RIF10 polyribonucleotide nucleotidyltransferase [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: RIF10
Official Full Name: polyribonucleotide nucleotidyltransferase
Primary source: TAIR:AT3G03710
Locus tag: AT3G03710
See related: Araport:AT3G03710
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: F20H23.26; PDE326; PIGMENT DEFECTIVE 326; PNP; POLYNUCLEOTIDE PHOSPHORYLASE; resistant to inhibition with FSM 10
Summary: Encodes a chloroplast polynucleotide phosphorylase (PNPase). Involved in response to phosphorus (P) starvation. Mutants impaired in the expression of this gene have been selected through their resistance to fosmidomycin, a strong inhibitor of DXR, an enzyme of the methylerythritol-dependent IPP biosynthesis pathway. The pathway enzymes were upregulated in the mutant seedlings.
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Genomic context

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See RIF10 in Genome Data Viewer

Location:: chromosome: 3

Exon count:: 24

Sequence:: Chromosome: 3; NC_003074.8 (919362..925372)

Chromosome 3 - NC_003074.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003074.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Chloroplast PNPase has a major role in maturing mRNA and rRNA 3'-ends, but also participates in RNA degradation through exonucleolytic digestion and polyadenylation.
Title: Mutational analysis of Arabidopsis chloroplast polynucleotide phosphorylase reveals roles for both RNase PH core domains in polyadenylation, RNA 3'-end maturation and intron degradation.
The activity of the chloroplast PNPase is involved in plant acclimation to phosphorus(P) availability and that it may help maintain an appropriate balance of P metabolites even under normal growth conditions.[PNPase]
Title: Abnormal physiological and molecular mutant phenotypes link chloroplast polynucleotide phosphorylase to the phosphorus deprivation response in Arabidopsis.

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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_111242.3

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables 3'-5'-RNA exonuclease activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables polyribonucleotide nucleotidyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within carotene biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cellular response to phosphate starvation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chlorophyll biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chloroplast RNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA catabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within xanthophyll biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chloroplast	HDA more info	PubMed
located_in chloroplast	ISM Inferred from Sequence Model more info
located_in chloroplast stroma	HDA more info	PubMed
located_in cytosol	HDA more info	PubMed

General protein information

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Preferred Names: polyribonucleotide nucleotidyltransferase

NP_187021.2

resistant to inhibition with FSM 10 (RIF10); FUNCTIONS IN: polyribonucleotide nucleotidyltransferase activity, 3'-5'-exoribonuclease activity, RNA binding, nucleic acid binding; INVOLVED IN: chlorophyll biosynthetic process, cellular response to phosphate starvation, xanthophyll biosynthetic process, carotene biosynthetic process, negative regulation of isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway; LOCATED IN: chloroplast stroma, chloroplast; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: K Homology, type 1, subgroup (InterPro:IPR018111), Nucleic acid-binding, OB-fold (InterPro:IPR012340), Exoribonuclease, phosphorolytic domain 2 (InterPro:IPR015847), Ribosomal protein S1, RNA-binding domain (InterPro:IPR003029), Polynucleotide phosphorylase, phosphorolytic RNA-binding, bacterial/organelle-type (InterPro:IPR015848), K Homology (InterPro:IPR004087), Nucleic acid-binding, OB-fold-like (InterPro:IPR016027), K Homology, type 1 (InterPro:IPR004088), Exoribonuclease, phosphorolytic domain 1 (InterPro:IPR001247), Ribosomal protein S5 domain 2-type fold (InterPro:IPR020568), Polyribonucleotide nucleotidyltransferase (InterPro:IPR012162); BEST Arabidopsis thaliana protein match is: polyribonucleotide nucleotidyltransferase, putative (TAIR:AT5G14580.1); Has 29137 Blast hits to 25785 proteins in 2865 species: Archae - 377; Bacteria - 19207; Metazoa - 333; Fungi - 67; Plants - 272; Viruses - 0; Other Eukaryotes - 8881 (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_003074.8 Reference assembly

Range

919362..925372

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_111242.3 → NP_187021.2 polyribonucleotide nucleotidyltransferase [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_187021.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q8GZQ3, Q9M497, Q9S749

UniProtKB/TrEMBL

A0A178VFS9, A0A5S9X8T3, A0A654F3U1

Conserved Domains (1) summary

PLN00207
Location:1 → 900

PLN00207; polyribonucleotide nucleotidyltransferase; Provisional