Structure and domain organization of Drosophila Tudor

Ren, Ren; Liu, Haiping; Wang, Wenjia; Wang, Mingzhu; Yang, Na; Dong, Yuhui; Gong, Weimin; Lehmann, Ruth; Xu, Rui-Ming

doi:10.1038/cr.2014.63

Cited by 15 publications

(16 citation statements)

References 16 publications

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“…Furthermore, here we show that six Tud domains (1, 3, 4, 6, 9 and 11) of Tud can bind to Aub. Consistent with previous methylated Aub peptide-Tud domains 7–11 binding studies 19,40 , we did not detect interaction of domain 10 to full-length Aub presumably due to this domain’s incomplete sDMA-binding pocket 40 and show Aub interaction with domains 9 and 11. Although we could not detect binding of Aub to the other five Tud domains of Tud protein (Supplementary Figs.…”

Section: Discussionsupporting

confidence: 92%

Protein components of ribonucleoprotein granules from Drosophila germ cells oligomerize and show distinct spatial organization during germline development

Wahiduzzaman

Tindell

et al. 2019

Sci Rep

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The assembly of large RNA-protein granules occurs in germ cells of many animals and these germ granules have provided a paradigm to study structure-functional aspects of similar structures in different cells. Germ granules in Drosophila oocyte’s posterior pole (polar granules) are composed of RNA, in the form of homotypic clusters, and proteins required for germline development. In the granules, Piwi protein Aubergine binds to a scaffold protein Tudor, which contains 11 Tudor domains. Using a super-resolution microscopy, we show that surprisingly, Aubergine and Tudor form distinct clusters within the same polar granules in early Drosophila embryos. These clusters partially overlap and, after germ cells form, they transition into spherical granules with the structural organization unexpected from these interacting proteins: Aubergine shell around the Tudor core. Consistent with the formation of distinct clusters, we show that Aubergine forms homo-oligomers and using all purified Tudor domains, we demonstrate that multiple domains, distributed along the entire Tudor structure, interact with Aubergine. Our data suggest that in polar granules, Aubergine and Tudor are assembled into distinct phases, partially mixed at their “interaction hubs”, and that association of distinct protein clusters may be an evolutionarily conserved mechanism for the assembly of germ granules.

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Section: Discussionsupporting

confidence: 92%

Protein components of ribonucleoprotein granules from Drosophila germ cells oligomerize and show distinct spatial organization during germline development

Wahiduzzaman

Tindell

et al. 2019

Sci Rep

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“…S1B), we mutated Leu364 to phenylalanine, but we did not observe the expected change in binding preference (Table S3). Similarly, the L2058F mutation (aromatic cage residue) of Drosophila Tud9 does not restore methylarginine binding (23). These results imply that additional structural differences also contribute to the methylarginine mark recognition.…”

Section: Molecular Basis Of the Recognition Of The Unmethylated Piwil1mentioning

confidence: 90%

Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2

Liu

Izumi

Huang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The P-element-induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway plays a central role in transposon silencing and genome protection in the animal germline. A family of Tudor domain proteins regulates the piRNA pathway through direct Tudor domain-PIWI interactions. Tudor domains are known to fulfill this function by binding to methylated PIWI proteins in an arginine methylation-dependent manner. Here, we report a mechanism of methylation-independent Tudor domain-PIWI interaction. Unlike most other Tudor domains, the extended Tudor domain of mammalian Tudor domain-containing protein 2 (TDRD2) preferentially recognizes an unmethylated arginine-rich sequence from PIWI-like protein 1 (PIWIL1). Structural studies reveal an unexpected Tudor domain-binding mode for the PIWIL1 sequence in which the interface of Tudor and staphylococcal nuclease domains is primarily responsible for PIWIL1 peptide recognition. Mutations disrupting the TDRD2-PIWIL1 interaction compromise piRNA maturation via 3'-end trimming in vitro. Our work presented here reveals the molecular divergence of the interactions between different Tudor domain proteins and PIWI proteins.

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“…In this system, the OB-fold (SN domain) and SH3-fold (Tudor domain) function as a single unit (Friberg et al, 2009;Liu et al, 2010). Notably, the Drosophila SND1 protein features 11 tandem extended Tudors, also known as maternal Tudors (Ren et al, 2014).…”

Section: Sequence Variation and Electrostatic Properties Of Sbb Surfmentioning

confidence: 99%

The Small β-Barrel Domain: A Survey-Based Structural Analysis

et al. 2019

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The small b-barrel (SBB) is an ancient protein structural domain characterized by extremes: it features a broad range of structural varieties, a deeply intricate evolutionary history, and it is associated with a bewildering array of cellular pathways. Here, we present a thorough, survey-based analysis of the structural properties of SBBs. We first consider the defining properties of the SBB, including various systems of nomenclature used to describe it, and we introduce the unifying concept of an ''urfold.'' To begin elucidating how vast functional diversity can be achieved by a relatively simple domain, we explore the anatomy of the SBB and its representative structural variants. Many SBB proteins assemble into cyclic oligomers as the biologically functional units; these oligomers often bind RNA, and typically exhibit great quaternary structural plasticity (homomeric and heteromeric rings, variable subunit stoichiometries, etc.). We conclude with three themes that emerge from the rich structure 4 function versatility of the SBB.Strand b1 is red, b2 is orange, b3 is yellow, and b4 is green; for the SH3 and OB folds, the fifth strand is also shown (gray). Branches along a sample path in this digraph are highlighted in tan (subtree at right), yielding the 1 Zhang and Kim, 2000); these two sheets, near the center of the image, are drawn simply to illustrate tree traversal. The base of the overall tree (at center) is a decision between the two possible configurations (parallel, antiparallel) for the simplest possible sheet-i.e., a tandem pair of strands (⇨∿∿⇨). Traversing the tree from this split ''root'' to the leaves corresponds to building-up the sheet, and the tree's branching structure elucidates the n!• •2 nÀ2 unique topologies that are possible for a sheet of n strands; the successive branches of this unrooted k-ary tree are of degrees 2, 6, 2, 2, 2. The positions of the SH3 and OB folds are indicated by cyan and purple paths (subtree at left). Other features of b-sheets are also elucidated by this hierarchical representation, such as the fact that there are 24 unique arrangements of two sequentially adjacent b-hairpin motifs (red circles, left subtree). If the origin for strand numbering is taken as arbitrary (e.g., labeling a sequence 2/3/4 does not differ from 1/2/3), then the OB topology (pink path, left) can be seen to cluster closely with the SH3; the yellow region delimits a putative SBB ''urfold'' basin in fold-space, subsuming the SH3 and OB folds.

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Structure and domain organization of Drosophila Tudor

Cited by 15 publications

References 16 publications

Protein components of ribonucleoprotein granules from Drosophila germ cells oligomerize and show distinct spatial organization during germline development

Protein components of ribonucleoprotein granules from Drosophila germ cells oligomerize and show distinct spatial organization during germline development

Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2

The Small β-Barrel Domain: A Survey-Based Structural Analysis

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