RPO41 DNA-directed RNA polymerase [Saccharomyces cerevisiae S288C] - Gene

Summary

Go to the top of the page Help

Official Symbol: RPO41
Official Full Name: DNA-directed RNA polymerase
Primary source: SGD:S000001858
Locus tag: YFL036W
See related: AllianceGenome:SGD:S000001858; FungiDB:YFL036W; VEuPathDB:YFL036W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables DNA primase activity. Involved in DNA replication, synthesis of primer; mitochondrial genome maintenance; and mitochondrial transcription. Located in mitochondrial nucleoid. Part of mitochondrial DNA-directed RNA polymerase complex. Human ortholog(s) of this gene implicated in combined oxidative phosphorylation deficiency 55. Orthologous to human POLRMT (RNA polymerase mitochondrial). [provided by Alliance of Genome Resources, Jan 2025]
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help

See RPO41 in Genome Data Viewer

Location:: chromosome: VI

Exon count:: 1

Sequence:: Chromosome: VI; NC_001138.5 (58782..62837)

Chromosome VI - NC_001138.5 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:: NC_001138.5

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Rpo41-Mtf1 is an attractive candidate for serving as the primase to initiate lagging strand DNA synthesis during normal replication and/or to restart stalled replication from downstream ssDNA.
Title: The Yeast Mitochondrial RNA Polymerase and Transcription Factor Complex Catalyzes Efficient Priming of DNA Synthesis on Single-stranded DNA.
results thus indicate that the PPR motifs do not play an essential role in the function of the NTE domain of the mitochondrial RNA polymerase Rpo41p.
Title: Pentatricopeptide Motifs in the N-Terminal Extension Domain of Yeast Mitochondrial RNA Polymerase Rpo41p Are Not Essential for Its Function.
Herein the authors found that Rpo41 transcribes RNAs that can be extended by Mip1 on single and double-stranded DNA.
Title: Yeast mitochondrial RNA polymerase primes mitochondrial DNA polymerase at origins of replication and promoter sequences.
The study examined a series of N-terminal deletion mutants of yeast mitochondrial RNA polymerase, Rpo41, and found that the N-terminal region does not abolish the effects of Mtf1; rather it contributes directly to enzyme catalysis.
Title: Yeast Mitochondrial Transcription Factor Mtf1 Determines the Precision of Promoter-Directed Initiation of RNA Polymerase Rpo41.
This study identifies the importance of the +1+2 AA promoter sequence interactions with Rpo41-Mtf1 in dictating pre-transcribing complex formation, which regulates the binding of initiating NTPs and the catalytic efficiency of transcription initiation.
Title: Interactions of the yeast mitochondrial RNA polymerase with the +1 and +2 promoter bases dictate transcription initiation efficiency.
While Rpo41 induces a slight bend upon binding both the DNAs, addition of the Mtf1 results in severe bending of the promoter and unbending of the non-promoter DNA
Title: Transcription factor-dependent DNA bending governs promoter recognition by the mitochondrial RNA polymerase.
Data show that he promoter DNA is sandwiched between Mtf1 and Rpo41 in the structural model.
Title: Mitochondrial transcription factor Mtf1 traps the unwound non-template strand to facilitate open complex formation.
Data show that both Rpo41p and Mtf1p contact with promoter DNA.
Title: Multiple functions of yeast mitochondrial transcription factor Mtf1p during initiation.
core mitochondrial RNA polymerase (Rpo41) has the intrinsic ability to initiate from promoters without its specificity factor (Mtf1)
Title: Intrinsic promoter recognition by a "core" RNA polymerase.

Submit: New GeneRIF Correction

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables 5'-3' RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA primase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-directed 5'-3' RNA polymerase activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-directed 5'-3' RNA polymerase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-directed 5'-3' RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase I activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase III activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase IV activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase V activity	IEA Inferred from Electronic Annotation more info
enables mitochondrial promoter sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables mitochondrial single subunit type RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables nucleotidyltransferase activity	IEA Inferred from Electronic Annotation more info
enables plastid single subunit type RNA polymerase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA replication, synthesis of primer	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in mitochondrial genome maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrial transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitochondrial transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in mitochondrial transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in plastid transcription	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase I	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase III	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase IV	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase V	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of DNA-directed RNA polymerase complex	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	HDA more info	PubMed
located_in intracellular membrane-bounded organelle	IEA Inferred from Electronic Annotation more info
part_of mitochondrial DNA-directed RNA polymerase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of mitochondrial DNA-directed RNA polymerase complex	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial matrix	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial nucleoid	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	HDA more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: DNA-directed RNA polymerase

NP_116617.1

EC 2.7.7.6

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; Rpo41p also synthesizes RNA primers for mitochondrial DNA replication

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001138.5 Reference assembly

Range

58782..62837

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179930.1 → NP_116617.1 TPA: DNA-directed RNA polymerase [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_116617.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VTJ4, P13433

UniProtKB/TrEMBL

A7A203, C8Z7P6, G2WDA5, N1P4I3

Conserved Domains (1) summary

COG5108
Location:79 → 1351

RPO41; Mitochondrial DNA-directed RNA polymerase [Transcription]