Koning Heidar J, Lai Jia Y, Marshall Andrew C, Stroeher Elke, Monahan Gavin, Pullakhandam Anuradha, Knott Gavin J, Ryan Timothy M, Fox Archa H, Whitten Andrew, Lee Mihwa, Bond Charles S
School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
WA Proteomics Facility, School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.
Nucleic Acids Res. 2025 Jan 11;53(2). doi: 10.1093/nar/gkae1198.
The proteins SFPQ (splicing Factor Proline/Glutamine rich) and NONO (non-POU domain-containing octamer-binding protein) are mammalian members of the Drosophila Behaviour/Human Splicing (DBHS) protein family, which share 76% sequence identity in their conserved 320 amino acid DBHS domain. SFPQ and NONO are involved in all steps of post-transcriptional regulation and are primarily located in mammalian paraspeckles: liquid phase-separated, ribonucleoprotein sub-nuclear bodies templated by NEAT1 long non-coding RNA. A combination of structured and low-complexity regions provide polyvalent interaction interfaces that facilitate homo- and heterodimerisation, polymerisation, interactions with oligonucleotides, mRNA, long non-coding RNA, and liquid phase-separation, all of which have been implicated in cellular homeostasis and neurological diseases including neuroblastoma. The strength and competition of these interaction modes define the ability of DBHS proteins to dissociate from paraspeckles to fulfil functional roles throughout the nucleus or the cytoplasm. In this study, we define and dissect the coiled-coil interactions which promote the polymerisation of DBHS proteins, using a crystal structure of an SFPQ/NONO heterodimer which reveals a flexible coiled-coil interaction interface which differs from previous studies. We support this through extensive solution small-angle X-ray scattering experiments using a panel of SFPQ/NONO heterodimer variants which are capable of tetramerisation to varying extents. The QM mutant displayed a negligible amount of tetramerisation (quadruple loss of function coiled-coil mutant L535A/L539A/L546A/M549A), the Charged Single Alpha Helix (ΔCSAH) variant displayed a dimer-tetramer equilibrium interaction, and the disulfide-forming variant displayed constitutive tetramerisation (R542C which mimics the pathological Drosophila nonAdiss allele). We demonstrate that newly characterised coiled-coil interfaces play a role in the polymerisation of DBHS proteins in addition to the previously described canonical coiled-coil interface. The detail of these interactions provides insight into a process critical for the assembly of paraspeckles as well as the behaviour of SFPQ as a transcription factor, and general multipurpose auxiliary protein with functions essential to mammalian life. Our understanding of the coiled coil behaviour of SFPQ also enhances the explanatory power of mutations (often disease-associated) observed in the DBHS family, potentially allowing for the development of future medical options such as targeted gene therapy.
蛋白质SFPQ(富含脯氨酸/谷氨酰胺的剪接因子)和NONO(含非POU结构域的八聚体结合蛋白)是果蝇行为/人类剪接(DBHS)蛋白家族的哺乳动物成员,它们在其保守的320个氨基酸的DBHS结构域中具有76%的序列同一性。SFPQ和NONO参与转录后调控的所有步骤,主要位于哺乳动物的副斑点中:由NEAT1长链非编码RNA模板化的液相分离的核糖核蛋白亚核体。结构化区域和低复杂性区域的组合提供了多价相互作用界面,促进同二聚化和异二聚化、聚合、与寡核苷酸、mRNA、长链非编码RNA的相互作用以及液相分离,所有这些都与细胞内稳态和包括神经母细胞瘤在内的神经疾病有关。这些相互作用模式的强度和竞争决定了DBHS蛋白从副斑点解离以在整个细胞核或细胞质中发挥功能作用的能力。在本研究中,我们利用SFPQ/NONO异二聚体的晶体结构定义并剖析了促进DBHS蛋白聚合的卷曲螺旋相互作用,该晶体结构揭示了一个灵活的卷曲螺旋相互作用界面,这与先前的研究不同。我们通过使用一组能够不同程度四聚化的SFPQ/NONO异二聚体变体进行广泛的溶液小角X射线散射实验来支持这一点。QM突变体显示出可忽略不计的四聚化量(功能丧失的四重卷曲螺旋突变体L535A/L539A/L546A/M549A),带电单α螺旋(ΔCSAH)变体显示出二聚体 - 四聚体平衡相互作用,而形成二硫键的变体显示出组成型四聚化(R542C,其模拟病理性果蝇nonAdiss等位基因)。我们证明,除了先前描述的典型卷曲螺旋界面外,新鉴定的卷曲螺旋界面在DBHS蛋白的聚合中也发挥作用。这些相互作用的细节为副斑点组装以及SFPQ作为转录因子和对哺乳动物生命至关重要的具有多种功能的通用辅助蛋白的行为所依赖的关键过程提供了深入了解。我们对SFPQ卷曲螺旋行为的理解也增强了对DBHS家族中观察到的突变(通常与疾病相关)的解释力,这可能有助于未来开发诸如靶向基因治疗等医学选择。
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