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DEBRANCHING RNA LARIATS 1; DBR1

DEBRANCHING RNA LARIATS 1; DBR1

Alternative titles; symbolsDEBRANCHING ENZYME 1, S. CEREVISIAE, HOMOLOG OFHGNC Approved Gene Symbol: DBR1Cytogenetic location: 3q22.3 Genomic coordinates (GR...

Alternative titles; symbols

  • DEBRANCHING ENZYME 1, S. CEREVISIAE, HOMOLOG OF

HGNC Approved Gene Symbol: DBR1

Cytogenetic location: 3q22.3 Genomic coordinates (GRCh38): 3:138,160,987-138,174,920 (from NCBI)

▼ Description
The RNA lariat debranching enzyme, or DBR1, specifically hydrolyzes 2-prime-to-5-prime branched phosphodiester bonds at the branch point of excised lariat intron RNA and converts them into linear molecules (Kim et al., 2000).

▼ Cloning and Expression
By searching EST databases for sequences similar to yeast and worm Dbr1, followed by RT-PCR screening of a HeLa cell cDNA library, Kim et al. (2000) isolated a cDNA encoding human DBR1. The deduced 545-amino acid protein is approximately 42% identical to the fission yeast, budding yeast, and worm enzymes, and is 79% identical to the mouse enzyme. It contains a conserved N terminus, especially within the first 200 residues. Immunoblot analysis showed expression of a 62-kD protein with debranching activity. EST database searching suggested that DBR1 is of extremely low abundance, may be enriched in certain tissues, and has high specific enzymatic activity. Complementation analysis indicated that DBR1 is functional in yeast.

Kim et al. (2001) cloned mouse Dbr1, which encodes a 515-amino acid protein with a calculated molecular mass of 58 kD. Mouse Dbr1 shares significant amino acid identity with its orthologs in other species, including 80% identity with human DBR1.

Zhang et al. (2018) found that the DBR1 gene is expressed throughout the body, with highest expression in human spinal cord and brainstem.

▼ Mapping
Gross (2014) mapped the DBR1 gene to chromosome 3q22.3 based on an alignment of the DBR1 sequence (GenBank AF180919) with the genomic sequence (GRCh38).

▼ Gene Function
Using purified recombinant protein, Kim et al. (2001) showed that mouse Dbr1 was an RNA lariat intron debranching enzyme. Mouse Dbr1 complemented the intron accumulation phenotype in a S. cerevisiae Dbrl-null strain, but the level of complementation depended on the copy number of the Dbr1 cDNA. Mouse Dbr1 also complemented both intron accumulation and slow growth phenotypes of an S. pombe Dbr1-null strain.

Armakola et al. (2012) reported results from 2 genomewide loss-of-function TDP43 (605078) toxicity suppressor screens in yeast. The strongest suppressor of TDP43 toxicity was deletion of DBR1, which encodes an RNA lariat debranching enzyme. Armakola et al. (2012) showed that, in the absence of DBR1 enzymatic activity, intronic lariats accumulate in the cytoplasm and likely act as decoys to sequester TDP43, preventing it from interfering with essential cellular RNAs and RNA-binding proteins. Knockdown of DBR1 in a human neuronal cell line or in primary rat neurons was also sufficient to rescue TDP43 toxicity. Armakola et al. (2012) concluded that their findings provided insight into TDP43-mediated cytotoxicity and suggested that decreasing DBR1 activity could be a potential therapeutic approach for ALS.

▼ Biochemical Features
Using purified recombinant protein, Clark et al. (2016) showed that Dbr1 from Entamoeba histolytica was a binuclear metalloprotein with Fe and Zn as its preferred cofactors. X-ray crystal structures of Dbr1 in complex with its substrates showed that Fe partitioned primarily to the beta pocket of the enzyme, and Zn to the alpha pocket of the enzyme. A water/hydroxide bridged the Fe and Zn ions in optimal position to attack the scissile phosphate in the substrates.

▼ Molecular Genetics
In 4 patients from 2 unrelated families with susceptibility to acute infection (viral)-induced encephalitis-11 (IIAE11; 619441) with a predilection for the brainstem, Zhang et al. (2018) identified homozygous missense mutations in the DBR1 gene (I120T, 607024.0001 and Y17H, 607024.0002). The mutations, which were found by a combination of linkage analysis and whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the families. In a Japanese girl (P7) with IIAE11 and additional clinical features, Zhang et al. (2018) identified compound heterozygous mutations in the DBR1 gene (L13G, 607024.0003 and R197X, 607024.0004). These mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, also segregated with the disorder in the family. The authors postulated that the more severe phenotype in P7 may be due in part to the patient carrying a nonsense mutation in combination with a missense mutation. In vitro expression and functional studies in E. coli, HEK293 cells, and patient fibroblasts showed that the DBR1 mutations resulted in lower levels of full-length DBR1 protein, likely due to instability, as well as significantly decreased DBR1 enzymatic activity compared to controls (less than 15%). Patient fibroblasts had increased intronic RNA lariats compared to controls, indicating impaired DBR1 debranching activity. Complementation studies confirmed that the missense mutations were hypomorphic and that the single nonsense mutation caused a profound loss of function. Detailed studies of fibroblasts derived from patients with missense mutations showed intact TLR3-(603029) and interferon (IFN)-mediated responses and signaling pathways. Patient cells were more susceptible to infection with neurotropic viruses, including HSV-1 and vesicular stomatitis virus (VSV); infection was associated with higher cellular lariat levels, including intronic lariat reads derived from HSV-1 transcripts. Zhang et al. (2018) concluded that DBR1 is part of a cell-intrinsic defense function in the brainstem involving host cell pre-mRNA processing that has an antiviral effect.

▼ ALLELIC VARIANTS ( 4 Selected Examples):

.0001 ENCEPHALITIS, ACUTE, INFECTION-INDUCED (VIRAL), SUSCEPTIBILITY TO, 11
DBR1, ILE120THR
In 2 members of a highly consanguineous Arab family (family A) with susceptibility to acute infection (viral)-induced encephalitis-11 (IIAE11; 619441), Zhang et al. (2018) identified a homozygous c.359T-C transition in exon 3 of the DBR1 gene, resulting in an ile120-to-thr (I120T) substitution at a highly conserved residue in the MPE core domain. The mutation, which was found by a combination of linkage analysis and whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not present in public databases, including gnomAD. Two additional family members had died of the disease in childhood, but DNA was not available for study. The patients had HSV-1 encephalitis with a predilection to the brainstem.

.0002 ENCEPHALITIS, ACUTE, INFECTION-INDUCED (VIRAL), SUSCEPTIBILITY TO, 11
DBR1, TYR17HIS
In 2 sisters, born of unrelated Portuguese parents (family B) with susceptibility to acute infection (viral)-induced encephalitis-11 (IIAE11; 619441), Zhang et al. (2018) identified a homozygous c.49T-C transition in exon 1, resulting in a tyr17-to-his (Y17H) substitution at a conserved residue in the MPE core domain. The mutation, which was found by a combination of linkage analysis and whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not present in public databases, including gnomAD. The patients had influenza B virus (IBV) encephalitis with a predilection to the brainstem.

.0003 ENCEPHALITIS, ACUTE, INFECTION-INDUCED (VIRAL), SUSCEPTIBILITY TO, 11
DBR1, LEU13GLY
In a Japanese girl (P7), born of unrelated parents, with susceptibility to acute infection (viral)-induced encephalitis-11 (IIAE11; 619441) Zhang et al. (2018) identified compound heterozygous mutations in the DBR1 gene: c.37-38CT-GG transversions in exon 1 of the DBR1 gene, resulting in a leu13-to-gly (L13G) substitution at a highly conserved residue in the MPE core domain, and a c.589C-T transition in exon 5, resulting in an arg197-to-ter (R197X; 607024.0004) substitution. The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. The L13G mutation was not present in the gnomAD database, whereas R197X was found in the heterozygous state in 6 individuals from gnomAD (frequency of 2.17 x 10(-5)). In addition to fatal viral encephalitis affecting the brainstem due to norovirus (NV) infection, the patient had intrauterine growth retardation, impaired intellectual development, curly hair, and congenital neutropenia. The authors postulated that the more severe phenotype in this patient may be due in part to the truncating mutation, which would have a more detrimental effect on DBR1 function. Patient cells were not available, but in vitro cellular expression studies in E. coli and HEK293 cells showed very low expression of the full-length DBR1 protein and impaired DBR1 debranching enzyme activity compared to controls, consistent with a hypomorphic effect.

.0004 ENCEPHALITIS, ACUTE, INFECTION-INDUCED (VIRAL), SUSCEPTIBILITY TO, 11
DBR1, ARG197TER
For discussion of the c.589C-T transition in exon 5 of the DBR1 gene, resulting in an arg197-to-ter (R197X) substitution, that was found in compound heterozygous state in a patient with susceptibility to acute infection (viral)-induced encephalitis-11 (IIAE11; 619441) by Zhang et al. (2018), see 607024.0003.

Tags: 3q22.3