1
|
Zhang H, Kumimoto RW, Anver S, Harmer SL. XAP5 CIRCADIAN TIMEKEEPER regulates RNA splicing and the circadian clock by genetically separable pathways. Plant Physiol 2023:kiad193. [PMID: 36974904 DOI: 10.1093/plphys/kiad193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/09/2023] [Accepted: 03/24/2023] [Indexed: 06/18/2023]
Abstract
The circadian oscillator allows organisms to synchronize their cellular and physiological activities with diurnal environmental changes. In plants, the circadian clock is primarily composed of multiple transcriptional-translational feedback loops. Regulators of post-transcriptional events, such as pre-mRNA splicing factors, are also involved in controlling the pace of the clock. However, in most cases the underlying mechanisms remain unclear. We have previously identified XAP5 CIRCADIAN TIMEKEEPER (XCT) as an Arabidopsis thaliana circadian clock regulator with uncharacterized molecular functions. Here, we report that XCT physically interacts with components of the spliceosome, including members of the Nineteen Complex (NTC). PacBio Iso-Seq data show that xct mutants have transcriptome-wide pre-mRNA splicing defects, predominantly aberrant 3' splice site selection. Expression of a genomic copy of XCT fully rescues those splicing defects, demonstrating that functional XCT is important for splicing. Dawn-expressed genes are significantly enriched among those aberrantly spliced in xct mutants, suggesting that the splicing activity of XCT may be circadian regulated. Furthermore, we show that loss-of-function mutations in PRP19A or PRP19B, two homologous core NTC components, suppress the short circadian period phenotype of xct-2. However, we do not see rescue of the splicing defects of core clock genes in prp19 xct mutants. Therefore, our results suggest that XCT may regulate splicing and the clock function through genetically separable pathways.
Collapse
Affiliation(s)
- Hongtao Zhang
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Roderick W Kumimoto
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Shajahan Anver
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Stacey L Harmer
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| |
Collapse
|
2
|
Amiour S, Chekroud K, Font-Verdera F, Anver S, Liébana R, Hafdi O, Viver T. Overview of the Diversity of Extremely Saline Soils from a Semi-Arid Region Using 16S rRNA Gene Sequencing: A Case Study of the Sebkhas in Algerian High Plateaus. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722100472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|
3
|
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. Correction: Functional profiling of long intergenic non-coding RNAs in fission yeast. eLife 2022; 11:77337. [PMID: 35085068 PMCID: PMC8794465 DOI: 10.7554/elife.77337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
|
4
|
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
|
5
|
Winkelmüller TM, Entila F, Anver S, Piasecka A, Song B, Dahms E, Sakakibara H, Gan X, Kułak K, Sawikowska A, Krajewski P, Tsiantis M, Garrido-Oter R, Fukushima K, Schulze-Lefert P, Laurent S, Bednarek P, Tsuda K. Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species. Plant Cell 2021; 33:1863-1887. [PMID: 33751107 PMCID: PMC8290292 DOI: 10.1093/plcell/koab073] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/24/2021] [Indexed: 05/20/2023]
Abstract
Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, by employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species to investigate PTI responses, we identified a set of genes that commonly respond to the MAMP flg22 and genes that exhibit species-specific expression signatures. Variation in flg22-triggered transcriptome responses across Brassicaceae species was incongruent with their phylogeny, while expression changes were strongly conserved within A. thaliana. We found the enrichment of WRKY transcription factor binding sites in the 5'-regulatory regions of conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene expression patterns during PTI. Our findings advance our understanding of the evolution of the transcriptome during biotic stress.
Collapse
Affiliation(s)
- Thomas M Winkelmüller
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Frederickson Entila
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Shajahan Anver
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Present address: Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anna Piasecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Baoxing Song
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Present address: Institute for Genomic Diversity, Cornell University, Ithaca, New York
| | - Eik Dahms
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, 230-0045 Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Karolina Kułak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Present address: Department of Computational Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Aneta Sawikowska
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-628 Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany
| | - Paul Schulze-Lefert
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, 430070 Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, 430070 Wuhan, China
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Author for correspondence:
| |
Collapse
|
6
|
Mine A, Nobori T, Salazar-Rondon MC, Winkelmüller TM, Anver S, Becker D, Tsuda K. An incoherent feed-forward loop mediates robustness and tunability in a plant immune network. EMBO Rep 2017; 18:464-476. [PMID: 28069610 DOI: 10.15252/embr.201643051] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/09/2016] [Accepted: 12/08/2016] [Indexed: 01/09/2023] Open
Abstract
Immune signaling networks must be tunable to alleviate fitness costs associated with immunity and, at the same time, robust against pathogen interferences. How these properties mechanistically emerge in plant immune signaling networks is poorly understood. Here, we discovered a molecular mechanism by which the model plant species Arabidopsis thaliana achieves robust and tunable immunity triggered by the microbe-associated molecular pattern, flg22. Salicylic acid (SA) is a major plant immune signal molecule. Another signal molecule jasmonate (JA) induced expression of a gene essential for SA accumulation, EDS5 Paradoxically, JA inhibited expression of PAD4, a positive regulator of EDS5 expression. This incoherent type-4 feed-forward loop (I4-FFL) enabled JA to mitigate SA accumulation in the intact network but to support it under perturbation of PAD4, thereby minimizing the negative impact of SA on fitness as well as conferring robust SA-mediated immunity. We also present evidence for evolutionary conservation of these gene regulations in the family Brassicaceae Our results highlight an I4-FFL that simultaneously provides the immune network with robustness and tunability in A. thaliana and possibly in its relatives.
Collapse
Affiliation(s)
- Akira Mine
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Center for Gene Research, Nagoya University, Chikusa-Ku Nagoya, Japan
| | - Tatsuya Nobori
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Maria C Salazar-Rondon
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Thomas M Winkelmüller
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Shajahan Anver
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dieter Becker
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| |
Collapse
|
7
|
Anver S, Roguev A, Zofall M, Krogan NJ, Grewal SIS, Harmer SL. Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts. EMBO Rep 2014; 15:894-902. [PMID: 24957674 DOI: 10.15252/embr.201438902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Chromatin regulatory proteins affect diverse developmental and environmental response pathways via their influence on nuclear processes such as the regulation of gene expression. Through a genome-wide genetic screen, we implicate a novel protein called X-chromosome-associated protein 5 (Xap5) in chromatin regulation. We show that Xap5 is a chromatin-associated protein acting in a similar manner as the histone variant H2A.Z to suppress expression of antisense and repeat element transcripts throughout the fission yeast genome. Xap5 is highly conserved across eukaryotes, and a plant homolog rescues xap5 mutant yeast. We propose that Xap5 likely functions as a chromatin regulator in diverse organisms.
Collapse
Affiliation(s)
- Shajahan Anver
- Department of Plant Biology, College of Biological Sciences University of California, Davis, CA, USA
| | - Assen Roguev
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Stacey L Harmer
- Department of Plant Biology, College of Biological Sciences University of California, Davis, CA, USA
| |
Collapse
|