severe growth defect (Lsm2-R63A), both involving amino acids that bind the 3'-terminal UUU trinucleotide. All other Ala mutations were benign with respect to vegetative growth. Tests of 235 pairwise combinations of benign Lsm mutants identified six instances of inter-Lsm synthetic lethality and 45 cases of nonlethal synthetic growth defects. Thus, Lsm2-8 ring function is buffered by a network of internal genetic redundancies. A salient finding was that otherwise lethal single-gene deletions lsm2Δ, lsm3Δ, lsm4Δ, lsm5, and lsm8Δ were rescued by overexpression of U6 snRNA from a high-copy plasmid. Moreover, U6 overexpression rescued myriad lsmΔ lsmΔ double-deletions and lsmΔ lsmΔ lsmΔ triple-deletions. We find that U6 overexpression also rescues a lethal deletion of the U6 snRNP protein subunit Prp24 and that Prp24 overexpression bypasses the essentiality of the U6-associated Lsm subunits. Our results indicate that abetting U6 snRNA is the only essential function of the yeast Lsm2-8 proteins.
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Affiliation(s)
- Allen J Roth
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
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100
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Wang J, Tian L, Zhang DD, Short DPG, Zhou L, Song SS, Liu Y, Wang D, Kong ZQ, Cui WY, Ma XF, Klosterman SJ, Subbarao KV, Chen JY, Dai XF. SNARE-Encoding Genes VdSec22 and VdSso1 Mediate Protein Secretion Required for Full Virulence in Verticillium dahliae. Mol Plant Microbe Interact 2018; 31:651-664. [PMID: 29419372 DOI: 10.1094/mpmi-12-17-0289-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Proteins that mediate cellular and subcellular membrane fusion are key factors in vesicular trafficking in all eukaryotic cells, including the secretion and transport of plant pathogen virulence factors. In this study, we identified vesicle-fusion components that included 22 soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), four Sec1/Munc18 (SM) family proteins, and 10 Rab GTPases encoded in the genome of the vascular wilt pathogen Verticillium dahliae Vd991. Targeted deletion of two SNARE-encoding genes in V. dahliae, VdSec22 and VdSso1, significantly reduced virulence of both mutants on cotton, relative to the wild-type Vd991 strain. Comparative analyses of the secreted protein content (exoproteome) revealed that many enzymes involved in carbohydrate hydrolysis were regulated by VdSec22 or VdSso1. Consistent with a role of these enzymes in plant cell-wall degradation, pectin, cellulose, and xylan utilization were reduced in the VdSec22 or VdSso1 mutant strains along with a loss of exoproteome cytotoxic activity on cotton leaves. Comparisons with a pathogenicity-related exoproteome revealed that several known virulence factors were not regulated by VdSec22 or VdSso1, but some of the proteins regulated by VdSec22 or VdSso1 displayed different characteristics, including the lack of a typical signal peptide, suggesting that V. dahliae employs more than one secretory route to transport proteins to extracellular sites during infection.
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Affiliation(s)
- Jie Wang
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Li Tian
- 3 College of Life Science, Qufu Normal University, Qufu, 273165, Shandong, China; and
| | - Dan-Dan Zhang
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dylan P G Short
- 2 Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA, U.S.A
| | - Lei Zhou
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shuang-Shuang Song
- 3 College of Life Science, Qufu Normal University, Qufu, 273165, Shandong, China; and
| | - Yan Liu
- 3 College of Life Science, Qufu Normal University, Qufu, 273165, Shandong, China; and
| | - Dan Wang
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhi-Qiang Kong
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei-Ye Cui
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xue-Feng Ma
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Steven J Klosterman
- 4 United States Department of Agriculture, Agricultural Research Service, Salinas, CA, U.S.A
| | - Krishna V Subbarao
- 2 Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA, U.S.A
| | - Jie-Yin Chen
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiao-Feng Dai
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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