RNT1 ribonuclease III [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: RNT1
Official Full Name: ribonuclease III
Primary source: SGD:S000004852
Locus tag: YMR239C
See related: AllianceGenome:SGD:S000004852; FungiDB:YMR239C; VEuPathDB:YMR239C
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 ribonuclease III activity. Involved in RNA metabolic process; chromatin organization; and regulation of fungal-type cell wall organization. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See RNT1 in Genome Data Viewer

Location:: chromosome: XIII

Exon count:: 1

Sequence:: Chromosome: XIII; NC_001145.3 (748262..749677, complement)

Chromosome XIII - NC_001145.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001145.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

To recognize the specific substrates, the double-stranded RNA-binding domain of Rnt1p is specialized, featuring a alphabetabetabetaalphaalphaalpha topology and a sequence-specific RNA-binding motif at the C-terminus.
Title: Structure and function of Rnt1p: An alternative to RNAi for targeted RNA degradation.
The functional cycle of eukaryotic Rnt1p includes five consecutive steps of double-stranded RNA processing.
Title: The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III.
Data indicate that mutant of the RNA processing machinery (RNT1), and RNA/DNA helicase SEN1 mutants that are unable to interact with Rnt1p, exhibit a flocculation phenotype.
Title: Flocculation in Saccharomyces cerevisiae is regulated by RNA/DNA helicase Sen1p.
the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions
Title: Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals.
The double stranded RNA binding domain and N-terminal domains of Rnt1p function as two rulers that measure the distance between the tetraloop and the cleavage site.
Title: Structure of a eukaryotic RNase III postcleavage complex reveals a double-ruler mechanism for substrate selection.
The Rnt1p double-stranded RNA binding domain has an extended hydrophobic core comprising helix alpha1, the alpha1-beta1 loop, and helix alpha3.
Title: Intrinsic dynamics of an extended hydrophobic core in the S. cerevisiae RNase III dsRBD contributes to recognition of specific RNA binding sites.
Results support a model for transcription termination in which cotranscriptional cleavage by Rnt1p provides access for exoribonucleases in the absence of polyadenylation signals.
Title: Yeast RNase III triggers polyadenylation-independent transcription termination.
A fail-safe transcription termination mechanism is mediated by Rnt1 cleavage of the nascent transcript in S. cerevisiae.
Title: Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae.
The results indicate that Rnt1p uses a network of nucleotide interactions to identify its substrate and support two distinct modes of binding.
Title: Yeast ribonuclease III uses a network of multiple hydrogen bonds for RNA binding and cleavage.
Rnt1p physically interacts with RNA polymerase I (RNAPI) and its deletion decreases the transcription of the rRNA gene and increases the number of rRNA genes with an open chromatin structure
Title: Deletion of Rnt1p alters the proportion of open versus closed rRNA gene repeats in yeast.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables double-stranded RNA binding	IEA Inferred from Electronic Annotation more info
enables endonuclease activity	IEA Inferred from Electronic Annotation more info
enables ribonuclease III activity	IBA Inferred from Biological aspect of Ancestor more info
enables ribonuclease III activity	IDA Inferred from Direct Assay more info	PubMed
enables ribonuclease III activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in U1 snRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in U4 snRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in U4 snRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in U5 snRNA 3'-end processing	IDA Inferred from Direct Assay more info	PubMed
involved_in U5 snRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in box C/D sno(s)RNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in box H/ACA sno(s)RNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info
involved_in rRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rRNA transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of fungal-type cell wall organization	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of fungal-type cell wall organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in termination of RNA polymerase II transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in termination of RNA polymerase II transcription, exosome-dependent	IDA Inferred from Direct Assay more info	PubMed
involved_in termination of RNA polymerase II transcription, exosome-dependent	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: ribonuclease III

NP_013966.1

EC 3.1.26.3

Nuclear dsRNA-specific ribonuclease (RNase III); involved in rDNA transcription, rRNA processing and U2 snRNA 3' end formation by cleavage of a stem-loop structure at the 3' end of U2 snRNA; involved in polyadenylation-independent transcription termination; involved in the cell wall stress response, regulating the degradation of cell wall integrity and morphogenesis checkpoint genes

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_001145.3 Reference assembly

Range

748262..749677 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001182746.1 → NP_013966.1 TPA: ribonuclease III [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_013966.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W065, Q02555, Q04008, Q05038

UniProtKB/TrEMBL

A6ZMV2, B3LMC7, C7GRB2, C8ZFA4, G2WKU7, N1P5W6

Conserved Domains (2) summary

COG0571
Location:183 → 440

Rnc; dsRNA-specific ribonuclease [Transcription]

pfam18497
Location:44 → 147

RNase_3_N; Ribonuclease III N-terminal domain