SUB2 ATP-dependent RNA helicase SUB2 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: SUB2
Official Full Name: ATP-dependent RNA helicase SUB2
Primary source: SGD:S000002242
Locus tag: YDL084W
See related: AllianceGenome:SGD:S000002242; FungiDB:YDL084W; VEuPathDB:YDL084W
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 RNA binding activity and RNA helicase activity. Involved in gene expression; subtelomeric heterochromatin formation; and transcription-coupled nucleotide-excision repair. Located in chromosome, telomeric region. Part of transcription export complex. Human ortholog(s) of this gene implicated in type 1 diabetes mellitus. Orthologous to several human genes including DDX39B (DExD-box helicase 39B). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See SUB2 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 1

Sequence:: Chromosome: IV; NC_001136.10 (305237..306577)

Chromosome IV - NC_001136.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001136.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex.
Title: Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex.
Both THO and Yra1-C stimulated Sub2's intrinsic ATPase activity. The authors propose that THO surveys common landmarks in each nuclear mRNP to localize Sub2 for targeted loading of Yra1.
Title: Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1.
RNA helicase Sub2p mutation is associated with growth, mRNA export, and genomic stability.
Title: Mutational analysis of the yeast RNA helicase Sub2p reveals conserved domains required for growth, mRNA export, and genomic stability.
This work establishes a genome-wide function for THO-Sub2 in transcription elongation and mRNP biogenesis that function to prevent the accumulation of transcription-mediated replication obstacles, including R-loops.
Title: Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles.
Data suggests that the THO complex/Sub2p function is required to coordinate events leading to the acquisition of export competence at a step that follows commitment to 3'-processing.
Title: THO/Sub2p functions to coordinate 3'-end processing with gene-nuclear pore association.
A genetic screen reveals extensive interactions between deletions of THO subunits and mRNA 3' end processing mutants.
Title: Nuclear mRNA surveillance in THO/sub2 mutants is triggered by inefficient polyadenylation.
suppresses heterochormatic silencing at telomeres in parallel with its functions in transcription elongation, splicing and mRNA transport.
Title: The Saccharomyces cerevisiae Sub2 protein suppresses heterochromatic silencing at telomeres and subtelomeric genes.
HSP104 molecules undergoing quality control in THO/sub2 mutants fall into two populations: One that is quickly degraded after transcription induction and another that escapes rapid decay and accumulates in foci associated with HSP104 transcription site.
Title: Dissecting mechanisms of nuclear mRNA surveillance in THO/sub2 complex mutants.
Overexpression of Tho1 or Sub2 may provide alternative ways for mRNP formation and export in the absence of a functional THO complex.
Title: Tho1, a novel hnRNP, and Sub2 provide alternative pathways for mRNP biogenesis in yeast THO mutants.

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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 ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IGI Inferred from Genetic Interaction more info	PubMed
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in mRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA export from nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA export from nucleus	IPI Inferred from Physical Interaction more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in subtelomeric heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription-coupled nucleotide-excision repair	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	HDA more info	PubMed
located_in nucleus	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of spliceosomal complex	IEA Inferred from Electronic Annotation more info
part_of transcription export complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ATP-dependent RNA helicase SUB2

NP_010199.1

EC 3.6.4.13

Component of the TREX complex required for nuclear mRNA export; member of the DEAD-box RNA helicase superfamily and is involved in early and late steps of spliceosome assembly; homolog of the human splicing factor hUAP56; relocalizes from nucleus to cytoplasm upon DNA replication stress

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_001136.10 Reference assembly

Range

305237..306577

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180143.1 → NP_010199.1 TPA: ATP-dependent RNA helicase SUB2 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010199.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A6ZXP4, D6VRR5, Q07478

UniProtKB/TrEMBL

B3LGX8, B5VFI3, C7GJN0, G2WC79, N1P450

Conserved Domains (2) summary

cd18787
Location:281 → 410

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd17950
Location:61 → 270

DEADc_DDX39; DEAD-box helicase domain of DEAD box protein 39