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HCF107 high chlorophyll fluorescent 107 [ Arabidopsis thaliana (thale cress) ]

Gene ID: 820961, updated on 18-Sep-2024

Summary

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Official Symbol
HCF107
Official Full Name
high chlorophyll fluorescent 107
Primary source
TAIR:AT3G17040
Locus tag
AT3G17040
See related
Araport:AT3G17040
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
high chlorophyll fluorescent 107
Summary
It is a RNA tetratricopeptide repeat-containing protein required for normal processing of transcripts from the polycistronic chloroplast psbB-psbT-psbH-petB-petD operon coding for proteins of the photosystem II and cytochrome b6/f complexes. Localizes to the chloroplast membrane. Involved in regulating plastidial gene expression and biogenesis. It binds in the psbT?psbH intercistronic region and blocks the progression of 5' -> 3' exoribonucleases, which defines the 5' end of processed psbH transcripts and also stabilizes the downstream RNA segment. In addition, HCF107 binding remodels the structure of the psbH 5' UTR in a way that can account for its ability to enhance psbH translation.
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Genomic context

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See HCF107 in Genome Data Viewer
Location:
chromosome: 3
Exon count:
7
Sequence:
Chromosome: 3; NC_003074.8 (5808666..5812780, complement)

Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene Adenine nucleotide alpha hydrolases-like superfamily protein Neighboring gene Nucleic acid-binding proteins superfamily Neighboring gene pseudo Neighboring gene Pectin lyase-like superfamily protein

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003074.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Expression of a nuclear-encoded psbH gene complements the plastidic RNA processing defect in the PSII mutant hcf107 in Arabidopsis thaliana. Levey T, et al. Plant J, 2014 Oct. PMID 25081859
  2. The nucleus-encoded HCF107 gene of Arabidopsis provides a link between intercistronic RNA processing and the accumulation of translation-competent psbH transcripts in chloroplasts. Felder S, et al. Plant Cell, 2001 Sep. PMID 11549768, Free PMC Article
  3. RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression. Hammani K, et al. Proc Natl Acad Sci U S A, 2012 Apr 10. PMID 22451905, Free PMC Article
  4. The nuclear gene HCF107 encodes a membrane-associated R-TPR (RNA tetratricopeptide repeat)-containing protein involved in expression of the plastidial psbH gene in Arabidopsis. Sane AP, et al. Plant J, 2005 Jun. PMID 15918885
  5. The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Monte E, et al. Proc Natl Acad Sci U S A, 2004 Nov 16. PMID 15505214, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A chloroplast-localized HAT protein, HCF107, is a sequence-specific RNA binding protein.
    Title: RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression.
  2. The identification of the HCF107 gene that is involved in the 5'-end processing/stability and/or translation of the psbH gene and in the translation of the psbB gene. [HCF107]
    Title: The nuclear gene HCF107 encodes a membrane-associated R-TPR (RNA tetratricopeptide repeat)-containing protein involved in expression of the plastidial psbH gene in Arabidopsis.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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NM_001202985.2
NM_001338272.1
NM_112580.5

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables mRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables mRNA binding IEA
Inferred from Electronic Annotation
more info
  
enables ribonuclease inhibitor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables single-stranded RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within RNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in RNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within mRNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within plastid organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of translation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of translation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to red light IEP
Inferred from Expression Pattern
more info
 PubMed 
Component Evidence Code Pubs
located_in chloroplast HDA PubMed 
located_in chloroplast ISM
Inferred from Sequence Model
more info
  
located_in chloroplast envelope IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chloroplast membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chloroplast stroma IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISM
Inferred from Sequence Model
more info
  
located_in plant-type vacuole HDA PubMed 

General protein information

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Preferred Names
high chlorophyll fluorescent 107
NP_001189914.1
  • high chlorophyll fluorescent 107 (HCF107); FUNCTIONS IN: binding; INVOLVED IN: plastid organization, RNA processing, regulation of translation; LOCATED IN: chloroplast envelope; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA-processing protein, HAT helix (InterPro:IPR003107), Tetratricopeptide-like helical (InterPro:IPR011990), Tetratricopeptide repeat-containing (InterPro:IPR013026), Tetratricopeptide repeat (InterPro:IPR019734); BEST Arabidopsis thaliana protein match is: pre-mRNA splicing factor-related (TAIR:AT4G03430.1).
NP_188329.1
  • high chlorophyll fluorescent 107 (HCF107); FUNCTIONS IN: binding; INVOLVED IN: plastid organization, RNA processing, regulation of translation; LOCATED IN: chloroplast, plasma membrane, chloroplast envelope; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA-processing protein, HAT helix (InterPro:IPR003107), Tetratricopeptide-like helical (InterPro:IPR011990), Tetratricopeptide repeat-containing (InterPro:IPR013026), Tetratricopeptide repeat (InterPro:IPR019734); BEST Arabidopsis thaliana protein match is: pre-mRNA splicing factor-related (TAIR:AT4G03430.1); Has 8355 Blast hits to 4834 proteins in 935 species: Archae - 387; Bacteria - 2714; Metazoa - 1907; Fungi - 1281; Plants - 751; Viruses - 0; Other Eukaryotes - 1315 (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

  1. NC_003074.8 Reference assembly

    Range
    5808666..5812780 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001338271.1 → NP_001327904.1  high chlorophyll fluorescent 107 [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A1I9LTR5

  2. NM_112580.5 → NP_188329.1  high chlorophyll fluorescent 107 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_188329.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q8RWG2, Q9LSP3
    UniProtKB/TrEMBL
    A0A178VC71
    Conserved Domains (4) summary
    COG0457
    Location:183 → 440
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:273 → 299
    TPR; TPR repeat [structural motif]
    pfam13428
    Location:342 → 380
    TPR_14; Tetratricopeptide repeat
    pfam13432
    Location:412 → 475
    TPR_16; Tetratricopeptide repeat

  3. NM_001202985.2 → NP_001189914.1  high chlorophyll fluorescent 107 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_001189914.1

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A178VC71, F4J3Z3
    Conserved Domains (4) summary
    COG0457
    Location:149 → 406
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:239 → 265
    TPR; TPR repeat [structural motif]
    pfam13428
    Location:308 → 346
    TPR_14; Tetratricopeptide repeat
    pfam13432
    Location:378 → 441
    TPR_16; Tetratricopeptide repeat

  4. NM_001338272.1 → NP_001327903.1  high chlorophyll fluorescent 107 [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A1I9LTR4
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8RWG2.1

Gene LinkOut

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