The role of SRP9/SRP14 in regulating Alu RNA

Abstract

SRP9/SRP14 is a protein heterodimer that plays a critical role in the signal recognition particle through its interaction with the scaffolding signal recognition particle RNA (7SL). SRP9/SRP14 binding to 7SL is mediated through a conserved structural motif that is shared with the primate-specific Alu RNA. Alu RNA are transcription products of Alu elements, a retroelement that comprises ~10% of the human genome. Alu RNA are involved in myriad biological processes and are dysregulated in several human disease states. This review focuses on the roles SRP9/SRP14 has in regulating Alu RNA diversification, maturation, and function. The diverse mechanisms through which SRP9/SRP14 regulates Alu RNA exemplify the breadth of protein-mediated regulation of non-coding RNA.

Keywords: RIG-I; SINE; adenylation; alternative splicing; retrotransposition; scAlu; stress granules; trafficking; translation; viral packaging.

Figure 1.

Organization of signal recognition particle (SRP) components across different domains of life. RNA helices are numbered according to previously described nomenclature [5]. Tertiary interactions as depicted previously between helices 3 and 4 are represented by a black curve and T₁ symbol [5]. Tertiary interactions between helices 6 and 8 are represented by a black circle and T₂ symbol. The symbol U describes the U-turn overlapping the UGUNR motif and is indicative of the τ-junction in the mammalian 7SL RNA [6]. SRP9/SRP14 heterodimer, Srp14p homodimer, and HBsu homodimer are positioned over the UGUNR motif [5]. SRP68/SRP72 heterodimer is positioned over the 5e helix [7]. SRP19 and Sec65p are positioned over the GNAR motif [8]. SRP54, Srp54p, and ffh are positioned over the 8b helix [9]. The positioning of Srp21p has not yet been clearly identified [10]. (A) Mammalian complex depicted by the Homo sapiens SRP. 7SL RNA secondary structure is presented as previously shown [11] and scaffolds the SRP9/SRP14 heterodimer, SRP68/SRP72 heterodimer, SRP19, and SRP54; (B) fungal complex represented by the Saccharomyces cerevisiae SRP. scR1 RNA secondary structure is displayed as previously shown [12] and scaffolds the Srp14p homodimer, Srp21p, Srp68p/Srp72p heterodimer, Sec65p, and Srp54p; (C) Archaeal complex demonstrated by the Methanococcus jannaschii SRP. 7S RNA secondary structure is shown as previously presented [13] and scaffolds SRP19, and SRP54; (D) gram-positive bacterial complex demonstrated by the Bacillus subtilis SRP. scRNA secondary structure is displayed as previously shown [5] and scaffolds the HBsu homodimer, and Ffh; (E) gram-negative bacterial complex is represented by the Escherichia coli SRP. The ffs secondary structure is demonstrated as previously shown [13] and scaffolds Ffh.

Figure 2.

Genomic regulatory Alu element regions and corresponding transcribed Alu RNA. Alu elements are transcriptionally aided by an upstream element that is not transcribed [58]. RNA polymerase III promoter elements, A- and B-boxes are found on the left arm of Alu RNA. The N⁶-methyladenylation (m⁶A) modification site overlaps the RNA region transcribed by the B-box [59]. An internal polyadenosine tract separates the left and right-arm monomers. The right arm is differentiated from the left arm by a 31-nucleotide insertion that interrupts a potential B-box [41]. The right arm is terminated with an additional polyadenosine tract. RNA polymerase III termination sequence (TTTT in humans) is partially transcribed and terminates the transcript [60]. The termination sequence is truncated and capped with an adenosine [61].

Figure 3.

Life cycle of Alu RNA regulated by SRP9/SRP14. Schematics of biomolecules (not to scale) depicting SRP9/SRP14 (red circles), DNA (double helix), Alu RNA (dimeric Alu RNA secondary structure), non-Alu RNA mRNA (cyan lines), and a ribosome (overlapping black oval and circle) are shown. SRP9/SRP14 is distributed non-specifically across the DNA. i) SRP9/SRP14 interacts with nascent nuclear Alu RNA, in the context of non-coding RNA and mRNA; ii) non-coding Alu RNA is trafficked into the nucleolus by SRP9/SRP14; ii-b) Alu RNA embedded in mRNA is alternatively spliced depending on the absence or presence of SRP9/SRP14; iii) inside the nucleolus, Alu RNA undergoes post-transcriptional modifications including an N⁶-methyladenylation (m⁶A) and addition of a 3’ adenosine; iv) non-coding Alu RNA is processed into small cytoplasmic Alu RNA (scAlu RNA). The location of this process has not been determined, but is possible to occur in the nucleolus, as suggested by similar localization patterns of full-length and small cytoplasmic Alu RNA [74]; v) non-coding Alu RNA, scAlu RNA, and mRNA embedded Alu RNA are trafficked into the cytoplasm; vi) Alu RNA is brought in close proximity to ribosomes by SRP9/SRP14; vii) ribosome translating ORF2 protein performs retrotransposition on Alu RNA; viii) ribosomes involved in translation are directly regulated by Alu RNA; ix) Alu RNA induces stress granule assembly, including components such as stalled ribosomes; x) cytoplasmic Alu RNA is packaged into vesicles that are exocytosed into the extracellular matrix as exosomes; xi) cytoplasmic Alu RNA is packaged with retroviruses and excreted into the extracellular matrix.