1
|
Cheng AP, Lederer B, Oberkofler L, Huang L, Johnson NR, Platten F, Dunker F, Tisserant C, Weiberg A. A fungal RNA-dependent RNA polymerase is a novel player in plant infection and cross-kingdom RNA interference. PLoS Pathog 2023; 19:e1011885. [PMID: 38117848 PMCID: PMC10766185 DOI: 10.1371/journal.ppat.1011885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/05/2023] [Revised: 01/04/2024] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Small RNAs act as fungal pathogen effectors that silence host target genes to promote infection, a virulence mechanism termed cross-kingdom RNA interference (RNAi). The essential pathogen factors of cross-kingdom small RNA production are largely unknown. We here characterized the RNA-dependent RNA polymerase (RDR)1 in the fungal plant pathogen Botrytis cinerea that is required for pathogenicity and cross-kingdom RNAi. B. cinerea bcrdr1 knockout (ko) mutants exhibited reduced pathogenicity and loss of cross-kingdom small RNAs. We developed a "switch-on" GFP reporter to study cross-kingdom RNAi in real-time within the living plant tissue which highlighted that bcrdr1 ko mutants were compromised in cross-kingdom RNAi. Moreover, blocking seven pathogen cross-kingdom small RNAs by expressing a short-tandem target mimic RNA in transgenic Arabidopsis thaliana led to reduced infection levels of the fungal pathogen B. cinerea and the oomycete pathogen Hyaloperonospora arabidopsidis. These results demonstrate that cross-kingdom RNAi is significant to promote host infection and making pathogen small RNAs an effective target for crop protection.
Collapse
Affiliation(s)
- An-Po Cheng
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Bernhard Lederer
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Lorenz Oberkofler
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Lihong Huang
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Nathan R. Johnson
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Fabian Platten
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Florian Dunker
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Constance Tisserant
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Arne Weiberg
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| |
Collapse
|
2
|
Liu Z, Li Y, Hou J, Liu T. Transboundary milRNAs: Indispensable molecules in the process of Trichoderma breve T069 mycoparasitism of Botrytis cinerea. Pestic Biochem Physiol 2023; 196:105599. [PMID: 37945247 DOI: 10.1016/j.pestbp.2023.105599] [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] [Received: 08/05/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 11/12/2023]
Abstract
Despite the increasing number of fungal microRNA-like small RNAs (milRNAs) being identified and reported, profiling of milRNAs in biocontrol fungi and their roles in the mycoparasitism of pathogenic fungi remains limited. Therefore, in this study, we constructed a GFP fluorescence strain to evaluate the critical period of mycoparasitism in the interaction system between T. breve T069 and B. cinerea. The results showed that the early stage of Trichoderma mycoparasitism occurred 12 h after hyphal contact and was characterized by hyphal parallelism, whereas the middle stage lasted 36 h was characterized by wrapping. The late stage of mycoparasitism occurred at 72 h was characterized by the degradation of B. cinerea mycelia. We subsequently identified the sRNAs of T. breve T069 and B. cinerea during the critical period of mycoparasitism using high-throughput sequencing. In ltR1, 45 potential milRNA targets were identified for 243 genes, and 73 milRNAs targeted 733 genes in ltR3. Additionally, to identify potential transboundary miRNAs in T. breve T069, we screened for miRNAs that were exclusively expressed and had precursor structures in the T. breve T069 genome but were absent in the B. cinerea genome. Next, we predicted the target genes of B. cinerea. Our findings showed that 14 potential transboundary milRNAs from T. breve T069 targeted 41 genes in B. cinerea. Notably, cme-MIR164a-p5_1ss17CT can target 15 genes, including Rim15 (BCIN_15g00280), Nop53 (BCIN_12g03770), Skn7 (BCIN_02g08650), and Vel3 (BCIN_03g06410), while ppe-MIR477b-p3_1ss11TC targeted polyketide synthase (BCIN_03g04360, PKS3). The target gene of PC-5p-27397_41 was a non-ribosomal peptide synthetase (BCIN_01g03730, Bcnrps6). PC-3p-0029 (Tri-milR29) targeted chitin synthetase 7. These genes play crucial roles in normal mycelial growth and pathogenicity of B. cinerea. In conclusion, this study highlights the significance of milRNAs in Trichoderma mycoparasitism of B. cinerea. This discovery provides a new strategy for the application of miRNAs in the prevention and treatment of fungal pathogens.
Collapse
Affiliation(s)
- Zhen Liu
- Key Laboratory of Green Prevention and Control of Tropical Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Yuejiao Li
- Key Laboratory of Green Prevention and Control of Tropical Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Jumei Hou
- Key Laboratory of Green Prevention and Control of Tropical Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China.
| | - Tong Liu
- Key Laboratory of Green Prevention and Control of Tropical Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China.
| |
Collapse
|
3
|
Purchal MK, Eyler DE, Tardu M, Franco MK, Korn MM, Khan T, McNassor R, Giles R, Lev K, Sharma H, Monroe J, Mallik L, Koutmos M, Koutmou KS. Pseudouridine synthase 7 is an opportunistic enzyme that binds and modifies substrates with diverse sequences and structures. Proc Natl Acad Sci U S A 2022; 119:e2109708119. [PMID: 35058356 PMCID: PMC8794802 DOI: 10.1073/pnas.2109708119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudouridine (Ψ) is a ubiquitous RNA modification incorporated by pseudouridine synthase (Pus) enzymes into hundreds of noncoding and protein-coding RNA substrates. Here, we determined the contributions of substrate structure and protein sequence to binding and catalysis by pseudouridine synthase 7 (Pus7), one of the principal messenger RNA (mRNA) modifying enzymes. Pus7 is distinct among the eukaryotic Pus proteins because it modifies a wider variety of substrates and shares limited homology with other Pus family members. We solved the crystal structure of Saccharomyces cerevisiae Pus7, detailing the architecture of the eukaryotic-specific insertions thought to be responsible for the expanded substrate scope of Pus7. Additionally, we identified an insertion domain in the protein that fine-tunes Pus7 activity both in vitro and in cells. These data demonstrate that Pus7 preferentially binds substrates possessing the previously identified UGUAR (R = purine) consensus sequence and that RNA secondary structure is not a strong requirement for Pus7-binding. In contrast, the rate constants and extent of Ψ incorporation are more influenced by RNA structure, with Pus7 modifying UGUAR sequences in less-structured contexts more efficiently both in vitro and in cells. Although less-structured substrates were preferred, Pus7 fully modified every transfer RNA, mRNA, and nonnatural RNA containing the consensus recognition sequence that we tested. Our findings suggest that Pus7 is a promiscuous enzyme and lead us to propose that factors beyond inherent enzyme properties (e.g., enzyme localization, RNA structure, and competition with other RNA-binding proteins) largely dictate Pus7 substrate selection.
Collapse
Affiliation(s)
- Meredith K Purchal
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel E Eyler
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Mehmet Tardu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Monika K Franco
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Megan M Korn
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Taslima Khan
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Ryan McNassor
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Rachel Giles
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Katherine Lev
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Hari Sharma
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Jeremy Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Leena Mallik
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109
| | - Markos Koutmos
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109;
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109
| | - Kristin S Koutmou
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109;
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| |
Collapse
|
4
|
Abstract
As part of a complex network of genome control, long regulatory RNAs exert significant influences on chromatin dynamics. Understanding how this occurs could illuminate new avenues for disease treatment and lead to new hypotheses that would advance gene regulatory research. Recent studies using the model fission yeast Schizosaccharomyces pombe (S. pombe) and powerful parallel sequencing technologies have provided many insights in this area. This review will give an overview of key findings in S. pombe that relate long RNAs to multiple levels of chromatin regulation: histone modifications, gene neighborhood regulation in cis and higher-order chromosomal ordering. Moreover, we discuss parallels recently found in mammals to help bridge the knowledge gap between the study systems.
Collapse
Affiliation(s)
| | - Tommy V. Vo
- Department of Biochemistry and Molecular Biology, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA;
| |
Collapse
|
5
|
Rodriguez-Lopez M, Anver S, Cotobal C, Kamrad S, Malecki M, Correia-Melo C, Hoti M, Townsend S, Marguerat S, Pong SK, Wu MY, Montemayor L, Howell M, Ralser M, Bähler J. Functional profiling of long intergenic non-coding RNAs in fission yeast. eLife 2022; 11:e76000. [PMID: 34984977 PMCID: PMC8730722 DOI: 10.7554/elife.76000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic genomes express numerous long intergenic non-coding RNAs (lincRNAs) that do not overlap any coding genes. Some lincRNAs function in various aspects of gene regulation, but it is not clear in general to what extent lincRNAs contribute to the information flow from genotype to phenotype. To explore this question, we systematically analysed cellular roles of lincRNAs in Schizosaccharomyces pombe. Using seamless CRISPR/Cas9-based genome editing, we deleted 141 lincRNA genes to broadly phenotype these mutants, together with 238 diverse coding-gene mutants for functional context. We applied high-throughput colony-based assays to determine mutant growth and viability in benign conditions and in response to 145 different nutrient, drug, and stress conditions. These analyses uncovered phenotypes for 47.5% of the lincRNAs and 96% of the protein-coding genes. For 110 lincRNA mutants, we also performed high-throughput microscopy and flow cytometry assays, linking 37% of these lincRNAs with cell-size and/or cell-cycle control. With all assays combined, we detected phenotypes for 84 (59.6%) of all lincRNA deletion mutants tested. For complementary functional inference, we analysed colony growth of strains ectopically overexpressing 113 lincRNA genes under 47 different conditions. Of these overexpression strains, 102 (90.3%) showed altered growth under certain conditions. Clustering analyses provided further functional clues and relationships for some of the lincRNAs. These rich phenomics datasets associate lincRNA mutants with hundreds of phenotypes, indicating that most of the lincRNAs analysed exert cellular functions in specific environmental or physiological contexts. This study provides groundwork to further dissect the roles of these lincRNAs in the relevant conditions.
Collapse
Affiliation(s)
- Maria Rodriguez-Lopez
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Shajahan Anver
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Cristina Cotobal
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Stephan Kamrad
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
- Charité Universitätsmedizin Berlin, Institute of BiochemistryBerlinGermany
| | - Michal Malecki
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Clara Correia-Melo
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
| | - Mimoza Hoti
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - StJohn Townsend
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
| | - Samuel Marguerat
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Sheng Kai Pong
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Mary Y Wu
- The Francis Crick Institute, High Throughput ScreeningLondonUnited Kingdom
| | - Luis Montemayor
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Michael Howell
- The Francis Crick Institute, High Throughput ScreeningLondonUnited Kingdom
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
- Charité Universitätsmedizin Berlin, Institute of BiochemistryBerlinGermany
| | - Jürg Bähler
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| |
Collapse
|
6
|
Zeng F, Li X, Pires-Alves M, Chen X, Hawk CW, Jin H. Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells. Cell Rep 2021; 37:109877. [PMID: 34706231 DOI: 10.1016/j.celrep.2021.109877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/21/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022] Open
Abstract
Conserved developmentally regulated guanosine triphosphate (GTP)-binding proteins (Drgs) and their binding partner Drg family regulatory proteins (Dfrps) are important for embryonic development, cellular growth control, differentiation, and proliferation. Here, we report that the yeast Drg1/Dfrp1 ortholog Rbg1/Tma46 facilitates translational initiation, elongation, and termination by suppressing prolonged ribosome pausing. Consistent with the genome-wide observations, deletion of Rbg1 exacerbates the growth defect resulting from translation stalling, and Rbg1 stabilizes mRNAs against no-go decay. Furthermore, we provide a cryoelectron microscopy (cryo-EM) structure of the 80S ribosome bound with Rbg1/Tma46 that reveals the molecular interactions responsible for Rbg1/Tma46 function. The Rbg1 subunit binds to the GTPase association center of the ribosome and the A-tRNA, and the N-terminal zinc finger domain of the Tma46 subunit binds to the 40S, establishing an interaction critical for the ribosomal association. Our results answer the fundamental question of how a paused ribosome resumes translation and show that Drg1/Dfrp1 play a critical role in ensuring orderly translation.
Collapse
Affiliation(s)
- Fuxing Zeng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Department of Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Blvd., Shenzhen 518055, People's Republic of China
| | - Xin Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Blvd., Shenzhen 518055, People's Republic of China
| | - Melissa Pires-Alves
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Christopher W Hawk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA.
| |
Collapse
|
7
|
García-Martínez J, Medina DA, Bellvís P, Sun M, Cramer P, Chávez S, Pérez-Ortín JE. The total mRNA concentration buffering system in yeast is global rather than gene-specific. RNA 2021; 27:1281-1290. [PMID: 34272303 PMCID: PMC8456998 DOI: 10.1261/rna.078774.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Gene expression in eukaryotes does not follow a linear process from transcription to translation and mRNA degradation. Instead it follows a circular process in which cytoplasmic mRNA decay crosstalks with nuclear transcription. In many instances, this crosstalk contributes to buffer mRNA at a roughly constant concentration. Whether the mRNA buffering concept operates on the total mRNA concentration or at the gene-specific level, and if the mechanism to do so is a global or a specific one, remain unknown. Here we assessed changes in mRNA concentrations and their synthesis rates along the transcriptome of aneuploid strains of the yeast Saccharomyces cerevisiae We also assessed mRNA concentrations and their synthesis rates in nonsense-mediated decay (NMD) targets in euploid strains. We found that the altered synthesis rates in the genes from the aneuploid chromosome and the changes in their mRNA stabilities were not counterbalanced. In addition, the stability of NMD targets was not specifically compensated by the changes in synthesis rate. We conclude that there is no genetic compensation of NMD mRNA targets in yeast, and total mRNA buffering uses mostly a global system rather than a gene-specific one.
Collapse
Affiliation(s)
- José García-Martínez
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, E46100 Burjassot, Spain
| | - Daniel A Medina
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, E46100 Burjassot, Spain
| | - Pablo Bellvís
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
| | - Mai Sun
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, 37077 Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, 37077 Göttingen, Germany
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
- Dirección de Evaluación y Acreditación, Agencia Andaluza del Conocimiento, planta 3ª C.P. 14006 Córdoba, Spain
| | - José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, E46100 Burjassot, Spain
| |
Collapse
|
8
|
Novačić A, Šupljika N, Bekavac N, Žunar B, Stuparević I. Interplay of the RNA Exosome Complex and RNA-Binding Protein Ssd1 in Maintaining Cell Wall Stability in Yeast. Microbiol Spectr 2021; 9:e0029521. [PMID: 34259554 PMCID: PMC8552689 DOI: 10.1128/spectrum.00295-21] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/18/2021] [Indexed: 11/20/2022] Open
Abstract
Yeast cell wall stability is important for cell division and survival under stress conditions. The expression of cell-wall-related proteins is regulated by several pathways involving RNA-binding proteins and RNases. The multiprotein RNA exosome complex provides the 3'→5' exoribonuclease activity that is critical for maintaining the stability and integrity of the yeast cell wall under stress conditions such as high temperatures. In this work, we show that the temperature sensitivity of RNA exosome mutants is most pronounced in the W303 genetic background due to the nonfunctional ssd1-d allele. This gene encodes the RNA-binding protein Ssd1, which is involved in the posttranscriptional regulation of cell-wall-related genes. Expression of the functional SSD1-V allele from its native genomic locus or from a centromeric plasmid suppresses the growth defects and aberrant morphology of RNA exosome mutant cells at high temperatures or upon treatment with cell wall stressors. Moreover, combined inactivation of the RNA exosome catalytic subunit Rrp6 and Ssd1 results in a synthetically sick phenotype of cell wall instability, as these proteins may function in parallel pathways (i.e., via different mRNA targets) to maintain cell wall stability. IMPORTANCE Stressful conditions such as high temperatures can compromise cellular integrity and cause bursting. In microorganisms surrounded by a cell wall, such as yeast, the cell wall is the primary shield that protects cells from environmental stress. Therefore, remodeling its structure requires inputs from multiple signaling pathways and regulators. In this work, we identify the interplay of the RNA exosome complex and the RNA-binding protein Ssd1 as an important factor in the yeast cell wall stress response. These proteins operate in independent pathways to support yeast cell wall stability. This work highlights the contribution of RNA-binding proteins in the regulation of yeast cell wall structure, providing new insights into yeast physiology.
Collapse
Affiliation(s)
- Ana Novačić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Nada Šupljika
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Nikša Bekavac
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Bojan Žunar
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Igor Stuparević
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
9
|
Sterrett MC, Enyenihi L, Leung SW, Hess L, Strassler SE, Farchi D, Lee RS, Withers ES, Kremsky I, Baker RE, Basrai MA, van Hoof A, Fasken MB, Corbett AH. A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex. RNA 2021; 27:1046-1067. [PMID: 34162742 PMCID: PMC8370739 DOI: 10.1261/rna.078618.120] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
RNA exosomopathies, a growing family of diseases, are linked to missense mutations in genes encoding structural subunits of the evolutionarily conserved, 10-subunit exoribonuclease complex, the RNA exosome. This complex consists of a three-subunit cap, a six-subunit, barrel-shaped core, and a catalytic base subunit. While a number of mutations in RNA exosome genes cause pontocerebellar hypoplasia, mutations in the cap subunit gene EXOSC2 cause an apparently distinct clinical presentation that has been defined as a novel syndrome SHRF (short stature, hearing loss, retinitis pigmentosa, and distinctive facies). We generated the first in vivo model of the SHRF pathogenic amino acid substitutions using budding yeast by modeling pathogenic EXOSC2 missense mutations (p.Gly30Val and p.Gly198Asp) in the orthologous S. cerevisiae gene RRP4 The resulting rrp4 mutant cells show defects in cell growth and RNA exosome function. Consistent with altered RNA exosome function, we detect significant transcriptomic changes in both coding and noncoding RNAs in rrp4-G226D cells that model EXOSC2 p.Gly198Asp, suggesting defects in nuclear surveillance. Biochemical and genetic analyses suggest that the Rrp4 G226D variant subunit shows impaired interactions with key RNA exosome cofactors that modulate the function of the complex. These results provide the first in vivo evidence that pathogenic missense mutations present in EXOSC2 impair the function of the RNA exosome. This study also sets the stage to compare exosomopathy models to understand how defects in RNA exosome function underlie distinct pathologies.
Collapse
Affiliation(s)
- Maria C Sterrett
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia 30322, USA
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Liz Enyenihi
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Sara W Leung
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Laurie Hess
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Sarah E Strassler
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia 30322, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Daniela Farchi
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Richard S Lee
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Elise S Withers
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Isaac Kremsky
- Loma Linda University School of Medicine, Loma Linda, California 92350, USA
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| |
Collapse
|
10
|
Allen GE, Panasenko OO, Villanyi Z, Zagatti M, Weiss B, Pagliazzo L, Huch S, Polte C, Zahoran S, Hughes CS, Pelechano V, Ignatova Z, Collart MA. Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A. Cell Rep 2021; 36:109633. [PMID: 34469733 DOI: 10.1016/j.celrep.2021.109633] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 03/18/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
In this work, we show that Not4 and Not5 from the Ccr4-Not complex modulate translation elongation dynamics and change ribosome A-site dwelling occupancy in a codon-dependent fashion. These codon-specific changes in not5Δ cells are very robust and independent of codon position within the mRNA, the overall mRNA codon composition, or changes of mRNA expression levels. They inversely correlate with codon-specific changes in cells depleted for eIF5A and positively correlate with those in cells depleted for ribosome-recycling factor Rli1. Not5 resides in punctate loci, co-purifies with ribosomes and Rli1, but not with eIF5A, and limits mRNA solubility. Overexpression of wild-type or non-complementing Rli1 and loss of Rps7A ubiquitination enable Not4 E3 ligase-dependent translation of polyarginine stretches. We propose that Not4 and Not5 modulate translation elongation dynamics to produce a soluble proteome by Rps7A ubiquitination, dynamic condensates that limit mRNA solubility and exclude eIF5A, and a moonlighting function of Rli1.
Collapse
Affiliation(s)
- George E Allen
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Olesya O Panasenko
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Zoltan Villanyi
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland; Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Marina Zagatti
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Benjamin Weiss
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Lucile Pagliazzo
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Susanne Huch
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
| | - Christine Polte
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Szabolcs Zahoran
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland; Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | | | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland.
| |
Collapse
|
11
|
Khonsari B, Klassen R, Schaffrath R. Role of SSD1 in Phenotypic Variation of Saccharomyces cerevisiae Strains Lacking DEG1-Dependent Pseudouridylation. Int J Mol Sci 2021; 22:ijms22168753. [PMID: 34445460 PMCID: PMC8396022 DOI: 10.3390/ijms22168753] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/16/2022] Open
Abstract
Yeast phenotypes associated with the lack of wobble uridine (U34) modifications in tRNA were shown to be modulated by an allelic variation of SSD1, a gene encoding an mRNA-binding protein. We demonstrate that phenotypes caused by the loss of Deg1-dependent tRNA pseudouridylation are similarly affected by SSD1 allelic status. Temperature sensitivity and protein aggregation are elevated in deg1 mutants and further increased in the presence of the ssd1-d allele, which encodes a truncated form of Ssd1. In addition, chronological lifespan is reduced in a deg1 ssd1-d mutant, and the negative genetic interactions of the U34 modifier genes ELP3 and URM1 with DEG1 are aggravated by ssd1-d. A loss of function mutation in SSD1, ELP3, and DEG1 induces pleiotropic and overlapping phenotypes, including sensitivity against target of rapamycin (TOR) inhibitor drug and cell wall stress by calcofluor white. Additivity in ssd1 deg1 double mutant phenotypes suggests independent roles of Ssd1 and tRNA modifications in TOR signaling and cell wall integrity. However, other tRNA modification defects cause growth and drug sensitivity phenotypes, which are not further intensified in tandem with ssd1-d. Thus, we observed a modification-specific rather than general effect of SSD1 status on phenotypic variation in tRNA modification mutants. Our results highlight how the cellular consequences of tRNA modification loss can be influenced by protein targeting specific mRNAs.
Collapse
|
12
|
Abstract
Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.
Collapse
MESH Headings
- Evolution, Molecular
- Gene Expression Regulation, Fungal
- Gene Expression Regulation, Plant
- Genome, Fungal
- Genome, Plant
- Introns
- Organelles/genetics
- Organelles/metabolism
- RNA Splicing
- RNA Stability
- RNA, Algal/genetics
- RNA, Algal/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Transcription, Genetic
Collapse
|
13
|
Werner BT, Koch A, Šečić E, Engelhardt J, Jelonek L, Steinbrenner J, Kogel KH. Fusarium graminearum DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence. PLoS One 2021; 16:e0252365. [PMID: 34351929 PMCID: PMC8341482 DOI: 10.1371/journal.pone.0252365] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 05/11/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
In filamentous fungi, gene silencing by RNA interference (RNAi) shapes many biological processes, including pathogenicity. Recently, fungal small RNAs (sRNAs) have been shown to act as effectors that disrupt gene activity in interacting plant hosts, thereby undermining their defence responses. We show here that the devastating mycotoxin-producing ascomycete Fusarium graminearum (Fg) utilizes DICER-like (DCL)-dependent sRNAs to target defence genes in two Poaceae hosts, barley (Hordeum vulgare, Hv) and Brachypodium distachyon (Bd). We identified 104 Fg-sRNAs with sequence homology to host genes that were repressed during interactions of Fg and Hv, while they accumulated in plants infected by the DCL double knock-out (dKO) mutant PH1-dcl1/2. The strength of target gene expression correlated with the abundance of the corresponding Fg-sRNA. Specifically, the abundance of three tRNA-derived fragments (tRFs) targeting immunity-related Ethylene overproducer 1-like 1 (HvEOL1) and three Poaceae orthologues of Arabidopsis thaliana BRI1-associated receptor kinase 1 (HvBAK1, HvSERK2 and BdSERK2) was dependent on fungal DCL. Additionally, RNA-ligase-mediated Rapid Amplification of cDNA Ends (RLM-RACE) identified infection-specific degradation products for the three barley gene transcripts, consistent with the possibility that tRFs contribute to fungal virulence via targeted gene silencing.
Collapse
Affiliation(s)
- Bernhard Timo Werner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Aline Koch
- Institute for Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Jonas Engelhardt
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Lukas Jelonek
- Institute of Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - Jens Steinbrenner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
- * E-mail:
| |
Collapse
|
14
|
Zinn-Brooks L, Roper ML. Circadian rhythm shows potential for mRNA efficiency and self-organized division of labor in multinucleate cells. PLoS Comput Biol 2021; 17:e1008828. [PMID: 34339411 PMCID: PMC8360590 DOI: 10.1371/journal.pcbi.1008828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 08/12/2021] [Accepted: 07/12/2021] [Indexed: 11/23/2022] Open
Abstract
Multinucleate cells occur in every biosphere and across the kingdoms of life, including in the human body as muscle cells and bone-forming cells. Data from filamentous fungi suggest that, even when bathed in a common cytoplasm, nuclei are capable of autonomous behaviors, including division. How does this potential for autonomy affect the organization of cellular processes between nuclei? Here we analyze a simplified model of circadian rhythm, a form of cellular oscillator, in a mathematical model of the filamentous fungus Neurospora crassa. Our results highlight a potential role played by mRNA-protein phase separation to keep mRNAs close to the nuclei from which they originate, while allowing proteins to diffuse freely between nuclei. Our modeling shows that syncytism allows for extreme mRNA efficiency-we demonstrate assembly of a robust oscillator with a transcription rate a thousand-fold less than in comparable uninucleate cells. We also show self-organized division of the labor of mRNA production, with one nucleus in a two-nucleus syncytium producing at least twice as many mRNAs as the other in 30% of cycles. This division can occur spontaneously, but division of labor can also be controlled by regulating the amount of cytoplasmic volume available to each nucleus. Taken together, our results show the intriguing richness and potential for emergent organization among nuclei in multinucleate cells. They also highlight the role of previously studied mechanisms of cellular organization, including nuclear space control and localization of mRNAs through RNA-protein phase separation, in regulating nuclear coordination.
Collapse
Affiliation(s)
- Leif Zinn-Brooks
- Department of Mathematics, Harvey Mudd College, Claremont, California, United States of America
| | - Marcus L. Roper
- Department of Mathematics, UCLA, Los Angeles, California, United States of America
| |
Collapse
|
15
|
Jaafar M, Paraqindes H, Gabut M, Diaz JJ, Marcel V, Durand S. 2'O-Ribose Methylation of Ribosomal RNAs: Natural Diversity in Living Organisms, Biological Processes, and Diseases. Cells 2021; 10:1948. [PMID: 34440717 PMCID: PMC8393311 DOI: 10.3390/cells10081948] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/21/2023] Open
Abstract
Recent findings suggest that ribosomes, the translational machineries, can display a distinct composition depending on physio-pathological contexts. Thanks to outstanding technological breakthroughs, many studies have reported that variations of rRNA modifications, and more particularly the most abundant rRNA chemical modification, the rRNA 2'O-ribose methylation (2'Ome), intrinsically occur in many organisms. In the last 5 years, accumulating reports have illustrated that rRNA 2'Ome varies in human cell lines but also in living organisms (yeast, plant, zebrafish, mouse, human) during development and diseases. These rRNA 2'Ome variations occur either within a single cell line, organ, or patient's sample (i.e., intra-variability) or between at least two biological conditions (i.e., inter-variability). Thus, the ribosomes can tolerate the absence of 2'Ome at some specific positions. These observations question whether variations in rRNA 2'Ome could provide ribosomes with particular translational regulatory activities and functional specializations. Here, we compile recent studies supporting the heterogeneity of ribosome composition at rRNA 2'Ome level and provide an overview of the natural diversity in rRNA 2'Ome that has been reported up to now throughout the kingdom of life. Moreover, we discuss the little evidence that suggests that variations of rRNA 2'Ome can effectively impact the ribosome activity and contribute to the etiology of some human diseases.
Collapse
Affiliation(s)
| | | | | | | | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.J.); (H.P.); (M.G.); (J.-J.D.)
| | - Sébastien Durand
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.J.); (H.P.); (M.G.); (J.-J.D.)
| |
Collapse
|
16
|
Xu Z, Asakawa S. A model explaining mRNA level fluctuations based on activity demands and RNA age. PLoS Comput Biol 2021; 17:e1009188. [PMID: 34297727 PMCID: PMC8336849 DOI: 10.1371/journal.pcbi.1009188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/04/2021] [Accepted: 06/17/2021] [Indexed: 11/19/2022] Open
Abstract
Cellular RNA levels typically fluctuate and are influenced by different transcription rates and RNA degradation rates. However, the understanding of the fundamental relationships between RNA abundance, environmental stimuli, RNA activities, and RNA age distributions is incomplete. Furthermore, the rates of RNA degradation and transcription are difficult to measure in transcriptomic experiments in living organisms, especially in studies involving humans. A model based on activity demands and RNA age was developed to explore the mechanisms of RNA level fluctuations. Using single-cell time-series gene expression experimental data, we assessed the transcription rates, RNA degradation rates, RNA life spans, RNA demand, accumulated transcription levels, and accumulated RNA degradation levels. This model could also predict RNA levels under simulation backgrounds, such as stimuli that induce regular oscillations in RNA abundance, stable RNA levels over time that result from long-term shortage of total RNA activity or from uncontrollable transcription, and relationships between RNA/protein levels and metabolic rates. This information contributes to existing knowledge. Detected cellular RNA levels usually fluctuate. The understanding of the fundamental relationships between RNA level fluctuations, the rates of RNA degradation and transcription, environmental stimuli, RNA activities, and RNA age distributions is incomplete. In the present research, we developed a model based on the demands of RNA (related to intrinsic and/or extrinsic information), RNA age (determines the survival time and biological activity of an RNA), transcription, and RNA degradation to explain the mechanism underlying intracellular RNA level fluctuations. We also explored applicability of the model for analysing dynamic processes between interacting biomolecules, such as the relationship between RNA and protein level fluctuations. Using single-cell time-series gene expression experimental data, we assessed some biological parameters, such as transcription rates, RNA degradation rates, and RNA life spans. This model could also predict RNA levels under simulation backgrounds, such as stimuli that induce regular oscillations in RNA abundance, stable RNA levels over time that result from long-term shortage of total RNA activity or from uncontrollable transcription, and relationships between RNA/protein levels and metabolic rates. This information contributes to existing knowledge and provides a new perspective for future studies.
Collapse
Affiliation(s)
- Zhongneng Xu
- Department of Ecology, Jinan University, Guangzhou, China
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail: ,
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
17
|
San Martin-Alonso M, Soler-Oliva ME, García-Rubio M, García-Muse T, Aguilera A. Harmful R-loops are prevented via different cell cycle-specific mechanisms. Nat Commun 2021; 12:4451. [PMID: 34294712 PMCID: PMC8298424 DOI: 10.1038/s41467-021-24737-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/01/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying how R-loops are generated is crucial to know how transcription compromises genome integrity. We show by genome-wide analysis of conditional yeast mutants that the THO transcription complex, prevents R-loop formation in G1 and S-phase, whereas the Sen1 DNA-RNA helicase prevents them only in S-phase. Interestingly, damage accumulates asymmetrically downstream of the replication fork in sen1 cells but symmetrically in the hpr1 THO mutant. Our results indicate that: R-loops form co-transcriptionally independently of DNA replication; that THO is a general and cell-cycle independent safeguard against R-loops, and that Sen1, in contrast to previously believed, is an S-phase-specific R-loop resolvase. These conclusions have important implications for the mechanism of R-loop formation and the role of other factors reported to affect on R-loop homeostasis.
Collapse
Affiliation(s)
- Marta San Martin-Alonso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-UPO, Seville, Spain
| | - María E Soler-Oliva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-UPO, Seville, Spain
| | - María García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-UPO, Seville, Spain
| | - Tatiana García-Muse
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-UPO, Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-UPO, Seville, Spain.
| |
Collapse
|
18
|
Wang W, Zhang F, Cui J, Chen D, Liu Z, Hou J, Zhang R, Liu T. Identification of microRNA-like RNAs from Trichoderma asperellum DQ-1 during its interaction with tomato roots using bioinformatic analysis and high-throughput sequencing. PLoS One 2021; 16:e0254808. [PMID: 34293017 PMCID: PMC8297844 DOI: 10.1371/journal.pone.0254808] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 01/27/2021] [Accepted: 07/04/2021] [Indexed: 11/19/2022] Open
Abstract
MicroRNA-like small RNAs (milRNAs) and their regulatory roles in the interaction between plant and fungus have recently aroused keen interest of plant pathologists. Trichoderma spp., one of the widespread biocontrol fungi, can promote plant growth and induce plant disease resistance. To investigate milRNAs potentially involved in the interaction between Trichoderma and tomato roots, a small RNA (sRNA) library expressed during the interaction of T. asperellum DQ-1 and tomato roots was constructed and sequenced using the Illumina HiSeqTM 2500 sequencing platform. From 13,464,142 sRNA reads, we identified 21 milRNA candidates that were similar to other known microRNAs in the miRBase database and 22 novel milRNA candidates that possessed a stable microRNA precursor hairpin structure. Among them, three milRNA candidates showed different expression level in the interaction according to the result of stem-loop RT-PCR indicating that these milRNAs may play a distinct regulatory role in the interaction between Trichoderma and tomato roots. The potential transboundary milRNAs from T. asperellum and their target genes in tomato were predicted by bioinformatics analysis. The results revealed that several interesting proteins involved in plant growth and development, disease resistance, seed maturation, and osmotic stress signal transduction might be regulated by the transboundary milRNAs. To our knowledge, this is the first report of milRNAs taking part in the process of interaction of T. asperellum and tomato roots and associated with plant promotion and disease resistance. The results might be useful to unravel the mechanism of interaction between Trichoderma and tomato.
Collapse
Affiliation(s)
- Weiwei Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan, PR China
- Key Laboratory of Germplasm Resources of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Haikou, Hainan, PR China
| | - Fengtao Zhang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan, PR China
| | - Jia Cui
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan, PR China
| | - Di Chen
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan, PR China
| | - Zhen Liu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan, PR China
| | - Jumei Hou
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan, PR China
| | - Rongyi Zhang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan, PR China
| | - Tong Liu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan, PR China
- * E-mail:
| |
Collapse
|
19
|
Baudin-Baillieu A, Namy O. Saccharomyces cerevisiae, a Powerful Model for Studying rRNA Modifications and Their Effects on Translation Fidelity. Int J Mol Sci 2021; 22:ijms22147419. [PMID: 34299038 PMCID: PMC8307265 DOI: 10.3390/ijms22147419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 12/31/2022] Open
Abstract
Ribosomal RNA is a major component of the ribosome. This RNA plays a crucial role in ribosome functioning by ensuring the formation of the peptide bond between amino acids and the accurate decoding of the genetic code. The rRNA carries many chemical modifications that participate in its maturation, the formation of the ribosome and its functioning. In this review, we present the different modifications and how they are deposited on the rRNA. We also describe the most recent results showing that the modified positions are not 100% modified, which creates a heterogeneous population of ribosomes. This gave rise to the concept of specialized ribosomes that we discuss. The knowledge accumulated in the yeast Saccharomyces cerevisiae is very helpful to better understand the role of rRNA modifications in humans, especially in ribosomopathies.
Collapse
|
20
|
Claude KL, Bureik D, Chatzitheodoridou D, Adarska P, Singh A, Schmoller KM. Transcription coordinates histone amounts and genome content. Nat Commun 2021; 12:4202. [PMID: 34244507 PMCID: PMC8270936 DOI: 10.1038/s41467-021-24451-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 08/10/2020] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
Biochemical reactions typically depend on the concentrations of the molecules involved, and cell survival therefore critically depends on the concentration of proteins. To maintain constant protein concentrations during cell growth, global mRNA and protein synthesis rates are tightly linked to cell volume. While such regulation is appropriate for most proteins, certain cellular structures do not scale with cell volume. The most striking example of this is the genomic DNA, which doubles during the cell cycle and increases with ploidy, but is independent of cell volume. Here, we show that the amount of histone proteins is coupled to the DNA content, even though mRNA and protein synthesis globally increase with cell volume. As a consequence, and in contrast to the global trend, histone concentrations decrease with cell volume but increase with ploidy. We find that this distinct coordination of histone homeostasis and genome content is already achieved at the transcript level, and is an intrinsic property of histone promoters that does not require direct feedback mechanisms. Mathematical modeling and histone promoter truncations reveal a simple and generalizable mechanism to control the cell volume- and ploidy-dependence of a given gene through the balance of the initiation and elongation rates.
Collapse
Affiliation(s)
- Kora-Lee Claude
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Daniela Bureik
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Petia Adarska
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Abhyudai Singh
- Department of Electrical & Computer Engineering, University of Delaware, Newark, DE, USA
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
| |
Collapse
|
21
|
Abstract
mRNA degradation is connected to the translation process up to the degree that 5'-3' mRNA degradation follows the last translating ribosome. To study 5'-3'co-translational mRNA decay and the associated ribosome dynamics, here we present an improved high-throughput 5'P degradome RNA sequencing protocol (HT-5Pseq). We exemplify its application in Saccharomyces cerevisiae, but in principle, it could be applied to any other eukaryotic organism. HT-5Pseq is easy, scalable, and uses affordable duplex-specific nuclease-based rRNA depletion. For complete details on the use and execution of this protocol, please refer to Zhang and Pelechano (2021).
Collapse
Affiliation(s)
- Yujie Zhang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| |
Collapse
|
22
|
Jordan C, de Carvalho VR, Mascarin GM, Dos Santos Oliveira LR, Dunlap CA, Wilcken CF. First record of a new microsporidium pathogenic to Gonipterus platensis in Brazil. Sci Rep 2021; 11:10971. [PMID: 34040020 PMCID: PMC8155060 DOI: 10.1038/s41598-021-90041-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/12/2021] [Indexed: 11/22/2022] Open
Abstract
Microsporidia are naturally occurring fungal-related parasites that can infect nearly all animal hosts, but their biocontrol potential of insect pests is routinely overlooked in agriculture and forestry. This research brings the first report describing the natural occurrence of a microsporidium causing disease in field-collected populations of the invasive eucalyptus snout beetle, Gonipterus platensis (Coleoptera: Curculionidae), a major destructive pest of eucalyptus plantations in Brazil. Adult beetles were collected during field surveys in commercial eucalyptus plantations in southern Brazil to be examined and dissected with typical symptoms to verify presence of microsporidian spores in haemolymph. From 14 plantations in different sites, the natural infection occurrence in these populations ranged from 0 to 65%, while a lab colony exhibited an infection incidence of 70%. Spore density in haemolymph of symptomatic insects averaged 2.1 (± 0.4) × 107 spores/beetle. Symptoms in infected adults were identified by an abnormal abdomen with malformation of the second pair of wings, impairing their flight activity. Electron transmission microscopy of the pathogen showed morphological features similar to species belonging to the genus Nosema or Vairimorpha. Phylogenetic analysis of the full-length small subunit ribosomal RNA gene suggests this pathogen's placement in the genus Vairimorpha, but with a sequence identity of ~ 94% with the nearest neighbours. The low level of sequence identity suggests this pathogen may represent a novel taxon in the genus and further requires whole genome sequencing for definitive taxonomic resolution. These findings provide insights on the natural occurrence of this novel pathogen of this invasive pest in Eucalyptus plantations in Brazil. Further studies are needed to determine potential of this microsporidium in the design of conservative or augmentative biological control programs for this invasive pest.
Collapse
Affiliation(s)
- Carolina Jordan
- School of Agricultural Sciences, São Paulo State University (UNESP), Campus of Botucatu, Av. Universitária, 3780, Altos do Paraíso, Fazenda Experimental Lageado, Botucatu, SP, 18610-034, Brazil.
| | - Vanessa Rafaela de Carvalho
- School of Agricultural Sciences, São Paulo State University (UNESP), Campus of Botucatu, Av. Universitária, 3780, Altos do Paraíso, Fazenda Experimental Lageado, Botucatu, SP, 18610-034, Brazil
| | - Gabriel Moura Mascarin
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP-340, km 127.5, Jaguariúna, SP, 13918-110, Brazil.
| | - Leiliane Rodrigues Dos Santos Oliveira
- Botucatu Medical School, Dept. Internal Medicine, Sao Paulo State University (UNESP), Campus of Botucatu, Av. Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, 18618-687, Brazil
| | - Christopher A Dunlap
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, 1815, N. University St, Peoria, IL, 61604, USA
| | - Carlos Frederico Wilcken
- School of Agricultural Sciences, São Paulo State University (UNESP), Campus of Botucatu, Av. Universitária, 3780, Altos do Paraíso, Fazenda Experimental Lageado, Botucatu, SP, 18610-034, Brazil
| |
Collapse
|
23
|
Cánovas-Márquez JT, Navarro-Mendoza MI, Pérez-Arques C, Lax C, Tahiri G, Pérez-Ruiz JA, Lorenzo-Gutiérrez D, Calo S, López-García S, Navarro E, Nicolás FE, Garre V, Murcia L. Role of the Non-Canonical RNAi Pathway in the Antifungal Resistance and Virulence of Mucorales. Genes (Basel) 2021; 12:genes12040586. [PMID: 33920552 PMCID: PMC8072676 DOI: 10.3390/genes12040586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
Mucorales are the causal agents for the lethal disease known as mucormycosis. Mortality rates of mucormycosis can reach up to 90%, due to the mucoralean antifungal drug resistance and the lack of effective therapies. A concerning urgency among the medical and scientific community claims to find targets for the development of new treatments. Here, we reviewed different studies describing the role and machinery of a novel non-canonical RNAi pathway (NCRIP) only conserved in Mucorales. Its non-canonical features are the independence of Dicer and Argonaute proteins. Conversely, NCRIP relies on RNA-dependent RNA Polymerases (RdRP) and an atypical ribonuclease III (RNase III). NCRIP regulates the expression of mRNAs by degrading them in a specific manner. Its mechanism binds dsRNA but only cuts ssRNA. NCRIP exhibits a diversity of functional roles. It represses the epimutational pathway and the lack of NCRIP increases the generation of drug resistant strains. NCRIP also regulates the control of retrotransposons expression, playing an essential role in genome stability. Finally, NCRIP regulates the response during phagocytosis, affecting the multifactorial process of virulence. These critical NCRIP roles in virulence and antifungal drug resistance, along with its exclusive presence in Mucorales, mark this pathway as a promising target to fight against mucormycosis.
Collapse
Affiliation(s)
- José Tomás Cánovas-Márquez
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - María Isabel Navarro-Mendoza
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; (M.I.N.-M.); (C.P.-A.)
| | - Carlos Pérez-Arques
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; (M.I.N.-M.); (C.P.-A.)
| | - Carlos Lax
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Ghizlane Tahiri
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - José Antonio Pérez-Ruiz
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Damaris Lorenzo-Gutiérrez
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Silvia Calo
- School of Natural and Exact Sciences, Pontificia Universidad Católica Madre y Maestra, Santiago de los Caballeros 51033, Dominican Republic;
| | - Sergio López-García
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Eusebio Navarro
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Francisco Esteban Nicolás
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
| | - Laura Murcia
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain; (J.T.C.-M.); (C.L.); (G.T.); (J.A.P.-R.); (D.L.-G.); (S.L.-G.); (E.N.); (F.E.N.); (V.G.)
- Correspondence:
| |
Collapse
|
24
|
Höfler S, Lukat P, Blankenfeldt W, Carlomagno T. High-resolution structure of eukaryotic Fibrillarin interacting with Nop56 amino-terminal domain. RNA 2021; 27:496-512. [PMID: 33483369 PMCID: PMC7962484 DOI: 10.1261/rna.077396.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Ribosomal RNA (rRNA) carries extensive 2'-O-methyl marks at functionally important sites. This simple chemical modification is thought to confer stability, promote RNA folding, and contribute to generate a heterogenous ribosome population with a yet-uncharacterized function. 2'-O-methylation occurs both in archaea and eukaryotes and is accomplished by the Box C/D RNP enzyme in an RNA-guided manner. Extensive and partially conflicting structural information exists for the archaeal enzyme, while no structural data is available for the eukaryotic enzyme. The yeast Box C/D RNP consists of a guide RNA, the RNA-primary binding protein Snu13, the two scaffold proteins Nop56 and Nop58, and the enzymatic module Nop1. Here we present the high-resolution structure of the eukaryotic Box C/D methyltransferase Nop1 from Saccharomyces cerevisiae bound to the amino-terminal domain of Nop56. We discuss similarities and differences between the interaction modes of the two proteins in archaea and eukaryotes and demonstrate that eukaryotic Nop56 recruits the methyltransferase to the Box C/D RNP through a protein-protein interface that differs substantially from the archaeal orthologs. This study represents a first achievement in understanding the evolution of the structure and function of these proteins from archaea to eukaryotes.
Collapse
MESH Headings
- Amino Acid Sequence
- Archaeal Proteins/chemistry
- Archaeal Proteins/genetics
- Archaeal Proteins/metabolism
- Binding Sites
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Crystallography, X-Ray
- Gene Expression
- Methylation
- Models, Molecular
- Nuclear Proteins/chemistry
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Pyrococcus furiosus/genetics
- Pyrococcus furiosus/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Alignment
- Structural Homology, Protein
- RNA, Guide, CRISPR-Cas Systems
Collapse
Affiliation(s)
- Simone Höfler
- Leibniz University Hannover, Institute for Organic Chemistry and Centre for Biomolecular Drug Research (BMWZ), D-30167 Hannover, Germany
| | - Peer Lukat
- Helmholtz Centre for Infection Research, Department of Structure and Function of Proteins, D-38124 Braunschweig, Germany
| | - Wulf Blankenfeldt
- Helmholtz Centre for Infection Research, Department of Structure and Function of Proteins, D-38124 Braunschweig, Germany
| | - Teresa Carlomagno
- Leibniz University Hannover, Institute for Organic Chemistry and Centre for Biomolecular Drug Research (BMWZ), D-30167 Hannover, Germany
- Helmholtz Centre for Infection Research, Group of NMR-based Structural Chemistry, D-38124 Braunschweig, Germany
| |
Collapse
|
25
|
Irwin NAT, Twynstra CS, Mathur V, Keeling PJ. The molecular phylogeny of Chionaster nivalis reveals a novel order of psychrophilic and globally distributed Tremellomycetes (Fungi, Basidiomycota). PLoS One 2021; 16:e0247594. [PMID: 33760841 PMCID: PMC7990227 DOI: 10.1371/journal.pone.0247594] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/19/2020] [Accepted: 02/09/2021] [Indexed: 12/04/2022] Open
Abstract
Snow and ice present challenging substrates for cellular growth, yet microbial snow communities not only exist, but are diverse and ecologically impactful. These communities are dominated by green algae, but additional organisms, such as fungi, are also abundant and may be important for nutrient cycling, syntrophic interactions, and community structure in general. However, little is known about these non-algal community members, including their taxonomic affiliations. An example of this is Chionaster nivalis, a unicellular fungus that is morphologically enigmatic and frequently observed in snow communities globally. Despite being described over one hundred years ago, the phylogeny and higher-level taxonomic classifications of C. nivalis remain unknown. Here, we isolated and sequenced the internal transcribed spacer (ITS) and the D1-D2 region of the large subunit ribosomal RNA gene of C. nivalis, providing a molecular barcode for future studies. Phylogenetic analyses using the ITS and D1-D2 region revealed that C. nivalis is part of a novel lineage in the class Tremellomycetes (Basidiomycota, Agaricomycotina) for which a new order Chionasterales ord. nov. (MB838717) and family Chionasteraceae fam. nov. (MB838718) are proposed. Comparisons between C. nivalis and sequences generated from environmental surveys revealed that the Chionasterales are globally distributed and probably psychrophilic, as they appear to be limited to the high alpine and arctic regions. These results highlight the unexplored diversity that exists within these extreme habitats and emphasize the utility of single-cell approaches in characterizing these complex algal-dominated communities.
Collapse
Affiliation(s)
- Nicholas A. T. Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Merton College, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Chantelle S. Twynstra
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
26
|
Jing Y, Lv Y, Ye J, Yao L, Chen L, Mi L, Fei Y, Yu Y, Dong B, Lv H, Ma J. Quantifying tagged mRNA export flux via nuclear pore complexes in single live cells. Biochem Biophys Res Commun 2021; 545:138-144. [PMID: 33548627 DOI: 10.1016/j.bbrc.2021.01.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/08/2023]
Abstract
The mRNA export flux through nuclear pore complexes (NPC) changes under DNA manipulation and hence affects protein translation. However, monitoring the flux of a specific mRNA in single live cell is beyond reach of traditional techniques. We developed a fluorescence-based detection method for measuring the export flux of mRNA through NPC in single live cell using a snapshot image, which had been tested on exogenous genes' expression in HeLa cells, with transfection or infection, and endogenous genes' expression in yeast cells, during incubation and carbon catabolite repression. With its speediness, explicitness and noninvasiveness, we believe that it would be valuable in direct monitoring of gene behavior, and the understanding of gene regulation at a single cell level.
Collapse
Affiliation(s)
- Yueyue Jing
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Yilin Lv
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Jingya Ye
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Sichuan, 610041, China
| | - Longfang Yao
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Liwen Chen
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Biao Dong
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Sichuan, 610041, China.
| | - Hong Lv
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
| | - Jiong Ma
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China; Institute of Biomedical Engineering and Technology, Academy for Engineer and Technology, Fudan University, Shanghai, China; Shanghai Engineering Research Center of Industrial Microorganisms, Multiscale Research Institute of Complex Systems (MRICS), School of Life Sciences, Fudan University, Shanghai, China.
| |
Collapse
|
27
|
Lee SY, Hung S, Esnault C, Pathak R, Johnson KR, Bankole O, Yamashita A, Zhang H, Levin HL. Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation. Cell Rep 2021; 30:2686-2698.e8. [PMID: 32101745 PMCID: PMC9497450 DOI: 10.1016/j.celrep.2020.01.094] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 04/18/2019] [Revised: 10/18/2019] [Accepted: 01/27/2020] [Indexed: 11/24/2022] Open
Abstract
Heterochromatin functions as a scaffold for factors responsible for gene
silencing and chromosome segregation. Heterochromatin can be assembled by
multiple pathways, including RNAi and RNA surveillance. We identified factors
that form heterochromatin using dense profiles of transposable element
integration in Schizosaccharomyces pombe. The candidates
include a large number of essential proteins such as four canonical mRNA
cleavage and polyadenylation factors. We find that Iss1, a subunit of the
poly(A) polymerase module, plays a role in forming heterochromatin in centromere
repeats that is independent of RNAi. Genome-wide maps reveal that Iss1
accumulates at genes regulated by RNA surveillance. Iss1 interacts with RNA
surveillance factors Mmi1 and Rrp6, and importantly, Iss1 contributes to RNA
elimination that forms heterochromatin at meiosis genes. Our profile of
transposable element integration supports the model that a network of mRNA
cleavage and polyadenylation factors coordinates RNA surveillance, including the
mechanism that forms heterochromatin at meiotic genes. Lee et al. use dense profiles of transposon integration to identify genes
important for the formation of heterochromatin. Among many candidates, Iss1 is a
canonical mRNA cleavage and polyadenylation factor found to be important for
heterochromatin at meiotic genes by recruiting the nuclear exosome.
Collapse
Affiliation(s)
- Si Young Lee
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stevephen Hung
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Caroline Esnault
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rakesh Pathak
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kory R Johnson
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Oluwadamilola Bankole
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Akira Yamashita
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Hongen Zhang
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry L Levin
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
28
|
Abstract
RNA editing is an important posttranscriptional process that alters the genetic information of RNA encoded by genomic DNA. Adenosine-to-inosine (A-to-I) editing is the most prevalent type of RNA editing in animal kingdom, catalyzed by adenosine deaminases acting on RNA (ADARs). Recently, genome-wide A-to-I RNA editing is discovered in fungi, involving adenosine deamination mechanisms distinct from animals. Aiming to draw more attention to RNA editing in fungi, here we discuss the considerations for deep sequencing data preparation and the available various methods for detecting RNA editing, with a special emphasis on their usability for fungal RNA editing detection. We describe computational protocols for the identification of candidate RNA editing sites in fungi by using two software packages REDItools and RES-Scanner with RNA sequencing (RNA-Seq) and genomic DNA sequencing (DNA-Seq) data.
Collapse
Affiliation(s)
- Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
29
|
Pérez-Arques C, Navarro-Mendoza MI, Murcia L, Navarro E, Garre V, Nicolás FE. The RNAi Mechanism Regulates a New Exonuclease Gene Involved in the Virulence of Mucorales. Int J Mol Sci 2021; 22:ijms22052282. [PMID: 33668930 PMCID: PMC7956310 DOI: 10.3390/ijms22052282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/16/2021] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
Mucormycosis is a lethal disease caused by Mucorales, which are emerging as human causes that explain the high mortality for this disease. Consequently, the research community is searching for virulence determinants that could be repurposed as targets to develop new treatments against mucormycosis. Our work explores an RNA interference (RNAi)-based approach to find targets involved in the virulence of Mucorales. A transcriptomewide analysis compared sRNAs and their target mRNAs in two Mucor lusitanicus different pathotypes, virulent and avirulent, generating a list of 75 loci selected by their differential sRNA accumulation in these strains. As a proof of concept and validity, an experimental approach characterized two loci showing opposite behavior, confirming that RNAi activity causes their differential expression in the two pathotypes. We generated deletion mutants for two loci and a knockin-strain overexpressing for one of these loci. Their functional analysis in murine virulence assays identified the gene wex1, a putative DEDDy exonuclease with RNase domains, as an essential factor for virulence. The identification of wex1 showed the potential of our approach to discover virulence factors not only in Mucorales but also in any other fungal model with an active RNAi machinery. More importantly, it adds a new layer to the biological processes controlled by RNAi in M. lusitanicus, confirming that the Dicer-dependent RNAi pathway can silence gene expression to promote virulence.
Collapse
|
30
|
Oizumi Y, Kaji T, Tashiro S, Takeshita Y, Date Y, Kanoh J. Complete sequences of Schizosaccharomyces pombe subtelomeres reveal multiple patterns of genome variation. Nat Commun 2021; 12:611. [PMID: 33504776 PMCID: PMC7840980 DOI: 10.1038/s41467-020-20595-1] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022] Open
Abstract
Genome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess single SH regions of a standard laboratory strain. In addition, some natural isolates of S. pombe were analyzed using previous sequencing data. Whole sequences of SH regions revealed that each SH region consists of two distinct parts with mosaics of multiple common segments or blocks showing high variation among subtelomeres and strains. Subtelomere regions show relatively high frequency of nucleotide variations among strains compared with the other chromosomal regions. Furthermore, we identified subtelomeric RecQ-type helicase genes, tlh3 and tlh4, which add to the already known tlh1 and tlh2, and found that the tlh1-4 genes show high sequence variation with missense mutations, insertions, and deletions but no severe effects on their RNA expression. Our results indicate that SH sequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.
Collapse
Affiliation(s)
- Yusuke Oizumi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takuto Kaji
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sanki Tashiro
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Institute of Molecular Biology, University of Oregon, 1370 Franklin Blvd, Eugene, OR, USA
| | - Yumiko Takeshita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuko Date
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Junko Kanoh
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
31
|
Jenjaroenpun P, Wongsurawat T, Wadley TD, Wassenaar TM, Liu J, Dai Q, Wanchai V, Akel NS, Jamshidi-Parsian A, Franco AT, Boysen G, Jennings ML, Ussery DW, He C, Nookaew I. Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Res 2021; 49:e7. [PMID: 32710622 DOI: 10.1101/487819] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/13/2020] [Accepted: 07/13/2020] [Indexed: 05/25/2023] Open
Abstract
Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct sequencing of native RNA using Oxford Nanopore Technologies (ONT) can allow for directly detecting the RNA base modifications, although these modifications might appear as sequencing errors. The percent Error of Specific Bases (%ESB) was higher for native RNA than unmodified RNA, which enabled the detection of ribonucleotide modification sites. Based on the %ESB differences, we developed a bioinformatic tool, epitranscriptional landscape inferring from glitches of ONT signals (ELIGOS), that is based on various types of synthetic modified RNA and applied to rRNA and mRNA. ELIGOS is able to accurately predict known classes of RNA methylation sites (AUC > 0.93) in rRNAs from Escherichiacoli, yeast, and human cells, using either unmodified in vitro transcription RNA or a background error model, which mimics the systematic error of direct RNA sequencing as the reference. The well-known DRACH/RRACH motif was localized and identified, consistent with previous studies, using differential analysis of ELIGOS to study the impact of RNA m6A methyltransferase by comparing wild type and knockouts in yeast and mouse cells. Lastly, the DRACH motif could also be identified in the mRNA of three human cell lines. The mRNA modification identified by ELIGOS is at the level of individual base resolution. In summary, we have developed a bioinformatic software package to uncover native RNA modifications.
Collapse
Affiliation(s)
- Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Taylor D Wadley
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Trudy M Wassenaar
- Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany
| | - Jun Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Qing Dai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Visanu Wanchai
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Nisreen S Akel
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Azemat Jamshidi-Parsian
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Aime T Franco
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Gunnar Boysen
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Michael L Jennings
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - David W Ussery
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| |
Collapse
|
32
|
Li P, Zhou X, Xu K, Zhang QC. RASP: an atlas of transcriptome-wide RNA secondary structure probing data. Nucleic Acids Res 2021; 49:D183-D191. [PMID: 33068412 PMCID: PMC7779053 DOI: 10.1093/nar/gkaa880] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 08/14/2020] [Revised: 09/13/2020] [Accepted: 09/26/2020] [Indexed: 02/06/2023] Open
Abstract
RNA molecules fold into complex structures that are important across many biological processes. Recent technological developments have enabled transcriptome-wide probing of RNA secondary structure using nucleases and chemical modifiers. These approaches have been widely applied to capture RNA secondary structure in many studies, but gathering and presenting such data from very different technologies in a comprehensive and accessible way has been challenging. Existing RNA structure probing databases usually focus on low-throughput or very specific datasets. Here, we present a comprehensive RNA structure probing database called RASP (RNA Atlas of Structure Probing) by collecting 161 deduplicated transcriptome-wide RNA secondary structure probing datasets from 38 papers. RASP covers 18 species across animals, plants, bacteria, fungi, and also viruses, and categorizes 18 experimental methods including DMS-seq, SHAPE-Seq, SHAPE-MaP, and icSHAPE, etc. Specially, RASP curates the up-to-date datasets of several RNA secondary structure probing studies for the RNA genome of SARS-CoV-2, the RNA virus that caused the on-going COVID-19 pandemic. RASP also provides a user-friendly interface to query, browse, and visualize RNA structure profiles, offering a shortcut to accessing RNA secondary structures grounded in experimental data. The database is freely available at http://rasp.zhanglab.net.
Collapse
MESH Headings
- Animals
- COVID-19/epidemiology
- COVID-19/prevention & control
- COVID-19/virology
- Computational Biology/methods
- Computational Biology/statistics & numerical data
- Databases, Genetic/statistics & numerical data
- Genome, Viral/genetics
- High-Throughput Nucleotide Sequencing/methods
- High-Throughput Nucleotide Sequencing/statistics & numerical data
- Humans
- Nucleic Acid Conformation
- Pandemics
- RNA/chemistry
- RNA/genetics
- RNA Probes/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Viral/chemistry
- RNA, Viral/genetics
- SARS-CoV-2/genetics
- SARS-CoV-2/physiology
- Transcriptome
Collapse
Affiliation(s)
- Pan Li
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaolin Zhou
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Kui Xu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| |
Collapse
|
33
|
Moreau K, Le Dantec A, Rahmouni AR. Deciphering the Dynamic Landscape of Transcription-Associated mRNP Quality Control Components Over the Whole Yeast Genome. Methods Mol Biol 2021; 2209:251-265. [PMID: 33201474 DOI: 10.1007/978-1-0716-0935-4_16] [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: 06/11/2023]
Abstract
In eukaryotic cells, aberrant mRNPs with processing and packaging defects are targeted co-transcriptionally by a surveillance system that triggers their nuclear retention and ultimately the degradation of their mRNA component by the 3'-5' activity of the exosome-associated exonuclease Rrp6. This mRNP quality control process is stimulated by the NNS complex (Nrd1-Nab3-Sen1), which otherwise mediates termination, processing, and decay of ncRNAs. The process involves also the exosome co-activator TRAMP complex (Trf4-Air2-Mtr4). Here, we describe a genome-wide approach to visualize the dynamic movement and coordination of these quality control components over the yeast chromosomes upon perturbation of mRNP biogenesis. The method provides valuable information on how the surveillance system is precisely coordinated both physically and functionally with the transcription machinery to detect the faulty events during perturbation of mRNP biogenesis. The overview shows also that the gathering of the quality control components over affected mRNA genes takes place at the expense of their commitment to be recruited at ncRNA genomic features, provoking termination and processing defects of ncRNAs.
Collapse
Affiliation(s)
- Kévin Moreau
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Orléans, France
| | - Aurélia Le Dantec
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Orléans, France
| | - A Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Orléans, France.
| |
Collapse
|
34
|
Abstract
This chapter provides an overview on different methods for the characterization of RNAs in Trichoderma reesei. In the first section, protocols for the extraction of total RNA from fungal mycelia and the identification of 5' and 3' ends of certain RNAs of interest via rapid amplification of cDNA ends (RACE) are presented. In the next section, this knowledge on the transcriptional start and end points is used for in vitro synthesis and fluorescence labeling of the RNA of interest. The in vitro synthesized RNA can then be applied for in vitro analyses such as RNA electrophoretic mobility shift assays (RNA-EMSA) and RNA in vitro footprinting. RNA-EMSA is a method suitable for the identification and characterization of RNA-protein interactions or interactions of an RNA with other nucleic acids. RNA in vitro footprinting allows exact mapping of protein-binding sites on RNA molecules and also the determination of RNA secondary and tertiary structures at singe-nucleotide resolution. All protocols presented in this chapter are optimized for the analysis of noncoding RNAs (ncRNAs), especially long ncRNAs (lncRNAs) or other specific RNA species of more than 200 nt in length.
Collapse
Affiliation(s)
- Petra Till
- Christian Doppler laboratory for optimized expression of carbohydrate-active enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
| |
Collapse
|
35
|
Smethurst DGJ, Kovalev N, McKenzie ER, Pestov DG, Shcherbik N. Iron-mediated degradation of ribosomes under oxidative stress is attenuated by manganese. J Biol Chem 2020; 295:17200-17214. [PMID: 33040024 PMCID: PMC7863898 DOI: 10.1074/jbc.ra120.015025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 06/28/2020] [Revised: 10/05/2020] [Indexed: 02/05/2023] Open
Abstract
Protein biosynthesis is fundamental to cellular life and requires the efficient functioning of the translational machinery. At the center of this machinery is the ribosome, a ribonucleoprotein complex that depends heavily on Mg2+ for structure. Recent work has indicated that other metal cations can substitute for Mg2+, raising questions about the role different metals may play in the maintenance of the ribosome under oxidative stress conditions. Here, we assess ribosomal integrity following oxidative stress both in vitro and in cells to elucidate details of the interactions between Fe2+ and the ribosome and identify Mn2+ as a factor capable of attenuating oxidant-induced Fe2+-mediated degradation of rRNA. We report that Fe2+ promotes degradation of all rRNA species of the yeast ribosome and that it is bound directly to RNA molecules. Furthermore, we demonstrate that Mn2+ competes with Fe2+ for rRNA-binding sites and that protection of ribosomes from Fe2+-mediated rRNA hydrolysis correlates with the restoration of cell viability. Our data, therefore, suggest a relationship between these two transition metals in controlling ribosome stability under oxidative stress.
Collapse
Affiliation(s)
- Daniel G J Smethurst
- Department of Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Nikolay Kovalev
- Department of Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Erica R McKenzie
- Civil and Environmental Engineering Department, Temple University, Philadelphia, Pennsylvania, USA
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Natalia Shcherbik
- Department of Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA.
| |
Collapse
|
36
|
Reed AJ, Sapia RJ, Dowis C, Solarez S, Gerasimova YV. Interrogation of highly structured RNA with multicomponent deoxyribozyme probes at ambient temperatures. RNA 2020; 26:1882-1890. [PMID: 32859694 PMCID: PMC7668264 DOI: 10.1261/rna.074864.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
Molecular analysis of RNA through hybridization with sequence-specific probes is challenging due to the intrinsic ability of RNA molecules to form stable secondary and tertiary structures. To overcome the energy barrier toward the probe-RNA complex formation, the probes are made of artificial nucleotides, which are more expensive than their natural counterparts and may still be inefficient. Here, we propose the use of a multicomponent probe based on an RNA-cleaving deoxyribozyme for the analysis of highly structured RNA targets. Efficient interrogation of two native RNA from Saccharomyces cerevisiae-a transfer RNA (tRNA) and 18S ribosomal RNA (rRNA)-was achieved at ambient temperature. We achieved detection limits of tRNA down to ∼0.3 nM, which is two orders of magnitude lower than that previously reported for molecular beacon probes. Importantly, no probe annealing to the target was required, with the hybridization assay performed at 37°C. Excess of nonspecific targets did not compromise the performance of the probe, and high interrogation efficiency was maintained by the probes even in complex matrices, such as cell lysate. A linear dynamic range of 0.3-150 nM tRNA was demonstrated. The probe can be adapted for differentiation of a single mismatch in the tRNA-probe complex. Therefore, this study opens a venue toward highly selective, sensitive, robust, and inexpensive assays for the interrogation of biological RNA.
Collapse
Affiliation(s)
- Adam J Reed
- Chemistry Department, University of Central Florida, Orlando, Florida 32765, USA
| | - Ryan J Sapia
- Chemistry Department, University of Central Florida, Orlando, Florida 32765, USA
| | - Charles Dowis
- Chemistry Department, University of Central Florida, Orlando, Florida 32765, USA
| | - Sheila Solarez
- Chemistry Department, University of Central Florida, Orlando, Florida 32765, USA
| | - Yulia V Gerasimova
- Chemistry Department, University of Central Florida, Orlando, Florida 32765, USA
| |
Collapse
|
37
|
Klim J, Zielenkiewicz U, Kurlandzka A, Kaczanowski S, Skoneczny M. Slow Adaptive Response of Budding Yeast Cells to Stable Conditions of Continuous Culture Can Occur without Genome Modifications. Genes (Basel) 2020; 11:genes11121419. [PMID: 33261040 PMCID: PMC7759791 DOI: 10.3390/genes11121419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 11/20/2022] Open
Abstract
Continuous cultures assure the invariability of environmental conditions and the metabolic state of cultured microorganisms, whereas batch-cultured cells undergo constant changes in nutrients availability. For that reason, continuous culture is sometimes employed in the whole transcriptome, whole proteome, or whole metabolome studies. However, the typical method for establishing uniform growth of a cell population, i.e., by limited chemostat, results in the enrichment of the cell population gene pool with mutations adaptive for starvation conditions. These adaptive changes can skew the results of large-scale studies. It is commonly assumed that these adaptations reflect changes in the genome, and this assumption has been confirmed experimentally in rare cases. Here we show that in a population of budding yeast cells grown for over 200 generations in continuous culture in non-limiting minimal medium and therefore not subject to selection pressure, remodeling of transcriptome occurs, but not as a result of the accumulation of adaptive mutations. The observed changes indicate a shift in the metabolic balance towards catabolism, a decrease in ribosome biogenesis, a decrease in general stress alertness, reorganization of the cell wall, and transactions occurring at the cell periphery. These adaptive changes signify the acquisition of a new lifestyle in a stable nonstressful environment. The absence of underlying adaptive mutations suggests these changes may be regulated by another mechanism.
Collapse
Affiliation(s)
- Joanna Klim
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (J.K.); (U.Z.)
| | - Urszula Zielenkiewicz
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (J.K.); (U.Z.)
| | - Anna Kurlandzka
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
| | - Szymon Kaczanowski
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
- Correspondence: ; Tel.: +48-22-5921217
| |
Collapse
|
38
|
de Curcio JS, Oliveira LN, Batista MP, Novaes E, de Almeida Soares CM. MiRNAs regulate iron homeostasis in Paracoccidioides brasiliensis. Microbes Infect 2020; 23:104772. [PMID: 33157279 DOI: 10.1016/j.micinf.2020.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 10/17/2020] [Accepted: 10/27/2020] [Indexed: 11/19/2022]
Abstract
During pathogen interaction with the host, several mechanisms are used to favor or inhibit the infectious process; one is called nutritional immunity, characterized by restriction of micronutrients to pathogens. Several studies on fungi of the Paracoccidioides complex, have demonstrated that these pathogens remodel their metabolic pathways to overcome the hostile condition imposed by the host. However, molecular mechanisms that control the regulation of those metabolic changes are not fully understood. Therefore, this work characterizes the expression profile of miRNAs during iron deprivation and describes metabolic pathways putatively regulated by those molecules. Through analysis of RNAseq, 45 miRNAs were identified and eight presented alterations in the expression profile during iron deprivation. Among the differentially regulated miRNAs, five were more abundant in yeast cells during iron deprivation and interestingly, the analyses of genes potentially regulated by those five miRNAs, pointed to metabolic pathways as oxidative phosphorylation, altered in response to iron deprivation. In addition, miRNAs with more abundance in iron presence, have as target genes encoding transcriptional factors related to iron homeostasis and uptake. Therefore, we suggest that miRNAs produced by Paracoccidioides brasiliensis may contribute to the adaptive responses of this fungus in iron starvation environment.
Collapse
Affiliation(s)
- Juliana S de Curcio
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, CEP: 74690-900, Goiânia, Goiás, Brazil
| | - Lucas Nojosa Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, CEP: 74690-900, Goiânia, Goiás, Brazil
| | - Mariana P Batista
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, CEP: 74690-900, Goiânia, Goiás, Brazil
| | - Evandro Novaes
- Departamento de Biologia, Universidade Federal de Lavras, Minas Gerais, CEP: 37200-000, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Campus II Samambaia, CEP: 74690-900, Goiânia, Goiás, Brazil.
| |
Collapse
|
39
|
Garg A. A lncRNA-regulated gene expression system with rapid induction kinetics in the fission yeast Schizosaccharomyces pombe. RNA 2020; 26:1743-1752. [PMID: 32788323 PMCID: PMC7566572 DOI: 10.1261/rna.076000.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
The fission yeast Schizosaccharomyces pombe is an excellent model organism for the study of eukaryotic cellular physiology. The organism is genetically tractable and several tools to study the functions of individual genes are available. One such tool is regulatable gene expression and overproduction of proteins. Limitations of currently available overexpression systems include delay in expression after induction, narrow dynamic range, and system-wide changes due to induction conditions. Here I describe a new long noncoding RNA (lncRNA)-regulated, thiamine-inducible expression system that integrates lncRNA-based transcriptional interference at the fission yeast tgp1 promoter with the fast repression kinetics of the thiamine-repressible nmt1 promoter. This hybrid system has rapid induction kinetics, broad dynamic range, and tunable expression via thiamine concentration. The lncRNA-regulated thiamine-inducible system will be advantageous for the study of individual genes and for potential applications in the production of heterologous proteins in fission yeast.
Collapse
Affiliation(s)
- Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| |
Collapse
|
40
|
Simms CL, Yan LL, Qiu JK, Zaher HS. Ribosome Collisions Result in +1 Frameshifting in the Absence of No-Go Decay. Cell Rep 2020; 28:1679-1689.e4. [PMID: 31412239 PMCID: PMC6701860 DOI: 10.1016/j.celrep.2019.07.046] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 03/21/2019] [Revised: 06/17/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
During translation, an mRNA is typically occupied by multiple ribosomes sparsely distributed across the coding sequence. This distribution, mediated by slow rates of initiation relative to elongation, ensures that they rarely collide with each other, but given the stochastic nature of protein synthesis, collision events do occur. Recent work from our lab suggested that collisions signal for mRNA degradation through no-go decay (NGD). We have explored the impact of stalling on ribosome function when NGD is compromised and found it to result in +1 frameshifting. We used reporters that limit the number of ribosomes on a transcript to show that +1 frameshifting is induced through ribosome collision in yeast and bacteria. Furthermore, we observe a positive correlation between ribosome density and frameshifting efficiency. It is thus tempting to speculate that NGD, in addition to its role in mRNA quality control, evolved to cope with stochastic collision events to prevent deleterious frameshifting events. Ribosome collisions, resulting from stalling, activate quality control processes to degrade the aberrant mRNA and the incomplete peptide. mRNA degradation proceeds through an endonucleolytic cleavage between the stacked ribosomes, which resolves the collisions. Simms et al. show that, when cleavage is inhibited, colliding ribosomes move out of frame.
Collapse
Affiliation(s)
- Carrie L Simms
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Liewei L Yan
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jessica K Qiu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| |
Collapse
|
41
|
Sohn BK, Basu U, Lee SW, Cho H, Shen J, Deshpande A, Johnson LC, Das K, Patel SS, Kim H. The dynamic landscape of transcription initiation in yeast mitochondria. Nat Commun 2020; 11:4281. [PMID: 32855416 PMCID: PMC7452894 DOI: 10.1038/s41467-020-17793-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 10/16/2019] [Accepted: 07/14/2020] [Indexed: 01/24/2023] Open
Abstract
Controlling efficiency and fidelity in the early stage of mitochondrial DNA transcription is crucial for regulating cellular energy metabolism. Conformational transitions of the transcription initiation complex must be central for such control, but how the conformational dynamics progress throughout transcription initiation remains unknown. Here, we use single-molecule fluorescence resonance energy transfer techniques to examine the conformational dynamics of the transcriptional system of yeast mitochondria with single-base resolution. We show that the yeast mitochondrial transcriptional complex dynamically transitions among closed, open, and scrunched states throughout the initiation stage. Then abruptly at position +8, the dynamic states of initiation make a sharp irreversible transition to an unbent conformation with associated promoter release. Remarkably, stalled initiation complexes remain in dynamic scrunching and unscrunching states without dissociating the RNA transcript, implying the existence of backtracking transitions with possible regulatory roles. The dynamic landscape of transcription initiation suggests a kinetically driven regulation of mitochondrial transcription.
Collapse
Affiliation(s)
- Byeong-Kwon Sohn
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Seung-Won Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hayoon Cho
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Aishwarya Deshpande
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Laura C Johnson
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Kalyan Das
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
- Institute for Basic Science, Ulsan, Republic of Korea.
| |
Collapse
|
42
|
Bowman EK, Deaner M, Cheng JF, Evans R, Oberortner E, Yoshikuni Y, Alper HS. Bidirectional titration of yeast gene expression using a pooled CRISPR guide RNA approach. Proc Natl Acad Sci U S A 2020; 117:18424-18430. [PMID: 32690674 PMCID: PMC7414176 DOI: 10.1073/pnas.2007413117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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] [Indexed: 11/18/2022] Open
Abstract
Most classic genetic approaches utilize binary modifications that preclude the identification of key knockdowns for essential genes or other targets that only require moderate modulation. As a complementary approach to these classic genetic methods, we describe a plasmid-based library methodology that affords bidirectional, graded modulation of gene expression enabled by tiling the promoter regions of all 969 genes that comprise the ito977 model of Saccharomyces cerevisiae's metabolic network. When coupled with a CRISPR-dCas9-based modulation and next-generation sequencing, this method affords a library-based, bidirection titration of gene expression across all major metabolic genes. We utilized this approach in two case studies: growth enrichment on alternative sugars, glycerol and galactose, and chemical overproduction of betaxanthins, leading to the identification of unique gene targets. In particular, we identify essential genes and other targets that were missed by classic genetic approaches.
Collapse
Affiliation(s)
- Emily K Bowman
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712
| | - Matthew Deaner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712
| | - Jan-Fang Cheng
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720
| | - Robert Evans
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720
| | - Ernst Oberortner
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720
| | - Yasuo Yoshikuni
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712;
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712
| |
Collapse
|
43
|
Abstract
Ribosomal subunits are assembled on a precursor rRNA that includes four spacers in addition to mature rRNA sequences. The 5' external transcribed spacer (5' ETS) is the most prominent one that recruits U3 snoRNA and a plethora of proteins during the early assembly of 90S small subunit preribosomes. Here, we have conducted a comprehensive mutational analysis of 5' ETS by monitoring the processing and assembly of a plasmid-expressed pre-18S RNA. Remarkably, nearly half of the 5' ETS sequences, when depleted individually, are dispensable for 18S rRNA processing. The dispensable elements largely bind at the surface of the 90S structure. Defective assembly of 5' ETS completely blocks the last stage of 90S formation yet has little effect on the early assembly of 5' and central domains of 18S rRNA. Our study reveals the functional regions of 5' ETS and provides new insight into the assembly hierarchy of 90S preribosomes.
Collapse
Affiliation(s)
- Jing Chen
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
- National Institute of Biological Sciences, Beijing 102206, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liman Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
44
|
Mahmoudi O, Wahab A, Chong KT. iMethyl-Deep: N6 Methyladenosine Identification of Yeast Genome with Automatic Feature Extraction Technique by Using Deep Learning Algorithm. Genes (Basel) 2020; 11:genes11050529. [PMID: 32397453 PMCID: PMC7288457 DOI: 10.3390/genes11050529] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 04/08/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
One of the most common and well studied post-transcription modifications in RNAs is N6-methyladenosine (m6A) which has been involved with a wide range of biological processes. Over the past decades, N6-methyladenosine produced some positive consequences through the high-throughput laboratory techniques but still, these lab processes are time consuming and costly. Diverse computational methods have been proposed to identify m6A sites accurately. In this paper, we proposed a computational model named iMethyl-deep to identify m6A Saccharomyces Cerevisiae on two benchmark datasets M6A2614 and M6A6540 by using single nucleotide resolution to convert RNA sequence into a high quality feature representation. The iMethyl-deep obtained 89.19% and 87.44% of accuracy on M6A2614 and M6A6540 respectively which show that our proposed method outperforms the state-of-the-art predictors, at least 8.44%, 8.96%, 8.69% and 0.173 on M6A2614 and 15.47%, 28.52%, 25.54 and 0.5 on M6A6540 higher in terms of four metrics Sp, Sn, ACC and MCC respectively. Meanwhile, M6A6540 dataset never used to train a model.
Collapse
Affiliation(s)
- Omid Mahmoudi
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (O.M.); (A.W.)
| | - Abdul Wahab
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (O.M.); (A.W.)
| | - Kil To Chong
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Korea
- Correspondence:
| |
Collapse
|
45
|
Roy KR, Chanfreau GF. Robust mapping of polyadenylated and non-polyadenylated RNA 3' ends at nucleotide resolution by 3'-end sequencing. Methods 2020; 176:4-13. [PMID: 31128237 PMCID: PMC6874744 DOI: 10.1016/j.ymeth.2019.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 02/20/2019] [Revised: 04/10/2019] [Accepted: 05/20/2019] [Indexed: 10/26/2022] Open
Abstract
3'-end poly(A)+ sequencing is an efficient and economical method for global measurement of mRNA levels and alternative poly(A) site usage. A common method involves oligo(dT)19V reverse-transcription (RT)-based library preparation and high-throughput sequencing with a custom primer ending in (dT)19. While the majority of library products have the first sequenced nucleotide reflect the bona fide poly(A) site (pA), a substantial fraction of sequencing reads arise from various mis-priming events. These can result in incorrect pA site calls anywhere from several nucleotides downstream to several kilobases upstream from the bona fide pA site. While these mis-priming events can be mitigated by increasing annealing stringency (e.g. increasing temperature from 37 °C to 42 °C), they still persist at an appreciable level (∼10%) and computational methods must be used to prevent artifactual calls. Here we present a bioinformatics workflow for precise mapping of poly(A)+ 3' ends and handling of artifacts due to oligo(dT) mis-priming and sample polymorphisms. We test pA site calling with three different read mapping programs (STAR, BWA, and BBMap), and show that the way in which each handles terminal mismatches and soft clipping has a substantial impact on identifying correct pA sites, with BWA requiring the least post-processing to correct artifacts. We demonstrate the use of this pipeline for mapping pA sites in the model eukaryote S. cerevisiae, and further apply this technology to non-polyadenylated transcripts by employing in vitro polyadenylation prior to library prep (IVP-seq). As proof of principle, we show that a fraction of tRNAs harbor CCU 3' tails instead of the canonical CCA tail, and globally identify 3' ends of splicing intermediates arising from inefficiently spliced transcripts.
Collapse
Affiliation(s)
- Kevin R Roy
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095-1570, United States
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095-1570, United States.
| |
Collapse
|
46
|
Appanah R, Lones EC, Aiello U, Libri D, De Piccoli G. Sen1 Is Recruited to Replication Forks via Ctf4 and Mrc1 and Promotes Genome Stability. Cell Rep 2020; 30:2094-2105.e9. [PMID: 32075754 PMCID: PMC7034062 DOI: 10.1016/j.celrep.2020.01.087] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 09/06/2019] [Accepted: 01/24/2020] [Indexed: 01/21/2023] Open
Abstract
DNA replication and RNA transcription compete for the same substrate during S phase. Cells have evolved several mechanisms to minimize such conflicts. Here, we identify the mechanism by which the transcription termination helicase Sen1 associates with replisomes. We show that the N terminus of Sen1 is both sufficient and necessary for replisome association and that it binds to the replisome via the components Ctf4 and Mrc1. We generated a separation of function mutant, sen1-3, which abolishes replisome binding without affecting transcription termination. We observe that the sen1-3 mutants show increased genome instability and recombination levels. Moreover, sen1-3 is synthetically defective with mutations in genes involved in RNA metabolism and the S phase checkpoint. RNH1 overexpression suppresses defects in the former, but not the latter. These findings illustrate how Sen1 plays a key function at replication forks during DNA replication to promote fork progression and chromosome stability.
Collapse
Affiliation(s)
- Rowin Appanah
- Warwick Medical School, University of Warwick, CV4 7AL Coventry, UK
| | | | - Umberto Aiello
- Institut Jacques Monod, CNRS, UMR7592, Université Paris Diderot, Paris Sorbonne Cité, Paris, France
| | - Domenico Libri
- Institut Jacques Monod, CNRS, UMR7592, Université Paris Diderot, Paris Sorbonne Cité, Paris, France
| | | |
Collapse
|
47
|
Mishra D, Satpathy G, Wig N, Fazal F, Ahmed NH, Panda SK. Evaluation of 16S rRNA broad range PCR assay for microbial detection in serum specimens in sepsis patients. J Infect Public Health 2020; 13:998-1002. [PMID: 32061569 DOI: 10.1016/j.jiph.2020.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 07/09/2019] [Revised: 12/23/2019] [Accepted: 01/15/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Early and accurate laboratory diagnosis and appropriate management of infection improves the survival rate in sepsis. In this study we evaluated broad range 16S rRNA and 16 S-23 S intergenic spacer region (ISR) PCR assays followed by nucleotide sequencing directly from patients' serum and automated blood culture for laboratory diagnosis in admitted sepsis patients. METHODS A broad range 16S rRNA PCR and 16 S-23 S ISR PCR assay followed by nucleotide sequencing was used directly from patients' serum in hospital admitted patients in 62 sepsis and 16 suspected blood stream infection (sBSI) patients. Automated blood culture was also used in the same patients. Nucleotide sequences were analyzed against NCBI Genbank database and organisms were identified using CLSI MM18A guidelines. RESULTS Bacterial culture were positive in 10/62 (16.12%) sepsis and 3/16 (18.75%) suspected BSI patients along with 3 detected fungi (2 in sepsis and 1 in suspected BSI group). PCR assay was positive in 36/62 (58.06%) sepsis and 6/16 (37.5%) suspected BSI patients respectively. All but 2 bacteria (both from culture negative patients) detected by PCR assay could be identified from nucleotide sequencing. Survival in sepsis patients was 77%. PCR assay could detect bacteria in 9/14 (64.28%) of sepsis patients with death. CONCLUSION Broad range PCR assay was far superior for early diagnosis of infection. The bacteria which could not be detected by culture and were not commonly reported from this centre, were detected by the broad range PCR assays. Detection of these rare bacteria/fungi had significant clinical correlation with patient's underlying clinical conditions, immune status and prognosis. The tests could provide definitive diagnosis of infection in >58% of sepsis patients, which helped in patient management and better survival.
Collapse
Affiliation(s)
- Deepanshi Mishra
- Ocular Microbiology, Dr. R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Gita Satpathy
- Ocular Microbiology, Dr. R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India; Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Farhan Fazal
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Nishat Hussain Ahmed
- Ocular Microbiology, Dr. R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Subrat Kumar Panda
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
48
|
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.
Collapse
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
| |
Collapse
|
49
|
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.
Collapse
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
| |
Collapse
|
50
|
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.
Collapse
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
| |
Collapse
|