A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons

ABSTRACT Intracellular and intercellular polarity requires that specific proteins be sorted to discreet locations within and between cells. One mechanism for sorting proteins is through RNA localization. In Saccharomyces cerevisiae, ASH1 mRNA localizes to the distal tip of the bud, resulting in the asymmetric sorting of the transcriptional repressor Ash1p. ASH1 mRNA localization requires four cis-acting localization elements and the trans-acting factors Myo4p, She3p, and She2p. Myo4p is a type V myosin motor that functions to directly transport ASH1 mRNA to the bud. She2p is an RNA-binding protein that directly interacts with the ASH1 mRNA cis-acting elements. Currently, the role for She3p in ASH1 mRNA localization is as an adaptor protein, since it can simultaneously associate with Myo4p and She2p. Here, we present data for two novel mutants of She3p, S348E and the double mutant S343E S361E, that are defective for ASH1 mRNA localization, and yet both of these mutants retain the ability to associate with Myo4p and She2p. These observations suggest that She3p possesses a novel activity required for ASH1 mRNA localization, and our data imply that this function is related to the ability of She3p to associate with ASH1 mRNA. Interestingly, we determined that She3p is phosphorylated, and global mass spectrometry approaches have determined that Ser 343, 348, and 361 are sites of phosphorylation, suggesting that the novel function for She3p could be negatively regulated by phosphorylation. The present study reveals that the current accepted model for ASH1 mRNA localization does not fully account for the function of She3p in ASH1 mRNA localization.

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Identification of vegetal RNA-localization elements in Xenopus oocytes

Methods ◽

10.1016/j.ymeth.2010.02.016 ◽

2010 ◽

Vol 51 (1) ◽

pp. 146-151 ◽

Cited By ~ 5

Author(s):

Maike Claußen ◽

Tomas Pieler

Keyword(s):

Xenopus Oocytes ◽

Rna Localization ◽

Localization Elements

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Recognition and long-range interactions of a minimal nanos RNA localization signal element

Development ◽

10.1242/dev.128.3.427 ◽

2001 ◽

Vol 128 (3) ◽

pp. 427-435 ◽

Cited By ~ 3

Author(s):

S. Evans Bergsten ◽

T. Huang ◽

S. Chatterjee ◽

E.R. Gavis

Keyword(s):

Long Range ◽

Germ Plasm ◽

Rna Localization ◽

Posterior Pole ◽

Drosophila Embryo ◽

Cis Acting ◽

Signal Element ◽

Long Range Interactions ◽

Localization Signal ◽

Localization Elements

Localization of nanos (nos) mRNA to the germ plasm at the posterior pole of the Drosophila embryo is essential to activate nos translation and thereby generate abdominal segments. nos RNA localization is mediated by a large cis-acting localization signal composed of multiple, partially redundant elements within the nos 3′ untranslated region. We identify a protein of approximately 75 kDa (p75) that interacts specifically with the nos +2′ localization signal element. We show that the function of this element can be delimited to a 41 nucleotide domain that is conserved between D. melanogaster and D. virilis, and confers near wild-type localization when present in three copies. Two small mutations within this domain eliminate both +2′ element localization function and p75 binding, consistent with a role for p75 in nos RNA localization. In the intact localization signal, the +2′ element collaborates with adjacent localization elements. We show that different +2′ element mutations not only abolish collaboration between the +2′ and adjacent +1 element but also produce long-range deleterious effects on localization signal function. Our results suggest that higher order structural interactions within the localization signal, which requires factors such as p75, are necessary for association of nos mRNA with the germ plasm.

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