XB-ART-60388
Cells
2023 Oct 13;1220:. doi: 10.3390/cells12202449.
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Thirty Years with ERH: An mRNA Splicing and Mitosis Factor Only or Rather a Novel Genome Integrity Protector?
Kozlowski P
.
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ERH is a 100 to about 110 aa nuclear protein with unique primary and three-dimensional structures that are very conserved from simple eukaryotes to humans, albeit some species have lost its gene, with most higher fungi being a noteworthy example. Initially, studies on Drosophila melanogaster implied its function in pyrimidine metabolism. Subsequently, research on Xenopus laevis suggested that it acts as a transcriptional repressor. Finally, studies in humans pointed to a role in pre-mRNA splicing and in mitosis but further research, also in Caenorhabditis elegans and Schizosaccharomyces pombe, demonstrated its much broader activity, namely involvement in the biogenesis of mRNA, and miRNA, piRNA and some other ncRNAs, and in repressive heterochromatin formation. ERH interacts with numerous, mostly taxon-specific proteins, like Mmi1 and Mei2 in S. pombe, PID-3/PICS-1, TOST-1 and PID-1 in C. elegans, and DGCR8, CIZ1, PDIP46/SKAR and SAFB1/2 in humans. There are, however, some common themes in this wide range of processes and partners, such as: (a) ERH homodimerizes to form a scaffold for several complexes involved in the metabolism of nucleic acids, (b) all these RNAs are RNA polymerase II transcripts, (c) pre-mRNAs, whose splicing depends on ERH, are enriched in transcripts of DNA damage response and DNA metabolism genes, and (d) heterochromatin is formed to silence unwanted transcription, e.g., from repetitive elements. Thus, it seems that ERH has been adopted for various pathways that serve to maintain genome integrity.
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Species referenced: Xenopus laevis
Genes referenced: dgcr8 erh tbl1x
GO keywords: RNA splicing
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Figure 1. Comparison of amino acid sequences of the ERH proteins from the indicated organisms. For C. elegans and P. patens, both of their ERH paralogs are shown; the other species possess only one ERH. The species belonging to the same taxon (Metazoa, Choanoflagellata, Fungi, Amoebozoa, Archaeplastida and SAR [9]) are grouped together using the same color background. For each protein, the UniProt (www.uniprot.org) identifier, its length and its homology to the human ERH are shown. Vertical bars with numbers above the alignment indicate every tenth amino acid residue in the human ERH polypeptide chain. Numbers at the end of each line in the upper section of the alignment indicate the position of the last amino acid residue from each sequence shown in this section. A space sign signifies no amino acid residue and a dot sign indicates a residue identical with that in the human ERH. Residues in the human ERH that are identical in all sequences are highlighted in green, while those that are identical or conserved substitutions in the other sequences are highlighted in yellow. The secondary structures of the human ERH (PDB ID: 2NML) are shown above the alignment (the 3 α-helices as pink barrels, the 310-helix as a violet barrel and the 4 β-strands as yellow arrows). The α-helices are designated as α1, α2 and α3 and the β-strands as β1, β2, β3 and β4 according to the order of their appearance in the polypeptide chain starting from the N-terminus; numbers in parentheses indicate the position of the structure in the chain. A dashed line denotes the α1-α2 loop. |
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Figure 2. Comparison of intron positions in the ERH genes from the indicated organisms. The species belonging to the same taxon (Metazoa, Choanoflagellata, Fungi, Amoebozoa, Archaeplastida and SAR [9]) are grouped together using the same color background. Introns are marked with triangles and numbers that indicate their phases (0, 1 and 2) and their positions are shown above a schematic based on the human ERH coding sequence (CDS), represented by a black solid line with a white segment to indicate the location of the 4- and 5-amino acid deletions present in the S. pombe and S. japonicus erh1 CDSs, respectively, and grey segments to indicate additional fragments present in some ERH CDSs; numbering is according to the human ERH CDS. Introns with the same phase and the same position in two or more CDSs are connected by dashed vertical lines. The C. elegans genes are represented by erh-1 only since they share exactly the same positions for all their introns. The Ensembl (www.ensembl.org) identifiers for the sequences of the ERH genes are: H. sapiens (Ensembl vertebrates: ENST00000557016.6), C. elegans (Ensembl Metazoa: T21C9.4.1), S. rosetta (Ensembl Protists: EGD79537), S. pombe (Ensembl Fungi: SPAC19G12.17.1), S. japonicus (Ensembl Fungi: EEB06811), D. discoideum (Ensembl Protists: EAL70175), A. thaliana (Ensembl Plants: AT5G10810.1), C. merolae (Ensembl Plants: CMR260CT), T. gondii (Ensembl Protists: ESS33368) and S. parasitica (Ensembl Protists: KDO23370). |
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Figure 3. Three-dimensional structure of ERH and its protein partner binding sites. (A) The structure of the human ERH monomer (PDB ID: 2NML) is a screenshot from RCSB PDB (www.rcsb.org, accessed on 8 October 2023) and the secondary structures are shown in different colors (the α-helices α1, α2 and α3 with pink, the 310-helix with violet, the β-strands β1, β2, β3 and β4 with yellow, and turns with blue). The α1-α2 loop and the N- and C-termini are also indicated. (B) The homo-dimeric assembly of the human ERH colored by chain (PDB ID: 2NML) is a screenshot from PDBe (www.ebi.ac.uk/pdbe, accessed on 8 October 2023). Arrows indicate the rough locations of the partner binding sites (only one from each pair of the binding sites is shown) and the ERH partners from different species are grouped together in boxes according to the binding sites based on the structural studies (the PDB identifiers for the structures with the partners are: 7CNC for the human ERH with DGCR8, 7X39 for the human ERH with CIZ1, 7O6N and 7EJS for the C. elegans ERH-2 with PID-3/PICS-1, 7EJO for the C. elegans ERH-2 with TOST-1 and 6AKJ for the S. pombe Erh1 with Mmi1). PID-1 competed with TOST-1 for the binding to ERH and PDIP46/SKAR interacted with ERH through the ERH homodimer interface, but these interactions have not yet been verified by crystal structures. |
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Figure 4. Diagrammatic summary of the ERH functions, including the proposed genome integrity maintenance. Question marks indicate processes in which the involvement of ERH has not been proven. The ERH icon was downloaded from PDBe (www.ebi.ac.uk/pdbe, accessed on 20 August 2023). The names of the ERH partners are on colored backgrounds according to the species (in S. pombe blue, in C. elegans green, and in H. sapiens dark orange for the direct binding partners and light orange for those that have not been demonstrated to interact with ERH directly). The names of the complexes are highlighted in grey and these comprising ERH are outlined with a dashed line. |
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