RPO41 encodes the catalytic core subunit of the Saccharomyces cerevisiae mitochondrial RNA polymerase, a nuclear-encoded, 1351-residue single-subunit enzyme homologous to the RNA polymerases of bacteriophages T7 and T3, imported into the mitochondrial matrix via an N-terminal targeting sequence. Rpo41 associates with the sigma-like specificity factor Mtf1 to form the holoenzyme that melts and initiates transcription at the nonanucleotide (ATATAAGTA) mitochondrial promoters; Mtf1 is released after initiation and Rpo41 alone carries out elongation. Rpo41 can recognise and initiate from promoters by itself on supercoiled or premelted templates, but requires Mtf1 to open closed duplex promoters. It is found in mitochondrial nucleoids and is required for transcription of all mitochondrial genes and for stable maintenance of the wild-type mitochondrial genome. Its transcripts can serve as primers for the mitochondrial DNA polymerase Mip1 in vitro, and its yeast-specific amino-terminal extension supports mtDNA stability by a mechanism separable from RNA synthesis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001018 mitochondrial promoter sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of mitochondrial promoter-specific DNA binding from PANTHER node PTN000010147, whose experimental donor is S. pombe rpo41. Reason: RPO41 sits in the same PANTHER subfamily (PTHR10102:SF0) as the donor, and the inference is independently supported in S. cerevisiae. Core Rpo41 has an intrinsic, promoter sequence-dependent ability to initiate on supercoiled or premelted templates, so recognition of the ATATAAGTA promoter is a property of Rpo41 itself, not only of Mtf1. On closed duplex DNA, Rpo41 alone binds promoter and non-promoter DNA similarly and selectivity emerges in the holoenzyme; the term is therefore correct but realised in the Rpo41-Mtf1 context. Supporting Evidence: PMID:15342628 Rpo41 requires the mitochondrial promoter sequence (ATATAAGTA) for this activity. PMID:21911502 Recent studies indicate that Rpo41 and Mtf1 together contact the promoter within and immediately adjacent to the −10 to +5 region |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO DNA binding from the phage-type RNA polymerase signature. Reason: Correct but general. Rpo41 binds DNA directly (measured by fluorescence anisotropy) and recognises the mitochondrial promoter sequence, so the informative term is mitochondrial promoter sequence-specific DNA binding, which the gene already carries by IBA. Proposed replacements: mitochondrial promoter sequence-specific DNA binding Supporting Evidence: PMID:21911502 We have used fluorescence-based approaches to quantify DNA binding, bending, and opening steps by the core mtRNAP subunit (Rpo41) and the transcription factor (Mtf1). PMID:15342628 Rpo41 requires the mitochondrial promoter sequence (ATATAAGTA) for this activity. |
| GO:0003899 DNA-directed RNA polymerase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of DNA-directed RNA polymerase activity from PTN000010146, to which this gene (SGD:S000001858) is itself an experimental donor. Reason: Core catalytic function, conserved across the phage/mitochondrial RNA polymerase family. The presence of SGD:S000001858 among the donors reflects the direct experimental evidence on this protein and indicates that the activity is inherited, not lineage-specific. Supporting Evidence: PMID:7929382 The yeast mitochondrial RNA polymerase is composed of two nuclear encoded subunits, a catalytic core (Rpo41p), which resembles the enzymes from bacteriophage T7 and T3 PMID:3308116 the mitochondrial enzyme is highly homologous to the DNA-directed RNA polymerases of bacteriophages T3 and T7 |
| GO:0003899 DNA-directed RNA polymerase activity | IDA PMID:2426263 Isolation of the nuclear gene encoding a subunit of the yeas... | ACCEPT | Summary: The gene was cloned using antisera against the 145 kDa subunit of the purified mitochondrial RNA polymerase. Reason: The protein is the large subunit of the biochemically purified mitochondrial RNA polymerase activity. Abstract-only cache; curators had the full text, and the activity is independently confirmed with recombinant protein in later work. Supporting Evidence: PMID:2426263 Antisera directed against the purified 145,000-dalton subunit of the Saccharomyces cerevisiae mitochondrial RNA polymerase have been used to immuno-screen a library of yeast genomic inserts |
| GO:0003899 DNA-directed RNA polymerase activity | IDA PMID:26184436 Yeast mitochondrial RNA polymerase primes mitochondrial DNA ... | ACCEPT | Summary: Purified Rpo41 synthesizes RNAs on single- and double-stranded DNA templates that Mip1 can extend. Reason: Direct in vitro RNA synthesis by purified Rpo41. Supporting Evidence: PMID:26184436 Herein we found that Rpo41 transcribes RNAs that can be extended by Mip1 on single and double-stranded DNA. |
| GO:0003899 DNA-directed RNA polymerase activity | IDA PMID:3517858 Yeast RPO41 gene product is required for transcription and m... | ACCEPT | Summary: Identification of RPO41 as the gene for the 145 kDa subunit of the mitochondrial RNA polymerase. Reason: Consistent with the purified-enzyme and recombinant-protein evidence. Abstract-only cache; curator judgment deferred to. Supporting Evidence: PMID:3517858 appears to contain most of the coding information for the 145-kDa subunit of the Saccharomyces cerevisiae mitochondrial RNA polymerase |
| GO:0003899 DNA-directed RNA polymerase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated annotation of DNA-directed RNA polymerase activity. Reason: Consistent with family membership and direct experimental evidence. Supporting Evidence: file:yeast/RPO41/RPO41-uniprot.txt Belongs to the phage and mitochondrial RNA polymerase family. PMID:27311715 Both Rpo41 and Rpo41-Mtf1 can synthesize short and long RNAs on ssDNA template |
| GO:0005737 cytoplasm | HDA PMID:22842922 Dissecting DNA damage response pathways by analysing protein... | MODIFY | Summary: High-throughput GFP localisation screen assigned the fusion to cytoplasm. Reason: Mitochondria are part of the cytoplasm in GO, so the term is not false, but it is far less specific than the established location. Rpo41 is a matrix protein (IDA) found in mtDNA nucleoids; there is no evidence for a cytosolic pool with a function. Proposed replacements: mitochondrial matrix Supporting Evidence: PMID:15692048 We have identified 22 mtDNA-associated proteins in yeast |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | MODIFY | Summary: Detected in the purified mitochondrial proteome. Reason: Correct but general; the gene already carries the more specific mitochondrial matrix (IDA) and mitochondrial nucleoid (IDA). Proposed replacements: mitochondrial matrix Supporting Evidence: PMID:7929382 The yeast mitochondrial RNA polymerase is composed of two nuclear encoded subunits |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | MODIFY | Summary: Detected in quantitative mitochondrial proteomics. Reason: Correct but general; replace with mitochondrial matrix, which the gene already carries by IDA. Proposed replacements: mitochondrial matrix |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | MODIFY | Summary: UniProt subcellular location mapping (Mitochondrion). Reason: Correct but general; replace with mitochondrial matrix, which the gene already carries by IDA. Proposed replacements: mitochondrial matrix |
| GO:0005739 mitochondrion | NAS PMID:7929382 Release of the yeast mitochondrial RNA polymerase specificit... | MODIFY | Summary: Author statement that Rpo41 is a subunit of the mitochondrial RNA polymerase. Reason: Correct but general; replace with mitochondrial matrix, which the gene already carries by IDA. Proposed replacements: mitochondrial matrix Supporting Evidence: PMID:7929382 The yeast mitochondrial RNA polymerase is composed of two nuclear encoded subunits |
| GO:0005759 mitochondrial matrix | IDA PMID:2426263 Isolation of the nuclear gene encoding a subunit of the yeas... | ACCEPT | Summary: Rpo41 is the large subunit of the RNA polymerase purified from yeast mitochondria. Reason: The mitochondrial RNA polymerase transcribes mtDNA in the matrix; consistent with nucleoid association. Abstract-only cache; curator judgment deferred to. Supporting Evidence: PMID:2426263 the purified 145,000-dalton subunit of the Saccharomyces cerevisiae mitochondrial RNA polymerase |
| GO:0005759 mitochondrial matrix | IDA PMID:3517858 Yeast RPO41 gene product is required for transcription and m... | ACCEPT | Summary: Rpo41 encodes the subunit of the mitochondrial RNA polymerase required for mtDNA transcription. Reason: Matrix location of the mtDNA transcription machinery. Abstract-only cache; curator judgment deferred to. Supporting Evidence: PMID:3517858 its product is required for transcription and maintenance of the mitochondrial genome |
| GO:0006269 DNA replication, synthesis of primer | IDA PMID:26184436 Yeast mitochondrial RNA polymerase primes mitochondrial DNA ... | KEEP AS NON CORE | Summary: In vitro, Rpo41 transcripts from replication origins and promoters prime DNA synthesis by Mip1. Reason: Rpo41 itself catalyses the primer synthesis in the reconstituted assays, so this is participation, not mere necessity, and a second laboratory showed efficient priming by Rpo41-Mtf1 on Rim1-coated ssDNA. However, the evidence is entirely in vitro, and genetic data indicate that transcriptional priming is not required for at least some mtDNA replication in vivo, so the role is kept as non-core rather than as a core function. Supporting Evidence: PMID:26184436 Rpo41 primes Mip1 at replication origins and promoter sequences in vitro. PMID:27311715 the Saccharomyces cerevisiae mitochondrial RNA polymerase (Rpo41) and its transcription factor (Mtf1) is an efficient primase that initiates DNA synthesis on ssDNA coated with the yeast mitochondrial ssDNA-binding protein, Rim1. PMID:7651397 priming by transcription is not a universal mechanism for mtDNA replication initiation |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO DNA-templated transcription. Reason: Correct but general; Rpo41 transcribes the mitochondrial genome, and the gene already carries mitochondrial transcription (IDA, IMP, IBA). Proposed replacements: mitochondrial transcription Supporting Evidence: PMID:3517858 its product is required for transcription and maintenance of the mitochondrial genome |
| GO:0006390 mitochondrial transcription | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of mitochondrial transcription; this gene is an experimental donor to the node. Reason: Core process, directly established in S. cerevisiae and inherited across the mitochondrial RNA polymerase subfamily. Supporting Evidence: PMID:3517858 its product is required for transcription and maintenance of the mitochondrial genome |
| GO:0006390 mitochondrial transcription | IDA PMID:21911502 Transcription factor-dependent DNA bending governs promoter ... | ACCEPT | Summary: Reconstituted Rpo41-Mtf1 transcribes from the mitochondrial promoter; promoter selection occurs by Mtf1-dependent DNA bending. Reason: Direct biochemical evidence for the transcription initiation step catalysed by the Rpo41-Mtf1 holoenzyme. Supporting Evidence: PMID:21911502 The two proteins are sufficient to catalyze transcription from the conserved nona-nucleotide promoter (5′-ATATAAGTA(+1)) of the yeast mitochondria that directs the synthesis of rRNA, tRNA, and respiratory chain protein mRNAs |
| GO:0006390 mitochondrial transcription | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning annotation of mitochondrial transcription. Reason: Consistent with experimental evidence for this gene (IMP, IDA). Supporting Evidence: PMID:3517858 its product is required for transcription and maintenance of the mitochondrial genome |
| GO:0006390 mitochondrial transcription | IMP PMID:3517858 Yeast RPO41 gene product is required for transcription and m... | ACCEPT | Summary: RPO41 disruption abolishes mitochondrial transcription. Reason: Genetic evidence that the catalytic subunit is required for mitochondrial transcription, combined with its own polymerase activity, establishes direct participation. Supporting Evidence: PMID:3517858 its product is required for transcription and maintenance of the mitochondrial genome |
| GO:0034062 5'-3' RNA polymerase activity | IEA GO_REF:0000116 | MODIFY | Summary: Rhea-mapped generic RNA polymerase activity. Reason: Correct but general; GO:0003899 DNA-directed RNA polymerase activity is a descendant that the gene carries by IDA and IBA. Proposed replacements: DNA-directed RNA polymerase activity Supporting Evidence: PMID:26184436 Herein we found that Rpo41 transcribes RNAs that can be extended by Mip1 on single and double-stranded DNA. |
| GO:0034245 mitochondrial DNA-directed RNA polymerase complex | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of membership of the mitochondrial RNA polymerase complex; this gene is an experimental donor. Reason: Rpo41 is the catalytic core of the two-subunit holoenzyme with Mtf1. Supporting Evidence: PMID:7929382 Rpo41p and Mtf1p interact to form a holoenzyme in solution prior to DNA binding and promoter recognition |
| GO:0034245 mitochondrial DNA-directed RNA polymerase complex | IDA PMID:7929382 Release of the yeast mitochondrial RNA polymerase specificit... | ACCEPT | Summary: Reconstituted Rpo41 and Mtf1 form a holoenzyme in solution. Reason: Direct biochemical evidence of complex formation from purified subunits. Supporting Evidence: PMID:7929382 Rpo41p and Mtf1p interact to form a holoenzyme in solution prior to DNA binding and promoter recognition |
| GO:0034245 mitochondrial DNA-directed RNA polymerase complex | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA annotation of mitochondrial RNA polymerase complex membership. Reason: Consistent with direct experimental evidence (IDA, IPI). Supporting Evidence: PMID:7929382 Rpo41p and Mtf1p interact to form a holoenzyme in solution prior to DNA binding and promoter recognition |
| GO:0034245 mitochondrial DNA-directed RNA polymerase complex | IPI PMID:7929382 Release of the yeast mitochondrial RNA polymerase specificit... | ACCEPT | Summary: Physical interaction of Rpo41 with Mtf1 in the holoenzyme. Reason: Rpo41-Mtf1 interaction defines the holoenzyme; Mtf1 is released after initiation, so the complex is the initiation-competent form. Supporting Evidence: PMID:7929382 After the formation of a 13-nucleotide transcript, Mtf1p is no longer associated with Rpo41p on the DNA. |
| GO:0042645 mitochondrial nucleoid | IDA PMID:15692048 Aconitase couples metabolic regulation to mitochondrial DNA ... | ACCEPT | Summary: Identified among mtDNA-associated (nucleoid) proteins. Reason: Consistent with its role in transcribing mtDNA. Abstract-only cache; curator judgment deferred to for the specific identification of Rpo41. Supporting Evidence: PMID:15692048 We have identified 22 mtDNA-associated proteins in yeast |
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Download this section (compressed HTML)Q: Does the mtDNA maintenance function of the Rpo41 amino-terminal extension reside in the domain itself or in a factor it recruits, and is it conserved in petite-negative yeasts such as S. pombe whose Rpo41 N-terminal regions are divergent?
Q: Is Rpo41-dependent primer synthesis used for mtDNA replication in vivo, given that rep/ori-driven biased inheritance persists in rpo41 null rho- strains?
Q: The S. pombe rpo41 review states that the S. cerevisiae enzyme cannot initiate on its own; PMID:15342628 shows promoter-dependent initiation by S. cerevisiae Rpo41 alone on supercoiled templates. Should the comparison be revised?
Experiment: Express a tagged Rpo41 amino-terminal extension in trans in the rpo41-delta3 (N-terminal deletion) strain, where it partially suppresses mtDNA loss, and identify co-purifying proteins by affinity purification-mass spectrometry to determine how the extension stabilises mtDNA independently of transcription.
Experiment: Test whether Rpo41 RNA synthesis is needed for mtDNA replication initiation in vivo by introducing active-site point mutants of Rpo41 into a strain carrying a hypersuppressive ori/rep rho- genome (stable without RPO41) and measuring replication and transmission of that genome relative to the null and wild type.
Mitochondrial RNA polymerase; single subunit enzyme similar to those of T3 and T7 bacteriophages; requires a specificity subunit encoded by MTF1 for promoter recognition; Mtf1p interacts with and stabilizes the Rpo41p-promoter complex, enhancing DNA bending and melting to facilitate pre-initiation open complex formation; synthesizes RNA primers for mitochondrial DNA replication; capable of DNA-primed RNA extension, resulting in 5' input DNA with extended RNA on the 3' end
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