RiceRBP: A Resource for Experimentally Identified RNA Binding Proteins in Oryza sativa

Doroshenk, Kelly A.; Crofts, Andrew J.; Morris, Robert T.; Wyrick, John J.; Okita, Thomas W.

doi:10.3389/fpls.2012.00090

Cited by 18 publications

(22 citation statements)

References 47 publications

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“…Furthermore, because of the observation that heparin inhibited the binding of OsTudor-SN (the characterized prolamine and glutelin RBP) to its target RNAs, the prolamine zipcode capture assays were also performed without heparin, which revealed 132 putative prolamine RBPs [38,39]. Among them, 77 proteins were newly identified RBP candidates, except for the 12 proteins found in the stringent prolamine zipcode capture experiment and the 43 proteins obtained by poly(U)sepharose affinity purification [39]. In conclusion, Okita's group obtained 148 cytoskeleton-associated RBPs and 138 cytoskeleton-associated prolamine mRNA-binding proteins from developing rice seeds through isolation with affinity chromatography followed by identification with proteomic approaches.…”

Section: Subproteomic Studies Of Mature and Developing Rice Seedsmentioning

confidence: 99%

Use of proteomics to understand seed development in rice

2013

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Rice is an important cereal crop and has become a model monocot for research into crop biology. Rice seeds currently feed more than half of the world's population and the demand for rice seeds is rapidly increasing because of the fast-growing world population. However, the molecular mechanisms underlying rice seed development is incompletely understood. Genetic and molecular studies have developed our understanding of substantial proteins related to rice seed development. Recent advancements in proteomics have revolutionized the research on seed development at the single gene or protein level. Proteomic studies in rice seeds have provided the molecular explanation for cellular and metabolic events as well as environmental stress responses that occur during embryo and endosperm development. They have also led to the new identification of a large number of proteins associated with regulating seed development such as those involved in stress tolerance and RNA metabolism. In the future, proteomics, combined with genetic, cytological, and molecular tools, will help to elucidate the molecular pathways underlying seed development control and help in the development of valuable and potential strategies for improving yield, quality, and stress tolerance in rice and other cereals. Here, we reviewed recent progress in understanding the mechanisms of seed development in rice with the use of proteomics.

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Section: Subproteomic Studies Of Mature and Developing Rice Seedsmentioning

confidence: 99%

Use of proteomics to understand seed development in rice

2013

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“…Results from genetic studies suggest that the glutelin and prolamine regulated transport pathways and default transport pathway share common protein components, with one or more unique proteins specifying a specific pathway (Crofts et al, 2005;Doroshenk et al, 2012).…”

Section: Multiple Rbp Complexes Bind To the Prolamine Mrna Zipcodesmentioning

confidence: 99%

Multiple RNA Binding Protein Complexes Interact with the Rice Prolamine RNA Cis-Localization Zipcode Sequences

Yang

Crofts

et al. 2014

Plant Physiol.

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RNAs for the storage proteins, glutelins and prolamines, contain zipcode sequences, which target them to specific subdomains of the cortical endoplasmic reticulum in developing rice (Oryza sativa) seeds. Fifteen RNA binding proteins (RBPs) specifically bind to the prolamine zipcode sequences and are likely to play an important role in the transport and localization of this storage protein RNA. To understand the underlying basis for the binding of multiple protein species to the prolamine zipcode sequences, the relationship of five of these RBPs, RBP-A, RBP-I, RBP-J, RBP-K, and RBP-Q, were studied. These five RBPs, which belong to the heterogeneous nuclear ribonucleoprotein class, bind specifically to the 59 coding regions as well as to the 39 untranslated region zipcode RNAs but not to a control RNA sequence. Coimmunoprecipitation-immunoblot analyses in the presence or absence of ribonuclease showed that these five RBPs are assembled into three multiprotein complexes to form at least two zipcode RNA-protein assemblies. One cytoplasmic-localized zipcode assembly contained two multiprotein complexes sharing a common core consisting of RBP-J and RBP-K and either RBP-A (A-J-K) or RBP-I (I-J-K). A second zipcode assembly of possibly nuclear origin consists of a multiprotein complex containing RBP-Q and modified forms of the other protein complexes. These results suggest that prolamine RNA transport is initiated in the nucleus to form a zipcode-protein assembly, which is remodeled in the cytoplasm to target the RNA to its proper location on the cortical endoplasmic reticulum.

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“…Expansin, a cell wall protein associated with cellular expansion and cell wall changes, and a transcription elongation factor (TFIIS) that stimulates RNA polymerase II also were identified. By contrast, the Tsn peptide module interacted with eight RBPs, RBP-23, RBP-43, RBP-59, RBP-61, RBP-100, RBP-152, RBP-157, and RBP-159 (Table I), identified in earlier studies from this laboratory (Doroshenk et al, 2009(Doroshenk et al, , 2012 as major RBPs present in developing rice endosperm. These findings suggest that the two OsTudor-SN modules play distinct biological roles.…”

Section: Resultsmentioning

confidence: 82%

Multifunctional RNA Binding Protein OsTudor-SN in Storage Protein mRNA Transport and Localization

et al. 2017

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The multifunctional RNA-binding protein Tudor-SN plays multiple roles in transcriptional and posttranscriptional processes due to its modular domain structure, consisting of four tandem Staphylococcus nuclease (SN)-like domains (4SN), followed by a carboxyl-terminal Tudor domain, followed by a fifth partial SN sequence (Tsn). In plants, it confers stress tolerance, is a component of stress granules and P-bodies, and may participate in stabilizing and localizing RNAs to specific subdomains of the cortical-endoplasmic reticulum in developing rice (Oryza sativa) endosperm. Here, we show that, in addition to the intact rice OsTudor-SN protein, the 4SN and Tsn modules exist as independent polypeptides, which collectively may coassemble to form a complex population of homodimer and heteroduplex species. The 4SN and Tsn modules exhibit different roles in RNA binding and as a protein scaffold for stress-associated proteins and RNA-binding proteins. Despite their distinct individual properties, mutations in both the 4SN and Tsn modules mislocalize storage protein mRNAs to the cortical endoplasmic reticulum. These results indicate that the two modular peptide regions of OsTudor-SN confer different cellular properties but cooperate in mRNA localization, a process linking its multiple functions in the nucleus and cytoplasm.mRNA localization is readily evident in structurally polarized somatic cells

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RiceRBP: A Resource for Experimentally Identified RNA Binding Proteins in Oryza sativa

Cited by 18 publications

References 47 publications

Use of proteomics to understand seed development in rice

Use of proteomics to understand seed development in rice

Multiple RNA Binding Protein Complexes Interact with the Rice Prolamine RNA Cis-Localization Zipcode Sequences

Multifunctional RNA Binding Protein OsTudor-SN in Storage Protein mRNA Transport and Localization

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