Diverse role of survival motor neuron protein

Abstract

The multifunctional Survival Motor Neuron (SMN) protein is required for the survival of all organisms of the animal kingdom. SMN impacts various aspects of RNA metabolism through the formation and/or interaction with ribonucleoprotein (RNP) complexes. SMN regulates biogenesis of small nuclear RNPs, small nucleolar RNPs, small Cajal body-associated RNPs, signal recognition particles and telomerase. SMN also plays an important role in DNA repair, transcription, pre-mRNA splicing, histone mRNA processing, translation, selenoprotein synthesis, macromolecular trafficking, stress granule formation, cell signaling and cytoskeleton maintenance. The tissue-specific requirement of SMN is dictated by the variety and the abundance of its interacting partners. Reduced expression of SMN causes spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. SMA displays a broad spectrum ranging from embryonic lethality to an adult onset. Aberrant expression and/or localization of SMN has also been associated with male infertility, inclusion body myositis, amyotrophic lateral sclerosis and osteoarthritis. This review provides a summary of various SMN functions with implications to a better understanding of SMA and other pathological conditions.

Keywords: Cajal body; DNA repair; Gem; SBP2; SMA; SMN; Selenoprotein; Signal recognition particle; Spinal muscular atrophy; Splicing; Survival Motor Neuron; TERC; TERT; TMG; Telomerase; Transcription; snRNP biogenesis; snoRNP biogenesis.

Figure 1. Structure of SMN protein and SMN transcripts

(A) Diagrammatic representation of the SMN protein. The numbers in the colored box indicate the exon. Domains are indicated above the boxes and proteins shown to interact with SMN are shown below. See text for further details about proteins. (B) Comparative modeling of the full-length SMN protein utilized multiple structure templates for the Gemin2 binding domain (blue) [20,21], the Tudor domain (green) [–24] and the YG Box domain (orange) [25]. Model calculations with RosettaCM included the structure templates for the domains and fragment libraries derived from sequence-based searches of the Protein Data Bank for modeling all other regions [26]. The SMN protein diagram shows the structural domains in color overlaid on a map of the labeled exons with the number of the last amino acid residue in each exon indicated above. The structural domains and amino ranges are indicated below the diagram. The full-length SMN protein model is shown as a cartoon representation with a rainbow color scheme from blue N-terminus to red C-terminus (labeled N and C, respectively) [27]. The structured domains are indicated with the PDB codes of the comparative modeling templates listed below each name. The unstructured regions highlighted include the lysine-rich region, and the Profilin2a binding region with the conserved proline-rich sequence indicated below the label. Selected amino acid side chains are shown as stick representations with blue for lysine amino groups and red for tyrosine hydroxyl groups. The conserved residues of the YG Box motif are indicated with the Cα atoms of the glycine residues shown a van der Waals spheres. (C) Diagrammatic representation of transcripts generated from SMN. The name of each transcript is indicated to the left. Start and stop codons are indicated for each transcript, the exon number is indicated above the colored boxes and the number of amino acids coded by each exon is indicated in the boxes. The EMLA degron [9] that renders SMNΔ7 unstable is indicated. Abbreviation: UTR, untranslated.

Figure 2. Alignment of SMN protein from various animal species

Exon numbers correspond to human SMN exons. Sequences were aligned with the ClustalW algorithm using MacVector software. The name of each species is indicated to the left of the sequence and accession numbers are indicated at the end of the sequence. Bold letters highlighted in grey indicate consensus amino acids. The highly conserved Gemin2 interaction, Tudor domain, polyproline-rich domain YG Box are denoted. Adapted from [50].

Figure 3. Proposed RNA metabolism roles of SMN

SMN is pictured at the center and is represented in all cases by a blue circle. All RNAs are represented by red line drawings, all DNA in black, and all proteins as colored ovals or circles. Starting from the top left, in clockwise order, the functions are as follows. (A) Transcription termination: SMN interacts with symmetrically dimethylated arginines in the C-terminal domain CTD of polymerase II, and is proposed to assist in targeting the Senataxin helicase to R-loops [90]. (B) U7 snRNP assembly: The SMN complex loads the Sm/Lsm ring onto U7 snRNA [116,117]. Afterwards, the mature snRNP functions in 3′ end processing of histone mRNAs [117]. (C) SRP biogenesis: the SMN complex is required for proper interaction between SRP54 and the 7S RNA, which is required for targeting of nascent polypeptides to the endoplasmic reticulum [123]. SRP54 is pictured as a purple oval. (D) Spliceosomal snRNP assembly: SMN functions along with the other components of the SMN complex [,,–115] in assembly of the heptameric Sm ring onto snRNA [109]. After assembly, mature snRNPs catalyze pre-mRNA splicing in the nucleus. (E) Telomerase biogenesis: Functional telomerase contains an RNA component (TERC) as well as several proteins. SMN interacts with telomerase-associated proteins GAR1, TERT, Dyskerin, and WRAP53, and is proposed to function in targeting telomerase to Cajal bodies (CBs) [82,107,119]. (F) Selenoprotein translation: SBP2 causes incorporation of selenocysteine (Sec) in the place of a stop codon. In addition, many selenoprotein mRNA 5′ ends are hypermethylated by TGS1 [100]. SMN interacts with both SBP2 and TGS1 [100]. (G) snoRNP biogenesis: H/ACA and C/D class snoRNPs consist of RNA and a characteristic set of protein cofactors for each class. SMN interacts with Fibrillarin, a component of C/D class snoRNPs [118], and GAR1 and Dyskerin within H/ACA class snoRNPs [82,107]. (H) RNA trafficking: SMN interacts with a number of RNA binding proteins known to assist in targeting of mRNAs to axon terminals [,–129], and appears to actively participate in the process [,–130]. (I) Stress granule formation: SMN is present in stress granules (SGs) and low levels of SMN impair the formation of SGs [46,120]. (J) Translation regulation: SMN regulates the level of CARM1 protein [121] through a translation-dependent mechanism proposed to involve a direct interaction between SMN and polysomes [122].

Figure 4. Proposed function of SMN in double-strand break repair

Double-strand DNA break repair is a multi-step process that involves replication of DNA from a homologous chromosome. First, one strand from each end is digested by exonucleases and the newly generated single-stranded DNA (ssDNA) region is bound by the RPA complex. Next, BRCA2 oligomers are recruited to RPA-bound ssDNA and help to nucleate RAD51 oligomerization on the ssDNA. RAD51 then continues to oligomerize and completely replaces RPA on the ssDNA. RAD51-coated ssDNA then attempts to pair with homologous regions of double-stranded DNA (dsDNA). A SMN-Gemin2 fusion protein increases the association of RAD51-ssDNA with heterologous dsDNA in vitro [222], and so is proposed to function at this stage. Once a homologous region of dsDNA is identified, it is invaded by the ssDNA and strand extension takes place. At this stage, there are multiple outcomes, depending on whether there is crossover between the homologous chromosomes and whether both ends of the break are extended. For brevity’s sake, the simplest outcome, synthesis dependent strand annealing, in which a single strand is extended and then re-anneals with its complementary strand, is portrayed here. For a more detailed overview of double-stranded break repair, see Godin et al 2016 [219].

Figure 5. SMN involvement in signaling pathways

(A) SMN involvement in regulation of actin dynamics. Rho-Associated Kinase (ROCK) phosphorylates Lim Kinase (LIMK) which in turn phosphorylates Cofilin (denoted by P in yellow circle) to contribute to actin dynamics regulation. SMN can prevent ROCK-mediated phosphorylation of Profilin2a (p2a) by interacting and forming a complex with p2a. When SMN is reduced, the interaction between p2a and ROCK increases, with a concomitant increase in p2a phosphorylation and a decrease in LIMK and Cofilin phosphorylation. Consequently, actin dynamics are deregulated and this leads to neurite outgrowth inhibition and neurodegeneration [228]. (B) SMN regulates the activation of c-Jun NH₂-Terminal Kinases 3 (JNK3) by an unknown mechanism. When SMN is reduced, there is an increase in phosphorylation and thus activation of JNK3 and a subsequent increase in c-Jun phosphorylation. This increased activation can lead to neurodegeneration [231]. (C) SMN binds to and can regulate the level of Ubiquitin-Like Modifier Activating Enzyme 1 (UBA1; denoted by the dashed arrow). UBA1 can subsequently initiate the ubiquitination pathway that leads to degradation of target proteins. A reduction in UBA1 alters ubiquitin homeostasis and may lead to neurodegeneration [232].