Alternative titles; symbols
Other entities represented in this entry:
HGNC Approved Gene Symbol: POLRMT
Cytogenetic location: 19p13.3 Genomic coordinates (GRCh38): 19:617,221-633,537 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 19p13.3 | Combined oxidative phosphorylation deficiency 55 | 619743 | Autosomal dominant; Autosomal recessive | 3 |
Tiranti et al. (1997) used a gene cloning strategy based on the screening of the expressed sequence tags database (dbEST), using sequences of mitochondrial housekeeping proteins of yeast, to identify the cDNA encoding the precursor of the human mitochondrial RNA polymerase. They identified a 3,831-bp human cDNA predicted to encode a protein of 1,230 amino acid residues. The protein sequence showed significant homology with sequences corresponding to mitochondrial RNA polymerases from lower eukaryotes and to RNA polymerases from several bacteriophages. Mitochondrial RNA polymerase carries out the central activity of mitochondrial gene expression and, by providing the RNA primers for initiation of replication, is also implicated in the maintenance and propagation of the mitochondrial genome. Thus, it is an attractive candidate for disorders of nucleo-mitochondrial intergenomic signaling.
Tiranti et al. (1997) assigned the POLRMT gene, symbolized mtRPOL by them, to chromosome 19 by PCR-based screening of a panel of human/rodent somatic cell hybrids; regionalization to 19p13.3 was performed with a second panel containing different portions of chromosome 19.
Fish et al. (2004) reported the discovery of a mitochondrial DNA heavy strand replication origin at nucleotide position 57 in the strand-displacement loop (D-loop) of several human cell lines (HeLa, A549, and 143B.TK-) and immortalized lymphocytes. The nascent chains starting at this origin, in contrast to those initiated at the previously described origins (Anderson et al., 1981), did not terminate prematurely at the 3-prime end of the D-loop but proceeded well beyond this control point, behaving as 'true' replicating strands. This origin is mainly responsible for mtDNA maintenance under steady-state conditions, whereas mtDNA synthesis from the formerly identified D-loop origins may be more important for recovery after mtDNA depletion and for accelerating mtDNA replication in response to physiologic demands.
Kravchenko et al. (2005) demonstrated that transcription of some mRNAs in human and rodents is mediated by a single-polypeptide nuclear RNA polymerase, which they designated spRNAP-IV. spRNAP-IV is expressed from an alternative transcript of the mitochondrial RNA polymerase gene POLRMT. The spRNAP-IV lacks 262 N-terminal amino acids of mitochondrial RNA polymerase, including the mitochondrial-targeting signal, and localizes to the nucleus. Transcription by spRNAP-IV is resistant to the RNA polymerase II (PolII; see 180660) inhibitor alpha-amanitin but is sensitive to short interfering RNA specific for the POLRMT gene. The promoters for spRNAP-IV differ substantially from those used by RNA PolII, do not respond to transcriptional enhancers, and contain a common functional sequence motif.
Minczuk et al. (2011) found that immobilized mitochondrial elongation factor TEFM (616422) affinity purified with POLRMT, PTCD3 (614918), and DHX30 (616423), in addition to a variable set of mitochondrial ribosomal proteins, from HEK cell mitochondrial extracts. RNase treatment dissociated PTCD3 and DHX30 from the stable POLRMT-TEFM dimer. Mutation analysis revealed that TEFM interacted with the C-terminal catalytic region of POLRMT. In the absence of TEFM, POLRMT yielded short RNA fragments of up to 75 nucleotides long. In the same amount of time, but in the presence of TEFM, POLRMT synthesized RNA products up to 400 nucleotides long. Minczuk et al. (2011) hypothesized that TEFM functions as a mitochondrial transcription elongation factor.
Crystal Structure
Ringel et al. (2011) reported the crystal structure of mtRNAP at 2.5-angstrom resolution, which revealed a T7-like catalytic C-terminal domain, an N-terminal domain that remotely resembles the T7 promoter-binding domain, a novel pentatricopeptide repeat domain, and a flexible N-terminal extension. The pentatricopeptide repeat domain sequesters an AT-rich recognition loop, which binds promoter DNA in T7 RNAP, probably explaining the need for TFAM (600438) during promoter binding. Consistent with this, substitution of a conserved arginine residue in the AT-rich recognition loop, or release of this loop by deletion of the N-terminal part of mtRNAP, had no effect on transcription. The fingers domain and the intercalating hairpin, which melts DNA in phage RNAPs, are repositioned, explaining the need for TFB2M (607055) during promoter melting. Ringel et al. (2011) concluded that their results provided a new venue for the mechanistic analysis of mitochondrial transcription, and also indicated how an early phage-like mtRNAP lost functions in promoter binding and melting, which were provided by initiation factors in trans during evolution, to enable mitochondrial gene regulation and the adaptation of mitochondrial function to changes in the environment.
In 8 patients from 7 unrelated families with combined oxidative phosphorylation deficiency-55 (COXPD55; 619743), Olahova et al. (2021) identified heterozygous, homozygous, or compound heterozygous mutations in the POLRMT gene (601778.0001-601778.0011). The mutations were identified by whole-exome sequencing, whole-genome sequencing, or sequencing of a panel of nuclear-encoded mitochondrial genes. Functional studies of recombinant POLRMT carried out in all but 2 of the mutations indicated abnormalities in transcription initiation and elongation.
Mitochondria of all organisms contain a genome that is distinct from that of the nucleus. The circular mitochondrial chromosome contains 37 genes that encode the RNA components of the mitochondrial translational apparatus, i.e., 22 transfer RNAs and 2 ribosomal RNA genes, as well as 13 polypeptide-encoding genes. All 13 polypeptides are essential components of 4 of the 5 complexes that form the mitochondrial oxidative phosphorylation (OXPHOS) pathway (complexes I, III, IV, and V). However, gene expression in mitochondria relies upon numerous nuclear genes that encode protein components required for transcription and translation of the mtDNA-encoded genes, as well as protein and RNA components required for replication of mtDNA. In addition, nuclear genes encode factors controlling the import, assembly, and turnover of OXPHOS complexes, and proteins acting as general regulators of mitochondrial function. Nuclear-encoded mitochondrial proteins are synthesized by cytoplasmic ribosomes, usually as precursors containing an N-terminal extension. Import into mitochondria is carried out by a complex, ATP-dependent transport system, followed by cleavage of the leader peptide, which eventually produces a mature, functional protein. Tiranti et al. (1997) noted that abnormalities in the nuclear genome repertoire controlling mitochondrial biogenesis were proposed as the cause of some human disorders characterized by the presence of mtDNA abnormalities and mendelian transmission. Both autosomal dominant (157640) and autosomal recessive (258450) forms of chronic progressive external ophthalmoplegia are associated with the accumulation of multiple deletions of mtDNA in stable tissues. Another example is tissue-specific mtDNA depletion (251880), an autosomal recessive disorder causing severe organ-specific syndromes in early infancy. Mendelian inheritance indicates the presence of transmissible mutations in nuclear genes that can ultimately damage the structural integrity of the mtDNA molecule or its copy number. Genes involved in the control of mtDNA replication and expression are considered attractive candidates for these disorders. The characterization of the collection of human proteins related to mitochondria, the so-called human mitochondrial proteome, is important in the elucidation of fundamental mechanisms of nucleo-mitochondrial intergenomic signaling, as well as to clinical researchers interested in mitochondrial disorders.
Tiranti et al. (1997) referred to 'cyberscreening' of sequence databases, based on yeast-human cross-species comparison, as a powerful, simple, rapid, and inexpensive method for the molecular dissection of the human mitochondrial proteome. Cyberscreening might also be referred to as 'cloning in silico.'
The term proteome appears first to have been used by Humphery-Smith et al. (1994) and his colleagues (Wasinger et al., 1995) to refer to the total protein complement of a genome. (They described methods that allowed proteins to be identified prior to detection of their respective genes.)
In a 17-year-old girl (patient 1) with combined oxidative phosphorylation deficiency-55 (COXPD55; 619743), who was previously reported by Bowden et al. (2013), Olahova et al. (2021) identified 3 mutations in the POLRMT gene: a c.1696C-T transition (c.1696C-T, NM_005035.3), resulting in a pro566-to-ser (P566S) substitution, in cis with a c.3578C-T transition (c.3578C-T, NM_005035.3), resulting in a ser1193-to-phe (S1193F) substitution, which were in trans with a c.2608G-A transition, resulting in an asp870-to-asn (D870N; 601778.0002) substitution. The mutations were found by whole-exome sequencing. The P566S and S1193F mutations were paternally inherited and the D870N mutation was maternally inherited. In the gnomAD database, the P566S mutation was present in 401/200,344 alleles, only in heterozygous state (allele frequency of 2.0 x 10(-3)), the S1193F mutation was present in 42/279,886 alleles, only in heterozygous state (allele frequency of 1.61 x 10(-3)), and the D870N mutation was present in 992/275,368 alleles (allele frequency of 3.6 x 10(-3)) and included 7 homozygotes. The mutations were predicted to affect stabilization of the core structure of POLRMT. Functional studies of recombinant POLRMT with the P556S/S1193F mutation resulted in mild reduction in initiation of transcription, and functional studies of recombinant POLRMT with the D870N mutation resulted in severely reduced transcription. The combination of the 2 mutant POLRMT forms resulted in intermediate reduction in transcription.
For discussion of the c.2608G-A transition (c.2608G-A, NM_005035.3) in the POLRMT gene, resulting in an asp870-to-asn (D870N) substitution, that was found in compound heterozygous state in a patient with oxidative phosphorylation deficiency-55 (COXPD55; 619743) by Olahova et al. (2021), see 601778.0001.
In a 20-year-old woman (patient 2) with oxidative phosphorylation deficiency-55 (COXPD55; 619743), Olahova et al. (2021) identified compound heterozygous mutations in the POLRMT gene: a c.748C-G transversion (c.748C-G, NM_005035.3), resulting in a his250-to-asp (H250D) substitution, and an 18-bp deletion (c.2225_2242del; 601778.0004), resulting in an in-frame deletion of amino acids Pro742_Pro747. The mutations, which were identified by sequencing of a gene panel of 406 nuclear-encoded mitochondrial genes, were shown by Sanger sequencing to be in trans. In the gnomAD database, the H250D mutation was present in 50/276,422 alleles (allele frequency of 1.81 x 10(-4)) and the Pro742_Pro747del mutation was present in 8/47,292 alleles (allele frequency of 1.69 x 10(-4)), only in heterozygous state. Functional studies of recombinant POLRMT with the H250D mutation resulted in a mild reduction in initiation of transcription, and functional studies of recombinant POLRMT with the Pro742_Pro747del mutation resulted in severely reduced transcription. The combination of the 2 mutant POLRMT forms resulted in intermediate reduction in transcription.
For discussion of the 18-bp deletion (c.2225_2242del, NM_005035.3) in the POLRMT gene, resulting in an in-frame deletion of amino acids Pro742_Pro747, that was found in compound heterozygous state in a patient with oxidative phosphorylation deficiency-55 (COXPD55; 619743) by Olahova et al. (2021), see 601778.0003.
In a 58-year-old man (patient 3) with oxidative phosphorylation deficiency-55 (COXPD55; 619743), Olahova et al. (2021) identified a heterozygous c.2641-1G-C transversion (c.2641-1G-C, NM_005035.3) in the splice acceptor site of intron 10 of the POLRMT gene, predicted to result in an in-frame deletion of amino acids Gly881_Lys883. The mutation was identified by whole-exome sequencing and confirmed by Sanger sequencing. Familial segregation studies were not done. The mutation was present in the gnomAD database at a frequency of 9.49 x 10(-6) in only heterozygous state. Studies in patient fibroblasts confirmed that the mutant transcript was not subject to nonsense-mediated decay. Functional studies of recombinant POLRMT with the c.2641-1G-C mutation resulted in severely reduced promoter-dependent transcription initiation activity but only mildly reduced single nucleotide incorporation activity. Olahova et al. (2021) concluded that the mutant POLRMT exerted a dominant-negative effect over the wildtype POLRMT, possibly due to an inability to switch between initiation and elongation activities.
In a 3-year-old boy (patient 4) with oxidative phosphorylation deficiency-55 (COXPD55; 619743), Olahova et al. (2021) identified a de novo heterozygous c.1832C-T transition (c.1832C-T, NM_005035.3) in the POLRMT gene, predicted to result in a ser611-to-phe (S611F) substitution. The de novo mutation was identified by trio whole-exome sequencing and confirmed by Sanger sequencing. The S611F mutation was absent in the gnomAD and 1000 Genomes Project databases. The mutation was predicted to affect protein-protein interactions involved in cofactor binding. Functional studies of recombinant POLRMT with the S611F mutation resulted in reduced promoter-dependent transcription initiation activity and reduced single-nucleotide incorporation activity.
In a 10-year-old Iranian boy (patient 5), born to consanguineous parents, with oxidative phosphorylation deficiency-55 (COXPD55; 619743), Olahova et al. (2021) identified a homozygous c.1923C-G transversion (c.1923C-G, NM_005035.3) in the POLRMT gene, predicted to result in a phe641-to-leu (F641L) substitution at a conserved residue. The mutation was identified by trio whole-exome sequencing and the parents were confirmed to be mutation carriers. The F641L mutation was present in 1/237,432 alleles in only heterozygous state in the gnomAD database (allele frequency of 4.21 x 10(-6)). The mutation was predicted to affect stabilization of the core structure of the protein. Functional studies of recombinant POLRMT with the F641L mutation resulted in reduced promoter-dependent transcription initiation activity and reduced single-nucleotide incorporation activity.
In a 14-year-old girl (patient 6) with oxidative phosphorylation deficiency-55 (COXPD55; 619743), Olahova et al. (2021) identified compound heterozygosity for 2 mutations in the POLRMT gene: a c.2775C-A transversion (c.2775C-A, NM_005035.3), resulting in a cys925-to-ter (C925X) substitution, and a c.2428C-T transition, resulting in a pro810-to-ser (P810S; 601778.0010). The mutations were identified by trio whole-exome sequencing and the parents were confirmed to be mutation carriers. In the gnomAD database, the C925X mutation was present in 4/31,368 alleles, only in heterozygous state (allele frequency of 1.28 x 10(-4)), and the P810S mutation was present in 386/264,146 alleles (allele frequency of 1.46 x 10(-3)), which included 4 homozygotes. The mutations were predicted to affect stabilization of the core structure of the protein. Functional studies of recombinant POLRMT with the P810S mutation resulted in reduced promoter-dependent transcription initiation activity and reduced single-nucleotide incorporation activity.
For discussion of the c.2428C-T transition (c.2428C-T, NM_005035.3) in the POLRMT gene, resulting in a pro810-to-ser (P810S) substitution, that was identified in compound heterozygous state in a patient with oxidative phosphorylation deficiency-55 (COXPD55 619743) by Olahova et al. (2021), see 601778.0008.
In 2 sibs (patients 7 and 8) with oxidative phosphorylation deficiency-55 (COXPD55; 619743), Olahova et al. (2021) identified compound heterozygosity for 2 mutations in the POLRMT gene: a c.445C-T transition (c.445C-T, NM_005035.3), resulting in a gln149-to-ter (Q149X) substitution, and a c.3037C-T transition, resulting in an arg1013-to-cys (R1013C; 601778.0011) substitution. The mutations were identified by whole-exome sequencing; parental segregation was not possible, but an unaffected sib was confirmed to be a mutation carrier. In the gnomAD database, the Q149X mutation was present in 1/249,286 alleles (allele frequency of 4.1 x 10(-6)), whereas the R1013C mutation was not present. The mutations were predicted to affect stabilization of the core structure of POLRMT. Functional studies of recombinant POLRMT with the R1013C mutation resulted in reduced promoter-dependent transcription initiation activity and reduced single-nucleotide incorporation activity.
For discussion of the c.3037C-T transition (c.3037C-T, NM_005035.3) in the POLRMT gene, resulting in an arg1013-to-cys (R1013C) substitution, that was identified in compound heterozygous state in 2 sibs with oxidative phosphorylation deficiency-55 (COXPD55; 619743) by Olahova et al. (2021), see 601778.0010.
Anderson, S., Bankier, A. T., Barrell, B. G., de Bruijn, M. H. L., Coulson, A. R., Drouin, J., Eperon, I. C., Nierlich, D. P., Roe, B. A., Sanger, F., Schreier, P. H., Smith, A. J. H., Staden, R., Young, I. G. Sequence and organization of the human mitochondrial genome. Nature 290: 457-465, 1981. [PubMed: 7219534] [Full Text: https://doi.org/10.1038/290457a0]
Bowden, S. A., Patel, H. P., Beebe, A., McBride, K. L. Successful medical therapy for hypophosphatemic rickets due to mitochondrial complex I deficiency induced de Toni-Debre-Fanconi syndrome. Case Rep. Pediat. 2013: 354314, 2013. [PubMed: 24386581] [Full Text: https://doi.org/10.1155/2013/354314]
Fish, J., Raule, N., Attardi, G. Discovery of a major D-loop replication origin reveals two modes of human mtDNA synthesis. Science 306: 2098-2101, 2004. [PubMed: 15604407] [Full Text: https://doi.org/10.1126/science.1102077]
Humphery-Smith, I., Guyonnet, F., Chastel, C. Polypeptide cartography of Spiroplasma taiwanense. Electrophoresis 15: 1212-1217, 1994. Note: Erratum: Electrophoresis 16: 1324 only, 1995. [PubMed: 7859730] [Full Text: https://doi.org/10.1002/elps.11501501183]
Kravchenko, J. E., Rogozin, I. B., Koonin, E. V., Chumakov, P. M. Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. (Letter) Nature 436: 735-739, 2005. [PubMed: 16079853] [Full Text: https://doi.org/10.1038/nature03848]
Minczuk, M., He, J., Duch, A. M., Ettema, T. J., Chlebowski, A., Dzionek, K., Nijtmans, L. G. J., Huynen, M. A., Holt, I. J. TEFM (c17orf42) is necessary for transcription of human mtDNA. Nucleic Acids Res. 39: 4284-4299, 2011. [PubMed: 21278163] [Full Text: https://doi.org/10.1093/nar/gkq1224]
Olahova, M., Peter, B., Szilagyi, Z., Diaz-Maldonado, H., Singh, M., Sommerville, E. W., Blakely, E. L., Collier, J. J., Hoberg, E., Stranecky, V., Hartmannova, H., Bleyer, A. J., and 27 others. POLRMT mutations impair mitochondrial transcription causing neurological disease. Nat. Commun. 12: 1135, 2021. [PubMed: 33602924] [Full Text: https://doi.org/10.1038/s41467-021-21279-0]
Ringel, R., Sologub, M., Morozov, Y. I., Litonin, D., Cramer, P., Temiakov, D. Structure of human mitochondrial RNA polymerase. Nature 478: 269-273, 2011. [PubMed: 21947009] [Full Text: https://doi.org/10.1038/nature10435]
Tiranti, V., Savoia, A., Forti, F., D'Apolito, M.-F., Centra, M., Rocchi, M., Zeviani, M. Identification of the gene encoding the human mitochondrial RNA polymerase (h-mtRPOL) by cyberscreening of the Expressed Sequence Tags database. Hum. Molec. Genet. 6: 615-625, 1997. [PubMed: 9097968] [Full Text: https://doi.org/10.1093/hmg/6.4.615]
Wasinger, V. C., Cordwell, S. J., Cerpa-Poljak, A., Yan, J. X., Gooley, A. A., Wilkins, M. R., Duncan, M. W., Harris, R., Williams, K. L., Humphery-Smith, I. Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16: 1090-1094, 1995. [PubMed: 7498152] [Full Text: https://doi.org/10.1002/elps.11501601185]