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Lühmann KL, Seemann S, Martinek N, Ostendorp S, Kehr J. The glycine-rich domain of GRP7 plays a crucial role in binding long RNAs and facilitating phase separation. Sci Rep 2024; 14:16018. [PMID: 38992080 PMCID: PMC11239674 DOI: 10.1038/s41598-024-66955-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024] Open
Abstract
Microscale thermophoresis (MST) is a well-established method to quantify protein-RNA interactions. In this study, we employed MST to analyze the RNA binding properties of glycine-rich RNA binding protein 7 (GRP7), which is known to have multiple biological functions related to its ability to bind different types of RNA. However, the exact mechanism of GRP7's RNA binding is not fully understood. While the RNA-recognition motif of GRP7 is known to be involved in RNA binding, the glycine-rich region (known as arginine-glycine-glycine-domain or RGG-domain) also influences this interaction. To investigate to which extend the RGG-domain of GRP7 is involved in RNA binding, mutation studies on putative RNA interacting or modulating sites were performed. In addition to MST experiments, we examined liquid-liquid phase separation of GRP7 and its mutants, both with and without RNA. Furthermore, we systemically investigated factors that might affect RNA binding selectivity of GRP7 by testing RNAs of different sizes, structures, and modifications. Consequently, our study revealed that GRP7 exhibits a high affinity for a variety of RNAs, indicating a lack of pronounced selectivity. Moreover, we established that the RGG-domain plays a crucial role in binding longer RNAs and promoting phase separation.
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Affiliation(s)
- Kim Lara Lühmann
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Silja Seemann
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Nina Martinek
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Steffen Ostendorp
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Julia Kehr
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany.
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2
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Burgardt R, Lambert D, Heuwieser C, Sack M, Wagner G, Weinberg Z, Wachter A. Positioning of pyrimidine motifs around cassette exons defines their PTB-dependent splicing in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2202-2218. [PMID: 38578875 DOI: 10.1111/tpj.16739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
Alternative splicing (AS) is a complex process that generates transcript variants from a single pre-mRNA and is involved in numerous biological functions. Many RNA-binding proteins are known to regulate AS; however, little is known about the underlying mechanisms, especially outside the mammalian clade. Here, we show that polypyrimidine tract binding proteins (PTBs) from Arabidopsis thaliana regulate AS of cassette exons via pyrimidine (Py)-rich motifs close to the alternative splice sites. Mutational studies on three PTB-dependent cassette exon events revealed that only some of the Py motifs in this region are critical for AS. Moreover, in vitro binding of PTBs did not reflect a motif's impact on AS in vivo. Our mutational studies and bioinformatic investigation of all known PTB-regulated cassette exons from A. thaliana and human suggested that the binding position of PTBs relative to a cassette exon defines whether its inclusion or skipping is induced. Accordingly, exon skipping is associated with a higher frequency of Py stretches within the cassette exon, and in human also upstream of it, whereas exon inclusion is characterized by increased Py motif occurrence downstream of said exon. Enrichment of Py motifs downstream of PTB-activated 5' splice sites is also seen for PTB-dependent intron removal and alternative 5' splice site events from A. thaliana, suggesting this is a common step of exon definition. In conclusion, the position-dependent AS regulatory mechanism by PTB homologs has been conserved during the separate evolution of plants and mammals, while other critical features, in particular intron length, have considerably changed.
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Affiliation(s)
- Rica Burgardt
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Dorothee Lambert
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Christina Heuwieser
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Maximilian Sack
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Gabriele Wagner
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Andreas Wachter
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
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3
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Loeser J, Bauer J, Janßen K, Rockenbach K, Wachter A. A transient in planta editing assay identifies specific binding of the splicing regulator PTB as a prerequisite for cassette exon inclusion. PLANT MOLECULAR BIOLOGY 2024; 114:22. [PMID: 38443687 PMCID: PMC10914923 DOI: 10.1007/s11103-024-01414-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/31/2023] [Indexed: 03/07/2024]
Abstract
The dynamic interaction of RNA-binding proteins (RBPs) with their target RNAs contributes to the diversity of ribonucleoprotein (RNP) complexes that are involved in a myriad of biological processes. Identifying the RNP components at high resolution and defining their interactions are key to understanding their regulation and function. Expressing fusions between an RBP of interest and an RNA editing enzyme can result in nucleobase changes in target RNAs, representing a recent addition to experimental approaches for profiling RBP/RNA interactions. Here, we have used the MS2 protein/RNA interaction to test four RNA editing proteins for their suitability to detect target RNAs of RBPs in planta. We have established a transient test system for fast and simple quantification of editing events and identified the hyperactive version of the catalytic domain of an adenosine deaminase (hADARcd) as the most suitable editing enzyme. Examining fusions between homologs of polypyrimidine tract binding proteins (PTBs) from Arabidopsis thaliana and hADARcd allowed determining target RNAs with high sensitivity and specificity. Moreover, almost complete editing of a splicing intermediate provided insight into the order of splicing reactions and PTB dependency of this particular splicing event. Addition of sequences for nuclear localisation of the fusion protein increased the editing efficiency, highlighting this approach's potential to identify RBP targets in a compartment-specific manner. Our studies have established the editing-based analysis of interactions between RBPs and their RNA targets in a fast and straightforward assay, offering a new system to study the intricate composition and functions of plant RNPs in vivo.
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Affiliation(s)
- Jorinde Loeser
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Julia Bauer
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Kim Janßen
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Kevin Rockenbach
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Andreas Wachter
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
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4
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Xu F, Wang L, Li Y, Shi J, Staiger D, Yu F. Phase separation of GRP7 facilitated by FERONIA-mediated phosphorylation inhibits mRNA translation to modulate plant temperature resilience. MOLECULAR PLANT 2024; 17:460-477. [PMID: 38327052 DOI: 10.1016/j.molp.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 01/07/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
Changes in ambient temperature profoundly affect plant growth and performance. Therefore, the molecular basis of plant acclimation to temperature fluctuation is of great interest. In this study, we discovered that GLYCINE-RICH RNA-BINDING PROTEIN 7 (GRP7) contributes to cold and heat tolerance in Arabidopsis thaliana. We found that exposure to a warm temperature rapidly induces GRP7 condensates in planta, which can be reversed by transfer to a lower temperature. Cell biology and biochemical assays revealed that GRP7 undergoes liquid-liquid phase separation (LLPS) in vivo and in vitro. LLPS of GRP7 in the cytoplasm contributes to the formation of stress granules that recruit RNA, along with the translation machinery component eukaryotic initiation factor 4E1 (eIF4E1) and the mRNA chaperones COLD SHOCK PROTEIN 1 (CSP1) and CSP3, to inhibit translation. Moreover, natural variations in GRP7 affecting the residue phosphorylated by the receptor kinase FERONIA alter its capacity to undergo LLPS and correlate with the adaptation of some Arabidopsis accessions to a wider temperature range. Taken together, our findings illustrate the role of translational control mediated by GRP7 LLPS to confer plants with temperature resilience.
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Affiliation(s)
- Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China; State Key Laboratory of Hybrid Rice, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, P.R. China
| | - Yingbin Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Junfeng Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China.
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5
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Rieger J, Fitz M, Fischer SM, Wallmeroth N, Flores-Romero H, Fischer NM, Brand LH, García-Sáez AJ, Berendzen KW, Mira-Rodado V. Exploring the Binding Affinity of the ARR2 GARP DNA Binding Domain via Comparative Methods. Genes (Basel) 2023; 14:1638. [PMID: 37628689 PMCID: PMC10454580 DOI: 10.3390/genes14081638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Plants have evolved signaling mechanisms such as the multi-step phosphorelay (MSP) to respond to different internal and external stimuli. MSP responses often result in gene transcription regulation that is modulated through transcription factors such as B-type Arabidopsis response regulator (ARR) proteins. Among these proteins, ARR2 is a key component that is expressed ubiquitously and is involved in many aspects of plant development. Although it has been noted that B-type ARRs bind to their cognate genes through a DNA-binding domain termed the GARP domain, little is known about the structure and function of this type of DNA-binding domain; thus, how ARRs bind to DNA at a structural level is still poorly understood. In order to understand how the MSP functions in planta, it is crucial to unravel both the kinetics as well as the structural identity of the components involved in such interactions. For this reason, this work focusses on resolving how the GARP domain of ARR2 (GARP2) binds to the promoter region of ARR5, one of its native target genes in cytokinin signaling. We have established that GARP2 specifically binds to the ARR5 promoter with three different bi-molecular interaction systems-qDPI-ELISA, FCS, and MST-and we also determined the KD of this interaction. In addition, structural modeling of the GARP2 domain confirms that GARP2 entails a HTH motif, and that protein-DNA interaction most likely occurs via the α3-helix and the N-terminal arm of this domain since mutations in this region hinder ARR2's ability to activate transcription.
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Affiliation(s)
- Janine Rieger
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Michael Fitz
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Stefan Markus Fischer
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Niklas Wallmeroth
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Hector Flores-Romero
- Interfaculty Institute of Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
- CECAD Research Center, Institute of Genetics, Cologne University, 51069 Cologne, Germany
| | - Nina Monika Fischer
- Institute for Bioinformatics and Medical Informatics, Tübingen University, 72076 Tübingen, Germany
| | - Luise Helene Brand
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Ana J. García-Sáez
- Interfaculty Institute of Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
- CECAD Research Center, Institute of Genetics, Cologne University, 51069 Cologne, Germany
| | | | - Virtudes Mira-Rodado
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
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6
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Köster T, Meyer K. Plant Ribonomics: Proteins in Search of RNA Partners. TRENDS IN PLANT SCIENCE 2018; 23:352-365. [PMID: 29429586 DOI: 10.1016/j.tplants.2018.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/08/2018] [Accepted: 01/15/2018] [Indexed: 06/08/2023]
Abstract
Research into the regulation of gene expression underwent a shift from focusing on DNA-binding proteins as key transcriptional regulators to RNA-binding proteins (RBPs) that come into play once transcription has been initiated. RBPs orchestrate all RNA-processing steps in the cell. To obtain a global view of in vivo targets, the RNA complement associated with particular RBPs is determined via immunoprecipitation of the RBP and subsequent identification of bound RNAs via RNA-seq. Here, we describe technical advances in identifying RBP in vivo targets and their binding motifs. We provide an up-to-date view of targets of nucleocytoplasmic RBPs collected in arabidopsis. We also discuss current experimental limitations and provide an outlook on how the approaches may advance our understanding of post-transcriptional networks.
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Affiliation(s)
- Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany.
| | - Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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7
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Meyer K, Köster T, Nolte C, Weinholdt C, Lewinski M, Grosse I, Staiger D. Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7. Genome Biol 2017; 18:204. [PMID: 29084609 PMCID: PMC5663106 DOI: 10.1186/s13059-017-1332-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022] Open
Abstract
Background Functions for RNA-binding proteins in orchestrating plant development and environmental responses are well established. However, the lack of a genome-wide view of their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we adapt individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) genome-wide to determine the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7. Results iCLIP identifies 858 transcripts with significantly enriched crosslink sites in plants expressing AtGRP7-GFP that are absent in plants expressing an RNA-binding-dead AtGRP7 variant or GFP alone. To independently validate the targets, we performed RNA immunoprecipitation (RIP)-sequencing of AtGRP7-GFP plants subjected to formaldehyde fixation. Of the iCLIP targets, 452 were also identified by RIP-seq and represent a set of high-confidence binders. AtGRP7 can bind to all transcript regions, with a preference for 3′ untranslated regions. In the vicinity of crosslink sites, U/C-rich motifs are overrepresented. Cross-referencing the targets against transcriptome changes in AtGRP7 loss-of-function mutants or AtGRP7-overexpressing plants reveals a predominantly negative effect of AtGRP7 on its targets. In particular, elevated AtGRP7 levels lead to damping of circadian oscillations of transcripts, including DORMANCY/AUXIN ASSOCIATED FAMILY PROTEIN2 and CCR-LIKE. Furthermore, several targets show changes in alternative splicing or polyadenylation in response to altered AtGRP7 levels. Conclusions We have established iCLIP for plants to identify target transcripts of the RNA-binding protein AtGRP7. This paves the way to investigate the dynamics of posttranscriptional networks in response to exogenous and endogenous cues. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1332-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Christine Nolte
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Claus Weinholdt
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Martin Lewinski
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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8
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Köster T, Marondedze C, Meyer K, Staiger D. RNA-Binding Proteins Revisited - The Emerging Arabidopsis mRNA Interactome. TRENDS IN PLANT SCIENCE 2017; 22:512-526. [PMID: 28412036 DOI: 10.1016/j.tplants.2017.03.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/10/2017] [Accepted: 03/09/2017] [Indexed: 06/07/2023]
Abstract
RNA-protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture - where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.
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Affiliation(s)
- Tino Köster
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Claudius Marondedze
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Cambridge, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Katja Meyer
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany.
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9
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Ihsan MZ, Ahmad SJN, Shah ZH, Rehman HM, Aslam Z, Ahuja I, Bones AM, Ahmad JN. Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:233. [PMID: 28289422 PMCID: PMC5326801 DOI: 10.3389/fpls.2017.00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/07/2017] [Indexed: 05/29/2023]
Abstract
The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plant's sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.
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Affiliation(s)
- Muhammad Z. Ihsan
- Cholistan Institute of Desert Studies, The Islamia University BahawalpurBahawalpur, Pakistan
| | - Samina J. N. Ahmad
- Plant Stress Physiology and Molecular Biology Lab, Department of Botany, University of Agriculture FaisalabadFaisalabad, Pakistan
- Integrated Genomics Cellular Developmental and Biotechnology Lab, Department of Entomology, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, Faculty of Meteorology, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Hafiz M. Rehman
- Department of Electronic and Biomedical Engineering, Chonnam National UniversityGwangju, South Korea
| | - Zubair Aslam
- Department of Agronomy, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Ishita Ahuja
- Department of Biology, Norwegian University of Science and TechnologyTrondheim, Norway
| | - Atle M. Bones
- Department of Biology, Norwegian University of Science and TechnologyTrondheim, Norway
| | - Jam N. Ahmad
- Plant Stress Physiology and Molecular Biology Lab, Department of Botany, University of Agriculture FaisalabadFaisalabad, Pakistan
- Integrated Genomics Cellular Developmental and Biotechnology Lab, Department of Entomology, University of Agriculture FaisalabadFaisalabad, Pakistan
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10
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Li X, Xing J, Qiu Z, He Q, Lin J. Quantification of Membrane Protein Dynamics and Interactions in Plant Cells by Fluorescence Correlation Spectroscopy. MOLECULAR PLANT 2016; 9:1229-1239. [PMID: 27381442 DOI: 10.1016/j.molp.2016.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/25/2016] [Accepted: 06/27/2016] [Indexed: 05/25/2023]
Abstract
Deciphering the dynamics of protein and lipid molecules on appropriate spatial and temporal scales may shed light on protein function and membrane organization. However, traditional bulk approaches cannot unambiguously quantify the extremely diverse mobility and interactions of proteins in living cells. Fluorescence correlation spectroscopy (FCS) is a powerful technique to describe events that occur at the single-molecule level and on the nanosecond to second timescales; therefore, FCS can provide data on the heterogeneous organization of membrane systems. FCS can also be combined with other microscopy techniques, such as super-resolution techniques. More importantly, FCS is minimally invasive, which makes it an ideal approach to detect the heterogeneous distribution and dynamics of key proteins during development. In this review, we give a brief introduction about the development of FCS and summarize the significant contributions of FCS in understanding the organization of plant cell membranes and the dynamics and interactions of membrane proteins. We also discuss the potential applications of this technique in plant biology.
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Affiliation(s)
- Xiaojuan Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jingjing Xing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 10049, China
| | - Zongbo Qiu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qihua He
- The Health Science Center, Peking University, Beijing 100191, China
| | - Jinxing Lin
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
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11
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Lewinski M, Hallmann A, Staiger D. Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues. Mol Genet Genomics 2015; 291:763-73. [DOI: 10.1007/s00438-015-1144-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/06/2015] [Indexed: 11/28/2022]
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12
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Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia. Proc Natl Acad Sci U S A 2015; 112:E5401-10. [PMID: 26324889 DOI: 10.1073/pnas.1514883112] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wheat varieties with a winter growth habit require long exposures to low temperatures (vernalization) to accelerate flowering. Natural variation in four vernalization genes regulating this requirement has favored wheat adaptation to different environments. The first three genes (VRN1-VRN3) have been cloned and characterized before. Here we show that the fourth gene, VRN-D4, originated by the insertion of a ∼290-kb region from chromosome arm 5AL into the proximal region of chromosome arm 5DS. The inserted 5AL region includes a copy of VRN-A1 that carries distinctive mutations in its coding and regulatory regions. Three lines of evidence confirmed that this gene is VRN-D4: it cosegregated with VRN-D4 in a high-density mapping population; it was expressed earlier than other VRN1 genes in the absence of vernalization; and induced mutations in this gene resulted in delayed flowering. VRN-D4 was found in most accessions of the ancient subspecies Triticum aestivum ssp. sphaerococcum from South Asia. This subspecies showed a significant reduction of genetic diversity and increased genetic differentiation in the centromeric region of chromosome 5D, suggesting that VRN-D4 likely contributed to local adaptation and was favored by positive selection. Three adjacent SNPs in a regulatory region of the VRN-D4 first intron disrupt the binding of GLYCINE-RICH RNA-BINDING PROTEIN 2 (TaGRP2), a known repressor of VRN1 expression. The same SNPs were identified in VRN-A1 alleles previously associated with reduced vernalization requirement. These alleles can be used to modulate vernalization requirements and to develop wheat varieties better adapted to different or changing environments.
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Nolte C, Staiger D. RNA around the clock - regulation at the RNA level in biological timing. FRONTIERS IN PLANT SCIENCE 2015; 6:311. [PMID: 25999975 PMCID: PMC4419606 DOI: 10.3389/fpls.2015.00311] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/19/2015] [Indexed: 05/21/2023]
Abstract
The circadian timing system in plants synchronizes their physiological functions with the environment. This is achieved by a global control of gene expression programs with a considerable part of the transcriptome undergoing 24-h oscillations in steady-state abundance. These circadian oscillations are driven by a set of core clock proteins that generate their own 24-h rhythm through periodic feedback on their own transcription. Additionally, post-transcriptional events are instrumental for oscillations of core clock genes and genes in clock output. Here we provide an update on molecular events at the RNA level that contribute to the 24-h rhythm of the core clock proteins and shape the circadian transcriptome. We focus on the circadian system of the model plant Arabidopsis thaliana but also discuss selected regulatory principles in other organisms.
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Affiliation(s)
| | - Dorothee Staiger
- *Correspondence: Dorothee Staiger, Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Universitaetsstrasse 25, Bielefeld D-33615, Germany
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