Crystal structure of a SFPQ/PSPC1 heterodimer provides insights into preferential heterodimerization of human DBHS family proteins

Jie, Huang; García, Gema Alejandra Botana; Perugini, Matthew A.; Fox, Archa H.; Bond, Charles S.; M, Lee

doi:10.1074/jbc.ra117.001451

Cited by 35 publications

(43 citation statements)

References 33 publications

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“…Sharing more than 70% sequence identity within the DBHS domain, the three DBHS proteins form obligate dimers, both homodimers as well as heterodimers. The structures of the DBHS proteins have previously been characterized: crystal structures have been obtained of the human NONO-PSPC1 heterodimer (Passon et al, 2012), SFPQ homodimer (Lee et al, 2015) and SFPQ-PSPC1 heterodimer (Huang et al, 2018), and of Caenorhabditis elegans NONO-1 (Knott et al, 2015). The structures confirmed the dimeric nature of the DBHS proteins and showed a novel arrangement of four RRMs in the dimer owing to the antiparallel configuration of the CC domain.…”

Section: Introductionmentioning

confidence: 86%

A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ

Hewage

Caria

2019

Acta Cryst Sect F

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behavior human splicing.PDB reference: dimerization domain of human SFPQ in space group C222 1 , 6ncqSupporting information: this article has supporting information at journals.iucr.org/f A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ Splicing factor proline/glutamine-rich (SFPQ) is an essential RNA-binding protein that is implicated in many aspects of nuclear function. The structures of SFPQ and two paralogs, non-POU domain-containing octamer-binding protein and paraspeckle component 1, from the Drosophila behavior human splicing protein family have previously been characterized. The unusual arrangement of the four domains, two RNA-recognition motifs (RRMs), a conserved region termed the NonA/paraspeckle (NOPS) domain and a C-terminal coiled coil, in the intertwined dimer provides a potentially unique RNA-binding surface. However, the molecular details of how the four RRMs in the dimeric SFPQ interact with RNA remain to be characterized. Here, a new crystal structure of the dimerization domain of human SFPQ in the C-centered orthorhombic space group C222 1 with one monomer in the asymmetric unit is presented. Comparison of the new crystal structure with the previously reported structure of SFPQ and analysis of the solution small-angle X-scattering data revealed subtle domain movements in the dimerization domain of SFPQ, supporting the concept of multiple conformations of SFPQ in equilibrium in solution. The domain movement of RRM1, in particular, may reflect the complexity of the RNA substrates of SFPQ. Taken together, the crystal and solution structure analyses provide a molecular basis for further investigation into the plasticity of nucleic acid binding by SFPQ in the absence of the structure in complex with its cognate RNA-binding partners. Figure 1Crystal structure of an SFPQ homodimer in space group C222 1 . (a) Domain architecture of SFPQ. (b) Stereoview of the crystal structure of SFPQ in space group C222 1 in cartoon representation. Residues modeled in the final structure are colored gold (RRM1), dark blue (RRM2), orange (NOPS) and red (coiled coil). The construct boundary used in this study is indicated with a square box and includes residues 276-535 of SFPQ. (c) Stereoview of the SFPQ dimer with the other monomer (gray) generated by the symmetry operation (Àx À 1, y, Àz À 1/2).

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Section: Introductionmentioning

confidence: 86%

A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ

Hewage

Caria

2019

Acta Cryst Sect F

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“…Moreover, the rescue activity of NONO required dimerization with DBHS family proteins, including SFPQ, PSPC1, and NONO itself, which is also required for the oligomerization of these proteins along the RNA molecule. CLIP-seq data showed that the C domain of NEAT1_2 contains multiple binding sites for NONO/SFPQ, which are likely to be essential for paraspeckle formation (Naganuma et al 2012;Passon et al 2012;Lee et al 2015;Huang et al 2018;Yamazaki et al 2018b). The in vitro-transcribed RNA derived from the C2 domain preferentially binds to NONO/SFPQ and induces the formation of higher-order structures that are sensitive to 1,6-hexanediol and depend on NONO/SFPQ (Yamazaki et al 2018b).…”

Section: A C Bmentioning

confidence: 99%

Architectural RNAs for Membraneless Nuclear Body Formation

Yamazaki

Nakagawa

Hirose

2019

Cold Spring Harb Symp Quant Biol

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Long noncoding RNAs (lncRNAs) are fundamental regulators of various cellular processes. A subset of lncRNAs, termed architectural RNAs (arcRNAs), function in the formation and maintenance of phase-separated membraneless organelles in multiple eukaryotic species. These membraneless organelles represent an important type of compartmentalization in the crowded cellular environment and have several distinct features. The NEAT1_2 lncRNA is a well-characterized arcRNA that functions as an essential scaffold of paraspeckle nuclear bodies. Here, we describe the biogenesis of paraspeckles on arcRNAs through phase separation, focusing on the specific functions of multiple NEAT1_2 RNA domains and their partner RNAbinding proteins. Finally, we present an updated model of paraspeckle formation and discuss future perspectives of research into arcRNA-instructed architectures of phase-separated nuclear bodies.

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“…I chose the repair. [229][230][231]233,[239][240][241][242][251][252][253][254][255][256] NONO, SFPQ and PSPC1 belong to a family of proteins known as drosophila behaviour/human splicing (DBHS). 230 DBHS proteins are characterized by an N-terminal RNA recognition motif, NonA/paraspeckle domain and a C-terminal coiled-coil domain and nuclear localization signal.…”

Section: Co-immunoprecipitation Of Klf1 In the K1er Cell Line Revealsmentioning

confidence: 99%

“…230 DBHS proteins are characterized by an N-terminal RNA recognition motif, NonA/paraspeckle domain and a C-terminal coiled-coil domain and nuclear localization signal. 230,231,239,252,253,256 Due to the high homology between these proteins they may all perform similar functions and have been shown to partially compensate each other. 233,255 The coiled-coil domain is exclusively involved in association of these proteins and allows for different dimerization states (e.g.…”

Section: Co-immunoprecipitation Of Klf1 In the K1er Cell Line Revealsmentioning

confidence: 99%

“…RCC2, EIF3L, SFPQ, NONO, MATR3 and PSPC1 are some examples of the proteins identified. Further literature searches revealed that SFPQ, NONO, MATR3 and PSPC1 all form a complex together within nuclear paraspeckles [229][230][231][232][233]. I then examined the number of peptides found for each enriched protein more specifically in the tamoxifen treated samples for the three cell lines(Figure 6.11).…”

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confidence: 99%

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“Krüppeling Erythropoiesis”: KLF1 function in development and disease

Huang¹

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KLF1 is a three-fingered C2H2 transcription factor essential for the differentiation of definitive erythroid cells. KLF1 regulates the expression of many genes involved in this process and loss of Klf1 results in perinatal death due to anaemia and severe -thalassaemia in mice. The three C2H2 zinc-fingers of KLF1 are interconnected by two linker peptides. The first linker that connects the first and second zinc finger of KLF1 contains the conserved TGEKP sequence. The second linker connects the second and third zinc fingers and sequence TGHRP is more variant. In human patients, there have been multiple mutations identified in the 2 nd linker of KLF1. These mutations result in non-spherocytic haemolytic anaemia (NSHA) with microcytosis, and high foetal haemoglobin. While we understand pathology resulting from KLF1 mutations in these patients, very little is known about the precise molecular function of the 2 nd linker mutation, and in general, linker mutations across all C2H2 proteins. C2H2 zinc fingers are the largest class of DNA-binding proteins in the mammalian genome. They are characterized by the presence of two anti-parallel -sheets and an -helix (fold). Two cysteine and two histidine residues in the -fold coordinate a zinc molecule and are highly conserved across the family giving the zinc fingers their identity. Additionally, the -helix is directly involved in DNA contact through 3 amino acid residues at positions-1, +3 and +6 relative to the start of the helix. The linker peptide between each finger allows flexibility so that the -helix of each zinc-finger can contact DNA, while providing additional stability to these interactions through forming hydrogen bonds with the preceding -helix. This mechanism is known as c-capping and closes the 'frayed' c-terminus end of the -helix upon contacting DNA. Our laboratory recently identified the mommeD45 mutation from a mouse ENU mutagenesis screen for modifiers of an alpha-globin transgene. The mutation results in a transversion of the histidine to an arginine (H350R) residue in the second linker of KLF1. The mutation appears relatively benign in the heterozygous state. However homozygous D45 mice develop a mild anemic phenotype, including splenomegaly and microcytosis. To generate a model of NSHA in mice, like that observed in human patients, I crossed the mommeD45 mouse to a Klf1 heterozygous loss of function mouse to produce compound

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Crystal structure of a SFPQ/PSPC1 heterodimer provides insights into preferential heterodimerization of human DBHS family proteins

Cited by 35 publications

References 33 publications

A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ

A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ

Architectural RNAs for Membraneless Nuclear Body Formation

“Krüppeling Erythropoiesis”: KLF1 function in development and disease

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