1
|
Ren D, Liu H, Sun X, Zhang F, Jiang L, Wang Y, Jiang N, Yan P, Cui J, Yang J, Li Z, Lu P, Luo X. Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:66-85. [PMID: 37970747 DOI: 10.1111/jipb.13583] [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: 06/03/2023] [Revised: 09/29/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023]
Abstract
RNA-binding proteins (RBPs) are components of the post-transcriptional regulatory system, but their regulatory effects on complex traits remain unknown. Using an integrated strategy involving map-based cloning, functional characterizations, and transcriptomic and population genomic analyses, we revealed that RBP-K (LOC_Os08g23120), RBP-A (LOC_Os11g41890), and RBP-J (LOC_Os10g33230) encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits. Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally. Additionally, RBP-J most likely affects GA pathways, resulting in considerable increases in grain and panicle lengths, but decreases in grain width and thickness. In contrast, RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport, with substantial effects on the rice grain filling process as well as grain length and weight. Evolutionarily, RBP-K is relatively ancient and highly conserved, whereas RBP-J and RBP-A are more diverse. Thus, the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency, efficiency, and versatility, as well as increased evolutionary potential. Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits. Furthermore, rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.
Collapse
Affiliation(s)
- Ding Ren
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hui Liu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xuejun Sun
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Fan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Ling Jiang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Peiwen Yan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinhao Cui
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zhikang Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Pingli Lu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| |
Collapse
|
2
|
Lachke SA. RNA-binding proteins and post-transcriptional regulation in lens biology and cataract: Mediating spatiotemporal expression of key factors that control the cell cycle, transcription, cytoskeleton and transparency. Exp Eye Res 2022; 214:108889. [PMID: 34906599 PMCID: PMC8792301 DOI: 10.1016/j.exer.2021.108889] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023]
Abstract
Development of the ocular lens - a transparent tissue capable of sustaining frequent shape changes for optimal focusing power - pushes the boundaries of what cells can achieve using the molecular toolkit encoded by their genomes. The mammalian lens contains broadly two types of cells, the anteriorly located monolayer of epithelial cells which, at the equatorial region of the lens, initiate differentiation into fiber cells that contribute to the bulk of the tissue. This differentiation program involves massive upregulation of select fiber cell-expressed RNAs and their subsequent translation into high amounts of proteins, such as crystallins. But intriguingly, fiber cells achieve this while also simultaneously undergoing significant morphological changes such as elongation - involving about 1000-fold length-wise increase - and migration, which requires modulation of cytoskeletal and cell adhesion factors. Adding further to the challenges, these molecular and cellular events have to be coordinated as fiber cells progress toward loss of their nuclei and organelles, which irreversibly compromises their potential for harnessing genetically hardwired information. A long-standing question is how processes downstream of signaling and transcription, which may also participate in feedback regulation, contribute toward orchestrating these cellular differentiation events in the lens. It is now becoming clear from findings over the past decade that post-transcriptional gene expression regulatory mechanisms are critical in controlling cellular proteomes and coordinating key processes in lens development and fiber cell differentiation. Indeed, RNA-binding proteins (RBPs) such as Caprin2, Celf1, Rbm24 and Tdrd7 have now been described in mediating post-transcriptional control over key factors (e.g. Actn2, Cdkn1a (p21Cip1), Cdkn1b (p27Kip1), various crystallins, Dnase2b, Hspb1, Pax6, Prox1, Sox2) that are variously involved in cell cycle, transcription, cytoskeleton maintenance and differentiation in the lens. Furthermore, deficiencies of these RBPs have been shown to result in various eye and lens defects and/or cataract. Because fiber cell differentiation in the lens occurs throughout life, the underlying regulatory mechanisms operational in development are expected to also be recruited for the maintenance of transparency in aged lenses. Indeed, in support of this, TDRD7 and CAPRIN2 loci have been linked to age-related cataract in humans. Here, I will review the role of key RBPs in the lens and their importance in understanding the pathology of lens defects. I will discuss advances in RBP-based gene expression control, in general, and the important challenges that need to be addressed in the lens to define the mechanisms that determine the epithelial and fiber cell proteome. Finally, I will also discuss in detail several key future directions including the application of bioinformatics approaches such as iSyTE to study RBP-based post-transcriptional gene expression control in the aging lens and in the context of age-related cataract.
Collapse
Affiliation(s)
- Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA.
| |
Collapse
|
3
|
Kumar S, Lande NV, Barua P, Pareek A, Chakraborty S, Chakraborty N. Proteomic dissection of rice cytoskeleton reveals the dominance of microtubule and microfilament proteins, and novel components in the cytoskeleton-bound polysome. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:75-86. [PMID: 34861586 DOI: 10.1016/j.plaphy.2021.11.037] [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: 09/16/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The plant cytoskeleton persistently undergoes remodeling to achieve its roles in supporting cell division, differentiation, cell expansion and organelle transport. However, the links between cell metabolism and cytoskeletal networks, particularly how the proteinaceous components execute such processes remain poorly understood. We investigated the cytoskeletal proteome landscape of rice to gain better understanding of such events. Proteins were extracted from highly enriched cytoskeletal fraction of four-week-old rice seedlings, and the purity of the fraction was stringently monitored. A total of 2577 non-redundant proteins were identified using both gel-based and gel-free approaches, which constitutes the most comprehensive dataset, thus far, for plant cytoskeleton. The data set includes both microtubule and microfilament-associated proteins and their binding proteins comprising hypothetical as well as novel cytoskeletal proteins. Further, various in-silico analyses were performed, and the proteins were functionally classified on the basis of their gene ontology. The catalogued proteins were validated through their sequence analysis. Extensive comparative analysis of our dataset with the non-redundant set of cytoskeletal proteins across plant species affirms unique as well as overlapping candidates. Together, these findings unveil new insights of how cytoskeletons undergo dynamic remodeling in rice to drive seedling development processes in rapidly changing in planta environment.
Collapse
Affiliation(s)
- Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nilesh Vikram Lande
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Pragya Barua
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akanksha Pareek
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
4
|
Lee Y, Okita TW, Szymanski DB. A co-fractionation mass spectrometry-based prediction of protein complex assemblies in the developing rice aleurone-subaleurone. THE PLANT CELL 2021; 33:2965-2980. [PMID: 34270775 PMCID: PMC8462808 DOI: 10.1093/plcell/koab182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Multiprotein complexes execute and coordinate diverse cellular processes such as organelle biogenesis, vesicle trafficking, cell signaling, and metabolism. Knowledge about their composition and localization provides useful clues about the mechanisms of cellular homeostasis and system-level control. This is of great biological importance and practical significance in heterotrophic rice (Oryza sativa) endosperm and aleurone-subaleurone tissues, which are a primary source of seed vitamins and stored energy. Dozens of protein complexes have been implicated in the synthesis, transport, and storage of seed proteins, lipids, vitamins, and minerals. Mutations in protein complexes that control RNA transport result in aberrant endosperm with shrunken and floury phenotypes, significantly reducing seed yield and quality. The purpose of this study was to broadly predict protein complex composition in the aleurone-subaleurone layers of developing rice seeds using co-fractionation mass spectrometry. Following orthogonal chromatographic separations of biological replicates, thousands of protein elution profiles were subjected to distance-based clustering to enable large-scale multimerization state measurements and protein complex predictions. The predicted complexes had predicted functions across diverse functional categories, including novel heteromeric RNA binding protein complexes that may influence seed quality. This effective and open-ended proteomics pipeline provides useful clues about system-level posttranslational control during the early stages of rice seed development.
Collapse
Affiliation(s)
- Youngwoo Lee
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Thomas W. Okita
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Daniel B. Szymanski
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| |
Collapse
|
5
|
He D, Li M, Damaris RN, Bu C, Xue J, Yang P. Quantitative ubiquitylomics approach for characterizing the dynamic change and extensive modulation of ubiquitylation in rice seed germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1430-1447. [PMID: 31677306 DOI: 10.1111/tpj.14593] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/26/2019] [Accepted: 10/16/2019] [Indexed: 05/22/2023]
Abstract
During seed germination, cells embark on extensive post-transcriptional and post-translational modifications (PTM), providing a perfect platform to study these events in embryo rebooting from relative quiescenct to highly active state. PR-619, a deubiquitylase inhibitor, delayed the rice seed germination and resulted in the accumulation of ubiquitylated proteins, which indicated the protein ubiquitylation is involved in this process. Using the K-Ɛ-GG antibody enrichment method integrated with high-resolution mass spectrometry, a list of 2576 lysine ubiquitylated (Kub) sites in 1171 proteins was compiled for rice embryos at 0, 12 and 24 h after imbibition (HAI). Of these, the abundance of 1419 Kub sites in 777 proteins changed significantly. Most of them substantially increased within the first 12 HAI, which is similar to the dynamic state previously observed for protein phosphorylation, implying that the first 12 HAI are essential for subsequent switch during rice seed germination. We also quantitatively analyzed the embryo proteome in these samples. Generally, a specific protein's abundance in the ubiquitylome was uncorrelated to that in the proteome. The differentially ubiquitinated proteins were greatly enriched in the categories of protein processing, DNA and RNA processing/regulation related, signaling, and transport. The DiGly footprint of the Kub sites was significantly reduced on K48, a linkage typically associated with proteasome-mediated degradation. These observations suggest ubiquitylation may modulate the protein function more than providing 26S degradation signals in the early stage of rice seed germination. Revealing this comprehensive ubiquitylome greatly increases our understanding of this critical PTM during seed germination.
Collapse
Affiliation(s)
- Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Rebecca N Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, 310018, China
| | - Jianyou Xue
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, 310018, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| |
Collapse
|
6
|
Chou HL, Tian L, Fukuda M, Kumamaru T, Okita TW. The Role of RNA-Binding Protein OsTudor-SN in Post-Transcriptional Regulation of Seed Storage Proteins and Endosperm Development. PLANT & CELL PHYSIOLOGY 2019; 60:2193-2205. [PMID: 31198964 DOI: 10.1093/pcp/pcz113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 05/28/2019] [Indexed: 05/28/2023]
Abstract
Tudor-SN is involved in a myriad of transcriptional and post-transcriptional processes due to its modular structure consisting of 4 tandem SN domains (4SN module) and C-terminal Tsn module consisting of Tudor-partial SN domains. We had previously demonstrated that OsTudor-SN is a key player for transporting storage protein mRNAs to specific ER subdomains in developing rice endosperm. Here, we provide genetic evidence that this multifunctional RBP is required for storage protein expression, seed development and protein body formation. The rice EM1084 line, possessing a nonsynonymous mutation in the 4SN module (SN3 domain), exhibited a strong reduction in grain weight and storage protein accumulation, while a mutation in the Tudor domain (47M) or the loss of the Tsn module (43M) had much smaller effects. Immunoelectron microscopic analysis showed the presence of a new protein body type containing glutelin and prolamine inclusions in EM1084, while 43M and 47M exhibited structurally modified prolamine and glutelin protein bodies. Transcriptome analysis indicates that OsTudor-SN also functions in regulating gene expression of transcriptional factors and genes involved in developmental processes and stress responses as well as for storage proteins. Normal protein body formation, grain weight and expression of many genes were partially restored in EM1084 transgenic line complemented with wild-type OsTudor-SN gene. Overall, our study showed that OsTudor-SN possesses multiple functional properties in rice storage protein expression and seed development and that the 4SN and Tsn modules have unique roles in these processes.
Collapse
Affiliation(s)
- Hong-Li Chou
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, DC, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, DC, USA
| | - Masako Fukuda
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, DC, USA
- Plant Genetics Laboratory, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, Japan
| | - Toshihiro Kumamaru
- Plant Genetics Laboratory, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, Japan
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, DC, USA
| |
Collapse
|
7
|
Chou HL, Tian L, Washida H, Fukuda M, Kumamaru T, Okita TW. The rice storage protein mRNAs as a model system for RNA localization in higher plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 284:203-211. [PMID: 31084873 DOI: 10.1016/j.plantsci.2019.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
The transport and targeting of mRNAs to specific intracellular locations is a ubiquitous process in prokaryotic and eukaryotic organisms. Despite the prevalent nature of RNA localization in guiding development, differentiation, cellular movement and intracellular organization of biochemical activities, only a few examples exist in higher plants. Here, we summarize past studies on mRNA-based protein targeting to specific subdomains of the cortical endoplasmic reticulum (ER) using the rice storage protein mRNAs as a model. Such studies have demonstrated that there are multiple pathways of RNA localization to the cortical ER that are controlled by cis-determinants (zipcodes) on the mRNA. These zipcode sequences are recognized by specific RNA binding proteins organized into multi-protein complexes. The available evidence suggests mRNAs are transported to their destination sites by co-opting membrane trafficking factors. Lastly, we discuss the major gaps in our knowledge on RNA localization and how information on the targeting of storage protein mRNAs can be used to further our understanding on how plant mRNAs are organized into regulons to facilitate protein localization and formation of multi-protein complexes.
Collapse
Affiliation(s)
- Hong-Li Chou
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States
| | - Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States
| | - Haruhiko Washida
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States
| | - Masako Fukuda
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States; Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395, Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395, Japan
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States.
| |
Collapse
|
8
|
Comparative proteomic analysis of the shoot apical meristem in maize between a ZmCCT-associated near-isogenic line and its recurrent parent. Sci Rep 2016; 6:30641. [PMID: 27468931 PMCID: PMC4965789 DOI: 10.1038/srep30641] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/07/2016] [Indexed: 11/27/2022] Open
Abstract
The ZmCCT, one of the most important genes affecting photoperiod response, delays flowering under long-day conditions in maize (Zea mays). In this study we used the isobaric tags for relative and absolute quantification (iTRAQ) technique-based proteomics approach to identify differentially expressed proteins between a near-isogenic line (NIL) and its recurrent parent, contrasting in alleles of ZmCCT. A total of 5,259 distinct proteins were identified. Among them, 386 proteins were differentially expressed between NIL-cml line (ZmCCT-positive) and H4 line (ZmCCT-negative). Functional categorization showed that the differentially proteins were mainly involved in energy production, photosynthesis, signal transduction, and cell organization and biogenesis. Our results showed that during shoot apical meristem (SAM) development cell division proteins, carbohydrate metabolism–related proteins, and flower inhibition-related proteins were more abundant in the ZmCCT-positive line than the ZmCCT-negative line. These results, taken together with morphological observations, showed that the effect of ZmCCT on flowering might be caused by its effect on one or all of these biological processes. Although the exact roles of these putative related proteins remain to be examined, our results obtained using the proteomics approach lead to a better understanding of the photoperiodicity mechanism in maize plants.
Collapse
|
9
|
Offermann S, Friso G, Doroshenk KA, Sun Q, Sharpe RM, Okita TW, Wimmer D, Edwards GE, van Wijk KJ. Developmental and Subcellular Organization of Single-Cell C₄ Photosynthesis in Bienertia sinuspersici Determined by Large-Scale Proteomics and cDNA Assembly from 454 DNA Sequencing. J Proteome Res 2015; 14:2090-108. [PMID: 25772754 DOI: 10.1021/pr5011907] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Kranz C4 species strictly depend on separation of primary and secondary carbon fixation reactions in different cell types. In contrast, the single-cell C4 (SCC4) species Bienertia sinuspersici utilizes intracellular compartmentation including two physiologically and biochemically different chloroplast types; however, information on identity, localization, and induction of proteins required for this SCC4 system is currently very limited. In this study, we determined the distribution of photosynthesis-related proteins and the induction of the C4 system during development by label-free proteomics of subcellular fractions and leaves of different developmental stages. This was enabled by inferring a protein sequence database from 454 sequencing of Bienertia cDNAs. Large-scale proteome rearrangements were observed as C4 photosynthesis developed during leaf maturation. The proteomes of the two chloroplasts are different with differential accumulation of linear and cyclic electron transport components, primary and secondary carbon fixation reactions, and a triose-phosphate shuttle that is shared between the two chloroplast types. This differential protein distribution pattern suggests the presence of a mRNA or protein-sorting mechanism for nuclear-encoded, chloroplast-targeted proteins in SCC4 species. The combined information was used to provide a comprehensive model for NAD-ME type carbon fixation in SCC4 species.
Collapse
Affiliation(s)
- Sascha Offermann
- †Institute of Botany, Leibniz University, Herrenhaeuser Strasse 2, Hannover 30419, Germany
| | - Giulia Friso
- ‡Department of Plant Biology, Cornell University, 332 Emerson Hall, Ithaca, New York 14853, United States
| | - Kelly A Doroshenk
- §Institute of Biological Chemistry, Washington State University, 299 Clark Hall, Pullman, Washington 99164, United States
| | - Qi Sun
- ∥Computational Biology Service Unit, Cornell University, 618 Rhodes Hall, Ithaca, New York 14853, United States
| | - Richard M Sharpe
- ⊥School of Biological Science, Washington State University, 303 Heald Hall, Pullman, Washington 99164, United States
| | - Thomas W Okita
- §Institute of Biological Chemistry, Washington State University, 299 Clark Hall, Pullman, Washington 99164, United States
| | - Diana Wimmer
- †Institute of Botany, Leibniz University, Herrenhaeuser Strasse 2, Hannover 30419, Germany
| | - Gerald E Edwards
- ⊥School of Biological Science, Washington State University, 303 Heald Hall, Pullman, Washington 99164, United States
| | - Klaas J van Wijk
- ‡Department of Plant Biology, Cornell University, 332 Emerson Hall, Ithaca, New York 14853, United States
| |
Collapse
|
10
|
Li M, He X, Liu H, Fu Z, He X, Lu X. Proteomic analysis of silkworm midgut cellular proteins interacting with the 5' end of infectious flacherie virus genomic RNA. Acta Biochim Biophys Sin (Shanghai) 2015; 47:80-90. [PMID: 25534780 DOI: 10.1093/abbs/gmu119] [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] [Indexed: 11/15/2022] Open
Abstract
The flacherie disease in the silkworm is caused by the infectious flacherie virus (IFV). IFV relies on its 5' region of genomic RNA to recruit host-related factors to implement viral translation and replication. To identify host proteins bound to the 5'-region of IFV RNA and identify proteins important for its function, mass spectrometry was used to identify proteins from silkworm midgut extracts that were obtained using RNA aptamer-labeled 5' region of IFV RNA. We found 325 protein groups (unique peptide≥2) bound to the 5' region of IFV RNA including translation-related factors (16 ribosomal subunits, 3 eukaryotic initiation factor subunits, 1 elongation factor subunit and 6 potential internal ribosome entry site trans-acting factors), cytoskeleton-related proteins, membrane-related proteins, metabolism enzymes, and other proteins. These results can be used to study the translation and replication related factors of IFV interacting with host silkworm and to control flacherie disease in silkworm.
Collapse
Affiliation(s)
- Mingqian Li
- Silkworm Pathology and Disease Control Laboratory, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinyi He
- Silkworm Pathology and Disease Control Laboratory, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Han Liu
- Silkworm Pathology and Disease Control Laboratory, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhangwuke Fu
- Silkworm Pathology and Disease Control Laboratory, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiangkang He
- Silkworm Pathology and Disease Control Laboratory, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xingmeng Lu
- Silkworm Pathology and Disease Control Laboratory, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
11
|
Tian L, Okita TW. mRNA-based protein targeting to the endoplasmic reticulum and chloroplasts in plant cells. CURRENT OPINION IN PLANT BIOLOGY 2014; 22:77-85. [PMID: 25282588 DOI: 10.1016/j.pbi.2014.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/06/2014] [Accepted: 09/15/2014] [Indexed: 05/12/2023]
Abstract
The targeting of proteins to subcellular organelles is specified by the presence of signal/leader peptide sequences normally located on the N-terminus. In the past two decades, messenger RNA (mRNA) localization, a pathway driven by cis-acting localization elements within the RNA sequence, has emerged as an alternative mechanism for protein targeting to specific locations in the cytoplasm, on the endoplasmic reticulum or to mitochondria and chloroplasts. In this review, we will summarize studies on mRNA-based protein targeting to the endoplasmic reticulum and chloroplast within plant cells.
Collapse
Affiliation(s)
- Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA.
| |
Collapse
|
12
|
Yeap WC, Namasivayam P, Ho CL. HnRNP-like proteins as post-transcriptional regulators. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 227:90-100. [PMID: 25219311 DOI: 10.1016/j.plantsci.2014.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 05/23/2023]
Abstract
Plant cells contain a diverse repertoire of RNA-binding proteins (RBPs) that coordinate a network of post-transcriptional regulation. RBPs govern diverse developmental processes by modulating the gene expression of specific transcripts. Recent gene annotation and RNA sequencing clearly showed that heterogeneous nuclear ribonucleoprotein (hnRNP)-like proteins which form a family of RBPs, are also expressed in higher plants and serve specific plant functions. In addition to their involvement in post-transcriptional regulation from mRNA capping to translation, they are also involved in telomere regulation, gene silencing and regulation in chloroplast. Here, we review the involvement of plant hnRNP-like proteins in post-transcription regulation of RNA processes and their functional roles in control of plant developmental processes especially plant-specific functions including flowering, chloroplastic-specific mRNA regulation, long-distance phloem transportation and plant responses to environmental stresses.
Collapse
Affiliation(s)
- Wan-Chin Yeap
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Sime Darby Technology Centre Sdn. Bhd., 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Parameswari Namasivayam
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Chai-Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| |
Collapse
|
13
|
Doroshenk KA, Tian L, Crofts AJ, Kumamaru T, Okita TW. Characterization of RNA binding protein RBP-P reveals a possible role in rice glutelin gene expression and RNA localization. PLANT MOLECULAR BIOLOGY 2014; 85:381-394. [PMID: 24682961 DOI: 10.1007/s11103-014-0191-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/22/2014] [Indexed: 06/03/2023]
Abstract
RNA binding proteins (RBPs) play an important role in mRNA metabolism including synthesis, maturation, transport, localization, and stability. In developing rice seeds, RNAs that code for the major storage proteins are transported to specific domains of the cortical endoplasmic reticulum (ER) by a regulated mechanism requiring RNA cis-localization elements, or zipcodes. Putative trans-acting RBPs that recognize prolamine RNA zipcodes required for restricted localization to protein body-ER have previously been identified. Here, we describe the identification of RBP-P using a Northwestern blot approach as an RBP that recognizes and binds to glutelin zipcode RNA, which is required for proper RNA localization to cisternal-ER. RBP-P protein expression coincides with that of glutelin during seed maturation and is localized to both the nucleus and cytosol. RNA-immunoprecipitation and subsequent RT-PCR analysis further demonstrated that RBP-P interacts with glutelin RNAs. In vitro RNA-protein UV-crosslinking assays showed that recombinant RBP-P binds strongly to glutelin mRNA, and in particular, 3' UTR and zipcode RNA. RBP-P also exhibited strong binding activity to a glutelin intron sequence, suggesting that RBP-P might participate in mRNA splicing. Overall, these results support a multifunctional role for RBP-P in glutelin mRNA metabolism, perhaps in nuclear pre-mRNA splicing and cytosolic localization to the cisternal-ER.
Collapse
Affiliation(s)
- Kelly A Doroshenk
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | | | | | | | | |
Collapse
|
14
|
Kim SR, An G. Rice chloroplast-localized heat shock protein 70, OsHsp70CP1, is essential for chloroplast development under high-temperature conditions. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:854-63. [PMID: 23394789 DOI: 10.1016/j.jplph.2013.01.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/06/2013] [Accepted: 01/11/2013] [Indexed: 05/20/2023]
Abstract
Heat is a primary abiotic stress that reduces crop yields. At the seedling stage, we identified heat-sensitive mutants that carried T-DNA inserted into a heat shock protein 70 gene, OsHsp70CP1. When grown under a constant high temperature (40°C), the seedling leaves developed severe chlorosis whereas plants grown at a constant 27°C showed a normal phenotype. This indicated that OsHsp70CP1 is essential for chloroplast differentiation from the proplastids under high temperatures. Transient expression analyses revealed that OsHsp70CP1 was localized to the stroma. OsHsp70CP1 was dominantly expressed in photosynthetic tissues; transcripts were greatly increased by heat stress. Some transcripts for plastid RNA metabolism were impaired in the mutant while others were not, demonstrating that a subset of nuclear-encoded proteins are substrates of OsHsp70CP1.
Collapse
Affiliation(s)
- Sung-Ryul Kim
- Crop Biotech Institute & Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Republic of Korea
| | | |
Collapse
|
15
|
Deng ZY, Gong CY, Wang T. Use of proteomics to understand seed development in rice. Proteomics 2013; 13:1784-800. [DOI: 10.1002/pmic.201200389] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/24/2012] [Accepted: 01/07/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Zhu Yun Deng
- Key Laboratory of Plant Molecular Physiology; Institute of Botany; Chinese Academy of Sciences; Haidianqu Beijing China
| | - Chun Yan Gong
- Key Laboratory of Plant Molecular Physiology; Institute of Botany; Chinese Academy of Sciences; Haidianqu Beijing China
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology; Institute of Botany; Chinese Academy of Sciences; Haidianqu Beijing China
| |
Collapse
|
16
|
Schönberger J, Hammes UZ, Dresselhaus T. In vivo visualization of RNA in plants cells using the λN₂₂ system and a GATEWAY-compatible vector series for candidate RNAs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:173-81. [PMID: 22268772 DOI: 10.1111/j.1365-313x.2012.04923.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The past decade has seen a tremendous increase in RNA research, which has demonstrated that RNAs are involved in many more processes than were previously thought. The dynamics of RNA synthesis towards their regulated activity requires the interplay of RNAs with numerous RNA binding proteins (RBPs). The localization of RNA, a mechanism for controlling translation in a spatial and temporal fashion, requires processing and assembly of RNA into transport granules in the nucleus, transport towards cytoplasmic destinations and regulation of its activity. Compared with animal model systems little is known about RNA dynamics and motility in plants. Commonly used methods to study RNA transport and localization are time-consuming, and require expensive equipment and a high level of experimental skill. Here, we introduce the λN₂₂ RNA stem-loop binding system for the in vivo visualization of RNA in plant cells. The λN₂₂ system consists of two components: the λN₂₂ RNA binding peptide and the corresponding box-B stem loops. We generated fusions of λN₂₂ to different fluorophores and a GATEWAY vector series for the simple fusion of any target RNA 5' or 3' to box-B stem loops. We show that the λN₂₂ system can be used to detect RNAs in transient expression assays, and that it offers advantages compared with the previously described MS2 system. Furthermore, the λN₂₂ system can be used in combination with the MS2 system to visualize different RNAs simultaneously in the same cell. The toolbox of vectors generated for both systems is easy to use and promises significant progress in our understanding of RNA transport and localization in plant cells.
Collapse
Affiliation(s)
- Johannes Schönberger
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | | | | |
Collapse
|
17
|
Davies E, Stankovic B, Vian A, Wood AJ. Where has all the message gone? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 185-186:23-32. [PMID: 22325863 DOI: 10.1016/j.plantsci.2011.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 08/09/2011] [Accepted: 08/10/2011] [Indexed: 05/31/2023]
Abstract
We provide a brief history of polyribosomes, ergosomes, prosomes, informosomes, maternal mRNA, stored mRNA, and RNP particles. Even though most published research focuses on total mRNA rather than polysomal mRNA and often assumes they are synonymous - i.e., if a functional mRNA is present, it must be translated - results from our laboratories comparing polysomal RNA and total mRNA in a range of "normal" issues show that some transcripts are almost totally absent from polysomes while others are almost entirely associated with polysomes. We describe a recent model from yeast showing various destinies for polysomal mRNA once it has been released from polysomes. The main points we want to emphasize are; a) when mRNA leaves polysomes to go to prosomes, P-bodies, stress granules, etc., it is not necessarily destined for degradation - it can be re-utilized; b) "normal" tissue, not just seeds and stressed tissue, contains functional non-polysomal mRNA; c) association of mRNA with different classes of polysomes affects their sub-cellular location and translatability; and d) drawbacks, misinterpretations, and false hopes arise from analysis of total mRNA rather than polysomal mRNA and from presuming that all polysomes are "created equal".
Collapse
Affiliation(s)
- Eric Davies
- Department of Plant Biology, North Carolina State University, Raleigh, NC, USA
| | | | | | | |
Collapse
|
18
|
Muench DG, Zhang C, Dahodwala M. Control of cytoplasmic translation in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:178-94. [DOI: 10.1002/wrna.1104] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
19
|
Cho SK, Kang IH, Carr T, Hannapel DJ. Using the Yeast Three-Hybrid System to Identify Proteins that Interact with a Phloem-Mobile mRNA. FRONTIERS IN PLANT SCIENCE 2012; 3:189. [PMID: 22969782 PMCID: PMC3427875 DOI: 10.3389/fpls.2012.00189] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/02/2012] [Indexed: 05/02/2023]
Abstract
Heterografting and RNA transport experiments have demonstrated the long-distance mobility of StBEL5 RNA, its role in controlling tuber formation, and the function of the 503-nt 3' untranslated region (UTR) of the RNA in mediating transport. Because the 3' UTR of StBEL5 is a key element in regulating several aspects of RNA metabolism, a potato leaf cDNA library was screened using the 3' UTR of StBEL5 as bait in the yeast three-hybrid (Y3H) system to identify putative partner RNA-binding proteins (RBPs). From this screen, 116 positive cDNA clones were isolated based on nutrient selection, HIS3 activation, and lacZ induction and were sequenced and classified. Thirty-five proteins that were predicted to function in either RNA- or DNA-binding were selected from this pool. Seven were monitored for their expression profiles and further evaluated for their capacity to bind to the 3' UTR of StBEL5 using β-galactosidase assays in the Y3H system and RNA gel-shift assays. Among the final selections were two RBPs, a zinc finger protein, and one protein, StLSH10, from a family involved in light signaling. In this study, the Y3H system is presented as a valuable tool to screen and verify interactions between target RNAs and putative RBPs. These results can shed light on the dynamics and composition of plant RNA-protein complexes that function to regulate RNA metabolism.
Collapse
Affiliation(s)
- Sung Ki Cho
- Plant Biology Major, Iowa State University Ames, IA, USA
| | | | | | | |
Collapse
|
20
|
Doroshenk KA, Crofts AJ, Morris RT, Wyrick JJ, Okita TW. RiceRBP: A Resource for Experimentally Identified RNA Binding Proteins in Oryza sativa. FRONTIERS IN PLANT SCIENCE 2012; 3:90. [PMID: 22645600 PMCID: PMC3355793 DOI: 10.3389/fpls.2012.00090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 04/20/2012] [Indexed: 05/05/2023]
Abstract
RNA binding proteins (RBPs) play an important role not only in nuclear gene expression, but also in cytosolic events, including RNA transport, localization, translation, and stability. Although over 200 RBPs are predicted from the Arabidopsis genome alone, relatively little is known about these proteins in plants as many exhibit no homology to known RBPs in other eukaryotes. Furthermore, RBPs likely have low expression levels making them difficult to identify and study. As part of our continuing efforts to understand plant cytosolic gene expression and the factors involved, we employed a combination of affinity chromatography and proteomic techniques to enrich for low abundance RBPs in developing rice seed. Our results have been compiled into RiceRBP (http://www.bioinformatics2.wsu.edu/RiceRBP), a database that contains 257 experimentally identified proteins, many of which have not previously been predicted to be RBPs. For each of the identified proteins, RiceRBP provides information on transcript and protein sequence, predicted protein domains, details of the experimental identification, and whether antibodies have been generated for public use. In addition, tools are available to analyze expression patterns for the identified genes, view phylogentic relationships and search for orthologous proteins. RiceRBP is a valuable tool for the community in the study of plant RBPs.
Collapse
Affiliation(s)
- Kelly A. Doroshenk
- Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | | | - Robert T. Morris
- School of Molecular Biosciences, Center for Reproductive Biology, Washington State UniversityPullman, WA, USA
| | - John J. Wyrick
- School of Molecular Biosciences, Center for Reproductive Biology, Washington State UniversityPullman, WA, USA
| | - Thomas W. Okita
- Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
- *Correspondence: Thomas W. Okita, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA. e-mail:
| |
Collapse
|
21
|
Finnie C, Sultan A, Grasser KD. From protein catalogues towards targeted proteomics approaches in cereal grains. PHYTOCHEMISTRY 2011; 72:1145-1153. [PMID: 21134685 DOI: 10.1016/j.phytochem.2010.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/09/2010] [Accepted: 11/11/2010] [Indexed: 05/27/2023]
Abstract
Due to their importance for human nutrition, the protein content of cereal grains has been a subject of intense study for over a century and cereal grains were not surprisingly one of the earliest subjects for 2D-gel-based proteome analysis. Over the last two decades, countless cereal grain proteomes, mostly derived using 2D-gel based technologies, have been described and hundreds of proteins identified. However, very little is still known about post-translational modifications, subcellular proteomes, and protein-protein interactions in cereal grains. Development of techniques for improved extraction, separation and identification of proteins and peptides is facilitating functional proteomics and analysis of sub-proteomes from small amounts of starting material, such as seed tissues. The combination of proteomics with structural and functional analysis is increasingly applied to target subsets of proteins. These "next-generation" proteomics studies will vastly increase our depth of knowledge about the processes controlling cereal grain development, nutritional and processing characteristics.
Collapse
Affiliation(s)
- Christine Finnie
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Bldg 224, DK-2800 Kgs. Lyngby, Denmark.
| | | | | |
Collapse
|
22
|
Agrawal GK, Rakwal R. Rice proteomics: A move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology. Proteomics 2011; 11:1630-49. [DOI: 10.1002/pmic.201000696] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 01/05/2011] [Accepted: 01/24/2011] [Indexed: 12/13/2022]
|
23
|
Protein profiling of the potato petiole under short day and long day photoperiods. J Proteomics 2011; 74:212-30. [DOI: 10.1016/j.jprot.2010.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 10/18/2010] [Accepted: 10/21/2010] [Indexed: 12/25/2022]
|
24
|
Morris RT, Doroshenk KA, Crofts AJ, Lewis N, Okita TW, Wyrick JJ. RiceRBP: a database of experimentally identified RNA-binding proteins in Oryza sativa L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:204-11. [PMID: 21421362 DOI: 10.1016/j.plantsci.2010.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 07/29/2010] [Accepted: 08/06/2010] [Indexed: 05/08/2023]
Abstract
RNA-binding proteins play critical roles at multiple steps during gene expression, including mRNA transport and translation. mRNA transport is particularly important in rice (Oryza sativa L.) in order to ensure the proper localization of the prolamine and glutelin seed storage proteins. However, relatively little information is available about RNA-binding proteins that have been isolated or characterized in plants. The RiceRBP database is a novel resource for the analysis of RNA-binding proteins in rice. RiceRBP contains 257 experimentally identified RNA-binding proteins, which are derived from at least 221 distinct rice genes. Many of the identified proteins catalogued in RiceRBP had not previously been annotated or predicted to bind RNA. RiceRBP provides tools to facilitate the analysis of the identified RNA-binding proteins, including information about predicted protein domains, phylogenetic relationships, and expression patterns of the identified genes. Importantly, RiceRBP also contains tools to search and analyze predicted RNA-binding protein orthologs in other plant species. We anticipate that the data and analysis tools provided by RiceRBP should facilitate the study of plant RNA-binding proteins. RiceRBP is available at http://www.bioinformatics2.wsu.edu/RiceRBP.
Collapse
Affiliation(s)
- Robert T Morris
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | | | | | | | | | | |
Collapse
|
25
|
Crofts AJ, Crofts N, Whitelegge JP, Okita TW. Isolation and identification of cytoskeleton-associated prolamine mRNA binding proteins from developing rice seeds. PLANTA 2010; 231:1261-76. [PMID: 20217123 DOI: 10.1007/s00425-010-1125-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 02/10/2010] [Indexed: 05/08/2023]
Abstract
The messenger RNA of the rice seed storage protein prolamine is targeted to the endoplasmic reticulum (ER) membranes surrounding prolamine protein bodies via a mechanism, which is dependent upon both RNA sorting signals and the actin cytoskeleton. In this study we have used an RNA bait corresponding to the previously characterized 5'CDS prolamine cis-localization sequence for the capture of RNA binding proteins (RBPs) from cytoskeleton-enriched fractions of developing rice seed. In comparison to a control RNA, the cis-localization RNA bait sequence led to the capture of a much larger number of proteins, 18 of which have been identified by tandem mass spectrometry. Western blots demonstrate that several of the candidate proteins analyzed to date show good to excellent specificity for binding to cis-localization sequences over the control RNA bait. Temporal expression studies showed that steady state protein levels for one RNA binding protein, RBP-A, paralleled prolamine gene expression. Immunoprecipitation studies showed that RBP-A is bound to prolamine and glutelin RNAs in vivo, supporting a direct role in storage protein gene expression. Using confocal immunofluorescence microscopy, RBP-A was found to be distributed to multiple compartments in the cell. In addition to the nucleus, RBP-A co-localizes with microtubules and is associated with cortical ER membranes. Collectively, these results indicate that employing a combination of in vitro binding and in vivo binding and localization studies is a valid strategy for the identification of putative prolamine mRNA binding proteins, such as RBP-A, which play a role in controlling expression of storage protein mRNAs in the cytoplasm.
Collapse
Affiliation(s)
- Andrew J Crofts
- Institute of Biological Chemistry, Washington State University, Clark Hall, Room #299, 100 Dairy Road, Pullman, WA 99164-6340, USA.
| | | | | | | |
Collapse
|