LBA1 RNA helicase [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Gene symbol: LBA1
Gene description: RNA helicase
Primary source: Araport:AT5G47010
Locus tag: AT5G47010
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1
Summary: Required for nonsense-mediated mRNA decay. Involved in RNA interference. lba1 mutants has reduced sugar-induced expression of Atb- amylase, is hypersensitive to glucose and abscisic acid and resistant to mannose, and shows early flowering, short day-sensitive growth, and seed germination phenotypes.
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Genomic context

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Location:: chromosome: 5

Exon count:: 29

Sequence:: Chromosome: 5; NC_003076.8 (19071824..19079453)

Chromosome 5 - NC_003076.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis.
Title: Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis.
TOP1alpha, UPF1, and TTG2 regulate seed size in a parental dosage-dependent manner.
Title: TOP1α, UPF1, and TTG2 regulate seed size in a parental dosage-dependent manner.
interactome reveals interaction networks between RNA degradation and translation repression factors
Title: The UPF1 interactome reveals interaction networks between RNA degradation and translation repression factors in Arabidopsis.
The involvement of UPF1, UPF2, and UPF3 in development and in response to stresses, wounding and infection by Pseudomonas syringae pv. tomato strain DC3000, were examined.
Title: Arabidopsis plants having defects in nonsense-mediated mRNA decay factors UPF1, UPF2, and UPF3 show photoperiod-dependent phenotypes in development and stress responses.
UPF1 and UPF3, which are key nonsense-mediated mRNA decay factors, may act as defense-related regulators associated with plant immunity.
Title: Nonsense-mediated mRNA decay factors, UPF1 and UPF3, contribute to plant defense.
Data show that in mutants impaired in the nonsense-mediated decay (NMD) components UPF1, levels of the alternatively spliced AtGRP7 and AtGRP8 transcripts are strongly elevated, implicating UPF1 in the decay of these clock-regulated transcripts.
Title: Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation.
lba1 is a missense mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay
Title: The lba1 mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay causes pleiotropic phenotypic changes and altered sugar signalling in Arabidopsis.
Nonsense-mediated mRNA decay and RNA interference (RNAi) in plants requires UPF1. [UPF1]
Title: UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis.
AtUPF1 is involved in the control of seed size and shape and is essential for seedling growth. [AtUPF1]
Title: Arabidopsis UPF1 RNA helicase for nonsense-mediated mRNA decay is involved in seed size control and is essential for growth.

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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

NM_124072.3

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables mRNA binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within RNA splicing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in defense response to bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in jasmonic acid mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in long-day photoperiodism	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to sucrose	IGI Inferred from Genetic Interaction more info	PubMed
involved_in response to wounding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in salicylic acid mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sugar mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within translation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in P-body	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISM Inferred from Sequence Model more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
NOT located_in cytosol	RCA inferred from Reviewed Computational Analysis more info	PubMed
located_in plasmodesma	HDA more info	PubMed

General protein information

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Preferred Names: RNA helicase

NP_199512.2

LOW-LEVEL BETA-AMYLASE 1 (LBA1); FUNCTIONS IN: in 6 functions; INVOLVED IN: sugar mediated signaling pathway, RNA interference, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, response to sucrose stimulus; LOCATED IN: plasma membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Restriction endonuclease, type I, R subunit/Type III, Res subunit (InterPro:IPR006935), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), RNA helicase UPF1, UPF2-interacting domain (InterPro:IPR018999); BEST Arabidopsis thaliana protein match is: DNA-binding protein, putative (TAIR:AT2G03270.1); Has 9640 Blast hits to 8330 proteins in 1330 species: Archae - 182; Bacteria - 2840; Metazoa - 3001; Fungi - 1369; Plants - 807; Viruses - 148; Other Eukaryotes - 1293 (source: NCBI BLink).

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_003076.8 Reference assembly

Range

19071824..19079453

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_124072.3 → NP_199512.2 RNA helicase [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_199512.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q8S3K7, Q9FJR0

UniProtKB/TrEMBL

A0A178USW1, A0A5S9YBP1

Conserved Domains (3) summary

COG1112
Location:164 → 929

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

pfam09606
Location:983 → 1202

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

cd18039
Location:488 → 723

DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1