NPL3 mRNA-binding protein NPL3 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: NPL3
Official Full Name: mRNA-binding protein NPL3
Primary source: SGD:S000002840
Locus tag: YDR432W
See related: AllianceGenome:SGD:S000002840; FungiDB:YDR432W; VEuPathDB:YDR432W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: MTR13; MTS1; NAB1; NOP3
Summary: Enables RNA polymerase II complex binding activity; eukaryotic initiation factor 4G binding activity; and nucleic acid binding activity. Involved in gene expression; negative regulation of translation; and regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in proliferative diabetic retinopathy and spermatogenic failure 3. Orthologous to human SRSF4 (serine and arginine rich splicing factor 4); SRSF5 (serine and arginine rich splicing factor 5); and SRSF6 (serine and arginine rich splicing factor 6). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See NPL3 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 1

Sequence:: Chromosome: IV; NC_001136.10 (1328783..1330027)

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?

RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during splicing.
Title: RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during splicing.
Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA.
Title: Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA.
A guard protein mediated quality control mechanism monitors 5'-capping of pre-mRNAs.
Title: A guard protein mediated quality control mechanism monitors 5'-capping of pre-mRNAs.
Activation of Prp28 ATPase by phosphorylated Npl3 at a critical step of spliceosome remodeling.
Title: Activation of Prp28 ATPase by phosphorylated Npl3 at a critical step of spliceosome remodeling.
The SR-protein Npl3 is an essential component of the meiotic splicing regulatory network in Saccharomyces cerevisiae.
Title: The SR-protein Npl3 is an essential component of the meiotic splicing regulatory network in Saccharomyces cerevisiae.
This study investigated the enzyme-substrate interaction between Hmt1p and nucleolar protein Npl3p, using chemical cross linking/mass spectrometry. This method can capture transient interprotein interactions that occur during the process of methylation, involving a disordered region in Npl3p with tandem SRGG repeats, and we confirm that Hmt1p and Npl3p exist as homomultimers.
Title: Characterization of the Interaction between Arginine Methyltransferase Hmt1 and Its Substrate Npl3: Use of Multiple Cross-Linkers, Mass Spectrometric Approaches, and Software Platforms.
Npl3 participates in DNA double-strand break resection by promoting the proper biogenesis of EXO1 mRNA.
Title: The RNA binding protein Npl3 promotes resection of DNA double-strand breaks by regulating the levels of Exo1.
a model in which Hmt1, via arginine methylation of Npl3, facilitates U1 snRNP engagement with the pre-mRNA to promote usage of non-consensus splice sites by the splicing machinery.
Title: Protein arginine methylation of Npl3 promotes splicing of the SUS1 intron harboring non-consensus 5' splice site and branch site.
Npl3 binds diverse sites on large numbers of transcripts, and the loss of Npl3 results in transcriptional readthrough on many genes.
Title: Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough.
Studied and discovered 21 native sites of arginine methylation on five putative Hmt1 substrate proteins (Gar1p, Nop1p, Npl3p, Nsr1p, Rps2p).
Title: Yeast proteins Gar1p, Nop1p, Npl3p, Nsr1p, and Rps2p are natively methylated and are substrates of the arginine methyltransferase Hmt1p.

Submit: New GeneRIF Correction See all GeneRIFs (25)

Pathways from PubChem

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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 RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables double-stranded telomeric DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables eukaryotic initiation factor 4G binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	HDA more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables poly(A) binding	IDA Inferred from Direct Assay more info	PubMed
enables telomeric repeat-containing RNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IGI Inferred from Genetic Interaction more info	PubMed
involved_in mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ribosome biogenesis	IEA Inferred from Electronic Annotation more info
involved_in translational termination	IGI Inferred from Genetic Interaction more info	PubMed
involved_in translational termination	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IMP Inferred from Mutant Phenotype more info	PubMed
located_in cytoplasmic stress granule	HDA more info	PubMed
located_in cytoplasmic stress granule	IEA Inferred from Electronic Annotation more info
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
part_of ribonucleoprotein complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: mRNA-binding protein NPL3

NP_010720.3

RNA-binding guard protein; promotes transcription elongation and regulates termination; binds eIF4G to repress translation initiation; role in nuclear export of poly(A) mRNA and in pre-mRNA splicing; links chromatin modification to mRNA processing; prevents R-loop-mediated genome instability and replication stress; binds TERRA, stabilizing R-loops at short telomeres; phosphorylated by Sky1p to promote shuttling and mRNA dissociation; protein abundance increases during 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

1328783..1330027

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180740.3 → NP_010720.3 TPA: mRNA-binding protein NPL3 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010720.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VT60, Q01560

UniProtKB/TrEMBL

A6ZZ27, B3LFM6, C8Z5Z3, G2WBG6, N1P7H2

Conserved Domains (3) summary

PHA03247
Location:11 → 87

PHA03247; large tegument protein UL36; Provisional

cd12339
Location:200 → 271

RRM2_SRSF1_4_like; RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

cd12340
Location:126 → 192

RBD_RRM1_NPL3; RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins