Matrin3: Disorder and ALS Pathogenesis

Abstract

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the degeneration of both upper and lower motor neurons in the brain and spinal cord. ALS is associated with protein misfolding and inclusion formation involving RNA-binding proteins, including TAR DNA-binding protein (TDP-43) and fused in sarcoma (FUS). The 125-kDa Matrin3 is a highly conserved nuclear DNA/RNA-binding protein that is implicated in many cellular processes, including binding and stabilizing mRNA, regulating mRNA nuclear export, modulating alternative splicing, and managing chromosomal distribution. Mutations in MATR3, the gene encoding Matrin3, have been identified as causal in familial ALS (fALS). Matrin3 lacks a prion-like domain that characterizes many other ALS-associated RNA-binding proteins, including TDP-43 and FUS, however, our bioinformatics analyses and preliminary studies document that Matrin3 contains long intrinsically disordered regions that may facilitate promiscuous interactions with many proteins and may contribute to its misfolding. In addition, these disordered regions in Matrin3 undergo numerous post-translational modifications, including phosphorylation, ubiquitination and acetylation that modulate the function and misfolding of the protein. Here we discuss the disordered nature of Matrin3 and review the factors that may promote its misfolding and aggregation, two elements that might explain its role in ALS pathogenesis.

Keywords: ALS; Matrin3; intrinsically disordered domains; protein misfolding; proteinopathy.

FIGURE 1

Matrin3 sequence and structure. (A) The relative locations of the domains/motifs of Matrin3 (nuclear export signal (NES), Zinc-finger motif (ZnF), RNA-recognition motif (RRM) and nuclear localization signal (NLS)) are indicated approximately. Motif assignment is based on Interpro (Blum et al., 2020) and numerical values indicate the boundaries. (B) AlphaFold2 structure prediction of Matrin3, with the two RRM and two ZnF motifs colored to match the sequence graphic. Zinc-coordinating residues are indicated as sticks in the ZnF motif structures.

FIGURE 2

Structural ensembles of Matrin3, FUS and TDP-43. (A) RNA-recognition motif (RRM) 1 from Matrin3 and the βαββαβ-structure is colored and indicated. (B) All RRMs in Matrin3, FUS, and TDP-43 are colored (blue: Matrin3-RRM1, yellow: Matrin3-RRM2, green: FUS, magenta: TDP-43-RRM1 and orange: TDP-43-RRM2) and superimposed. Significant homology is evident and FUS shows the greatest deviation within the ensemble (green). (C) C2H2 Zinc-finger motif (ZnF) 1 from Matrin3 and the ββα-structure is colored and indicated. Zinc-coordinating residues (two cysteines and two histidines) are indicated as sticks. (D) The disordered RanBP2-type ZnF found in FUS is shown. Zinc-coordinating residues (four cysteines) are indicated as sticks. (E) Both ZnF motifs in Matrin3 are colored (blue: ZnF1 and yellow: ZnF2) and superimposed, significant homology is evident. All structures are based on AlphaFold2 (Jumper et al., 2021) predictions.

FIGURE 3

Shared interaction partners between Matrin3, FUS and TDP-43. Venn diagram showing the overlapping protein interaction partners shared between three primary ALS proteins. The appreviation ‘H’ is used for “HNRNP” (i.e., HNRNPA1 = H_A1). Interaction assignment is based on the STRING protein-protein interaction network (Szklarczyk et al., 2018).

FIGURE 4

Sequence disorder analysis. (A) Charge-hydropathy plot. The plot is based on the method introduced by Uversky et al. (Uversky et al., 2000; Uversky, 2017) and compares the mean net charge and mean Kyte-Doolittle hydropathy (Kyte and Doolittle, 1982) (scaled between 0 and 1). Linear boundaries are used to separate various groups of proteins (from left to right extended IDPs, compact soluble proteins, and insoluble proteins). A random sample of ordered (blue) and disordered (red) proteins was taken from the Swiss-Prot (The UniProt Consortium, 2018) and Disprot 7.0 (Piovesan et al., 2016) databases respectively and plotted. Matrin3, FUS and TDP-43 are indicated. (B) ODR ratio distribution plot. The same sample as in (A) was used to compute the ratio of the order-promoting to disorder-promoting residues with value truncation at 0 and 2. Disordered proteins (red) show a lower ratio (i.e., more disorderpromoting) than ordered proteins (blue).

FIGURE 5

TDP-43 and Matrin3 disorder prediction. Four webservers MFDp2 (Mizianty et al., 2010; Mizianty et al., 2011; Mizianty et al., 2013), PONDR-Fit (Xue et al., 2010), IUPred2A (Mészáros et al., 2018), and DISOPRED3 (Jones and Cozzetto, 2014; Buchan and Jones, 2019) were chosen based on documented performance (Nielsen and Mulder, 2019). A confidence value below 0.5 indicates a residue is likely to belong to an ordered region, while a value above 0.5 indicates a residue is likely to belong to a disordered region. Motifs are indicated and colored in grey as a background on the plot. Motif assignment is based on the InterPro (Blum et al., 2020) and numerical values indicate the boundaries.

FIGURE 6

Mutation and post-translational modifications of Matrin3. (A) Variant data was plotted as a function of residue index. Variants include those reported to be associated with ALS within the relevant literature and those identified in the ALS Knowledge Portal (Farhan et al., 2019) and/or Project MinE (Project MinE ALS Sequencing Consortium, 2018) ALS whole genomes. Variants observed in the ALS Knowledge Portal or Project MinE ALS whole genomes were only included if the variant had not been observed in the respective study’s control cohort. All previously reported variants were missense variants. Red and blue points indicate variants that were absent or occurred at low frequency (minor allele frequency < 0.001) in the gnomAD (v2.1 non-neuro) database. (B) Phopshositeplus (Hornbeck et al., 2014) data was plotted as a function of residue index. High- and low throughput studies were simply summed and the height of the most modified residue S188 (390 references/counts) was reduced for plotting purposes. Motifs are indicated and colored in grey as a background on the plot. Motif assignment is based on the InterPro (Blum et al., 2020) and numerical values indicate the boundaries.