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Psy1 phytoene synthase 1, chloroplastic [ Solanum lycopersicum (tomato) ]

Gene ID: 543988, updated on 9-Nov-2023

Summary

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Gene symbol
Psy1
Gene description
phytoene synthase 1, chloroplastic
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Solanum lycopersicum
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Solanum subgen. Lycopersicon
Also known as
psy; TOM5; GTOM5; PTOM5
Summary
This gene encodes phytoene synthase, the first enzyme in the carotenoid biosynthetic pathway which converts geranylgeranyl diphosphate (GGPP) to phytoene. Its disruption leads to lack of lycopene in fruits causing yellow flesh phenotype. This gene is one of the three phytoene synthase genes found in tomato. phytoene synthase 1 is most expressed in chromoplast-containing tissues, particularly in fruit. Alternative splicing and the use of alternative promoters results in multiple transcript variants.[provided by RefSeq, Dec 2016]
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Genomic context

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Location:
chromosome: 3
Exon count:
7
Annotation release Status Assembly Chr Location
103 current SL3.0 (GCF_000188115.4) 3 NC_015440.3 (4350836..4355976)
102 previous assembly SL2.50 (GCF_000188115.3) 3 NC_015440.2 (4324965..4330008)

Chromosome 3 - NC_015440.3Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101257636 Neighboring gene expansin A3 Neighboring gene butyrate--CoA ligase AAE11, peroxisomal-like Neighboring gene acyl-CoA synthetase Neighboring gene probable polyamine oxidase 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Identified trans-splicing of YELLOW-FRUITED TOMATO 2 encoding the PHYTOENE SYNTHASE 1 protein alters fruit color by map-based cloning, functional complementation and RACE. Chen L, et al. Plant Mol Biol, 2019 Aug. PMID 31154655
  2. A chimeric transcript containing Psy1 and a potential mRNA is associated with yellow flesh color in tomato accession PI 114490. Kang B, et al. Planta, 2014 Nov. PMID 24663441
  3. Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression. Fray RG, et al. Plant Mol Biol, 1993 Jul. PMID 8343597
  4. Sequence of pTOM5, a ripening related cDNA from tomato. Ray J, et al. Nucleic Acids Res, 1987 Dec 23. PMID 3697097, Free PMC Article
  5. A tomato gene expressed during fruit ripening encodes an enzyme of the carotenoid biosynthesis pathway. Bartley GE, et al. J Biol Chem, 1992 Mar 15. PMID 1544888

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Transcription of lncRNA ACoS-AS1 is essential to trans-splicing between SlPsy1 and ACoS-AS1 that causes yellow fruit in tomato.
    Title: Transcription of lncRNA ACoS-AS1 is essential to trans-splicing between SlPsy1 and ACoS-AS1 that causes yellow fruit in tomato.
  2. PHYTOENE SYNTHASE 1 expression is activated by SlBBX20.
    Title: A tomato B-box protein SlBBX20 modulates carotenoid biosynthesis by directly activating PHYTOENE SYNTHASE 1, and is targeted for 26S proteasome-mediated degradation.
  3. trans-splicing of YFT2 alters tomato fruit color, providing new insights into fruit color development [yft2]
    Title: Identified trans-splicing of YELLOW-FRUITED TOMATO 2 encoding the PHYTOENE SYNTHASE 1 protein alters fruit color by map-based cloning, functional complementation and RACE.
  4. Data indicate that the chimeric phytoene synthase 1 mRNA (Psy1/Unknown) has a lower function than PSY1 in a bacterial expression system.
    Title: A chimeric transcript containing Psy1 and a potential mRNA is associated with yellow flesh color in tomato accession PI 114490.
  5. SlSGR1 plays a pivotal regulatory role in color formation and fruit ripening regulation in tomato, and further suggest that SlSGR1 activity is mediated through direct interaction with PSY1.
    Title: A STAY-GREEN protein SlSGR1 regulates lycopene and β-carotene accumulation by interacting directly with SlPSY1 during ripening processes in tomato.
  6. Data show that Psy1 genes have an highly conserved structure and Psy1 transcript could be detected in chromoplast-containing tissues, particularly in fruit where it activates and boosts lycopene accumulation.
    Title: Phytoene synthase genes in tomato (Solanumlycopersicum L.) - new data on the structures, the deduced amino acid sequences and the expression patterns.
  7. The synthesis of carotenoid in plants starts with the formation of the 15-cis-isomer of phytoene by the action of the phytoene synthase (PSY). In tomato, two active forms of PSY have been described each encoded by its own gene, Psy1 and Psy2. [Psy1]
    Title: Phytoene synthase genes in tomato (Solanumlycopersicum L.) - new data on the structures, the deduced amino acid sequences and the expression patterns.
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General gene information

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Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables farnesyltranstransferase activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables geranylgeranyl-diphosphate geranylgeranyltransferase activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in carotenoid biosynthetic process IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
phytoene synthase 1, chloroplastic
Names
chloroplast 15-cis-phytoene synthase
fruit-ripening-specific protein pTOM5
mutant phytoene synthase
phytoene synthetase
plastid phytoene synthase 1
NP_001234812.1
NP_001334763.1
NP_001334765.1
NP_001334767.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001247883.2 → NP_001234812.1  phytoene synthase 1, chloroplastic

    See identical proteins and their annotated locations for NP_001234812.1

    Status: REVIEWED

    Source sequence(s)
    AEKE03003139, AK247060, BP884132
    UniProtKB/Swiss-Prot
    P08196, Q40166
    UniProtKB/TrEMBL
    A1Z0Z3, A1Z0Z4, A6YRZ8
    Conserved Domains (1) summary
    PLN02632
    Location:75 → 405
    PLN02632; phytoene synthase

  2. NM_001347834.1 → NP_001334763.1  phytoene synthase 1, chloroplastic

    Status: REVIEWED

    Source sequence(s)
    AEKE03003139, BP878210, BP879539, BP884188, BP893499, BW685976, BW686438
    UniProtKB/Swiss-Prot
    P08196, Q40166
    UniProtKB/TrEMBL
    A1Z0Z3, A1Z0Z4, A6YRZ8

  3. NM_001347836.1 → NP_001334765.1  phytoene synthase 1, chloroplastic

    Status: REVIEWED

    Source sequence(s)
    BT012712
    UniProtKB/Swiss-Prot
    P08196, Q40166
    UniProtKB/TrEMBL
    A1Z0Z3, A1Z0Z4, A6YRZ8

  4. NM_001347838.1 → NP_001334767.1  phytoene synthase 1, chloroplastic

    Status: REVIEWED

    Source sequence(s)
    AEKE03003139, M84744
    UniProtKB/Swiss-Prot
    P08196, Q40166
    UniProtKB/TrEMBL
    A1Z0Z3, A1Z0Z4, A6YRZ8

RefSeqs of Annotated Genomes: Solanum lycopersicum Annotation Release 103 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference SL3.0 Primary Assembly

Genomic

  1. NC_015440.3 Reference SL3.0 Primary Assembly

    Range
    4350836..4355976
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001247307.1: Suppressed sequence

    Description
    NM_001247307.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P08196.2 GenPept UniProtKB/Swiss-Prot:P08196

Gene LinkOut

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Other Literature Sources
Molecular Biology Databases
Research Materials