TOP1ALPHA DNA topoisomerase I alpha [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: TOP1ALPHA
Official Full Name: DNA topoisomerase I alpha
Primary source: TAIR:AT5G55300
Locus tag: AT5G55300
See related: Araport:AT5G55300
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: DNA topoisomerase 1 beta; DNA topoisomerase I alpha; MGO1; MGOUN 1; MTE17.1; MTE17_1; TOP1; TOP1BETA; TOPOISOMERASE 1
Summary: Encodes a type-I DNA topoisomerase I. Disruptions in this gene affect phyllotaxis and plant architecture suggesting that the gene plays a critical role in the maintenance of a regular pattern of organ initiation. Isolated as a protein oxidized during seed germination; proteomics approach revealed differences in de novo synthesis levels of this protein in condition with vs. without salicylic acid in the period from 0 to 40 hrs. following seed imbibition. Functions in stem cell maintenance at all stages of shoot and floral meristems and in the regulation of gene silencing.
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Genomic context

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See TOP1ALPHA in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 16

Sequence:: Chromosome: 5; NC_003076.8 (22424502..22429514, complement)

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?

Profiling thimet oligopeptidase-mediated proteolysis in Arabidopsis thaliana.
Title: Profiling thimet oligopeptidase-mediated proteolysis in Arabidopsis thaliana.
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.
TOP1alpha has a role in regulating FLOWERING LOCUS C expression by coupling histone modification and transcription machinery
Title: TOP1α regulates FLOWERING LOCUS C expression by coupling histone modification and transcription machinery.
TOP1alpha is required for the survival of stele stem cells and regulates the differentiation state and number of columella stem cells.
Title: TOPOISOMERASE1α Acts through Two Distinct Mechanisms to Regulate Stele and Columella Stem Cell Maintenance.
TOP1ALPHA role in flowering
Title: DNA Topoisomerase Iα Affects the Floral Transition.
Pleiotropic effect of the fas5 mutation on different stages of ontogeny and different organs suggests that the FAS5 gene plays a complex regulatory role at all stages of the A. thaliana shoot development. [Fas5]
Title: [Pleiotropic effect of the fas5 mutation on the shoot development of Arabidopsis thaliana].
In the floral meristem, the binding of AG to WUS is reduced in top1a-2, which results in reduced H3K27me3 levels at WUS and prolonged WUS expression, and consequently loss of floral determinacy.
Title: DNA topoisomerase I affects polycomb group protein-mediated epigenetic regulation and plant development by altering nucleosome distribution in Arabidopsis.
Further studies with Arabidopsis top1alpha mutants showed that TOP1alpha silences endogenous RdDM loci by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at TEs and repeats
Title: DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis.
MGO1 encodes a putative Arabidopsis type IB topoisomerase that functions together with WUS in stem cell regulation. [MGO1]
Title: MGOUN1 encodes an Arabidopsis type IB DNA topoisomerase required in stem cell regulation and to maintain developmentally regulated gene silencing.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001203614.1

Supported by ESTs:

NM_001203615.1

Supported by ESTs:

NM_124912.5

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA topoisomerase type I (single strand cut, ATP-independent) activity	IEA Inferred from Electronic Annotation more info
enables DNA topoisomerase type I (single strand cut, ATP-independent) activity	IGI Inferred from Genetic Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA topological change	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA topological change	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within chromatin remodeling	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryo development ending in seed dormancy	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within flower morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within leaf morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within meristem structural organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within plant organ formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within post-embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of meristem growth	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within shoot system morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within stem cell population maintenance	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: DNA topoisomerase I alpha

NP_001190543.1

DNA topoisomerase I alpha (TOP1ALPHA); FUNCTIONS IN: protein binding, DNA topoisomerase type I activity; INVOLVED IN: in 8 processes; LOCATED IN: chromosome; EXPRESSED IN: 29 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: DNA topoisomerase I, DNA binding, mixed alpha/beta motif, eukaryotic-type (InterPro:IPR013030), DNA topoisomerase I, DNA binding, eukaryotic-type (InterPro:IPR008336), DNA topoisomerase I, C-terminal (InterPro:IPR001631), DNA topoisomerase I, catalytic core, eukaryotic-type (InterPro:IPR013500), DNA topoisomerase I, active site (InterPro:IPR018521), DNA topoisomerase I, catalytic core, alpha/beta subdomain, eukaryotic-type (InterPro:IPR014727), DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type (InterPro:IPR014711), DNA breaking-rejoining enzyme, catalytic core (InterPro:IPR011010), DNA topoisomerase I, C-terminal, eukaryotic-type (InterPro:IPR013499); BEST Arabidopsis thaliana protein match is: DNA topoisomerase 1 beta (TAIR:AT5G55310.1).

NP_001190544.1

DNA topoisomerase I alpha (TOP1ALPHA); FUNCTIONS IN: protein binding, DNA topoisomerase type I activity; INVOLVED IN: in 8 processes; LOCATED IN: chromosome; EXPRESSED IN: 29 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: DNA topoisomerase I, C-terminal (InterPro:IPR001631), DNA topoisomerase I, catalytic core, alpha/beta subdomain, eukaryotic-type (InterPro:IPR014727), DNA topoisomerase I, catalytic core, eukaryotic-type (InterPro:IPR013500), DNA topoisomerase I, active site (InterPro:IPR018521), DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type (InterPro:IPR014711), DNA breaking-rejoining enzyme, catalytic core (InterPro:IPR011010), DNA topoisomerase I, C-terminal, eukaryotic-type (InterPro:IPR013499); BEST Arabidopsis thaliana protein match is: DNA topoisomerase 1 beta (TAIR:AT5G55310.1).

NP_200341.1

DNA topoisomerase I alpha (TOP1ALPHA); FUNCTIONS IN: protein binding, DNA topoisomerase type I activity; INVOLVED IN: in 12 processes; LOCATED IN: chromosome; EXPRESSED IN: 30 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: DNA topoisomerase I, DNA binding, mixed alpha/beta motif, eukaryotic-type (InterPro:IPR013030), DNA topoisomerase I, DNA binding, eukaryotic-type (InterPro:IPR008336), DNA topoisomerase I, C-terminal (InterPro:IPR001631), DNA topoisomerase I, active site (InterPro:IPR018521), DNA topoisomerase I, catalytic core, alpha/beta subdomain, eukaryotic-type (InterPro:IPR014727), DNA topoisomerase I, catalytic core, eukaryotic-type (InterPro:IPR013500), DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type (InterPro:IPR014711), DNA topoisomerase I, C-terminal, eukaryotic-type (InterPro:IPR013499), DNA breaking-rejoining enzyme, catalytic core (InterPro:IPR011010); BEST Arabidopsis thaliana protein match is: DNA topoisomerase 1 beta (TAIR:AT5G55310.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (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

22424502..22429514 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_124912.5 → NP_200341.1 DNA topoisomerase I alpha [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_200341.1

Status: REVIEWED

UniProtKB/Swiss-Prot

P30181, Q56XA9, Q8RX06

UniProtKB/TrEMBL

A0A178UCZ4, A0A654GB41

Conserved Domains (2) summary

smart00435
Location:510 → 886

TOPEUc; DNA Topoisomerase I (eukaryota)

cl02774
Location:370 → 582

Topoisomer_IB_N; N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and ...
NM_001203614.1 → NP_001190543.1 DNA topoisomerase I alpha [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001190543.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A178UCZ4, F4K3F4

Conserved Domains (4) summary

smart00435
Location:510 → 886

TOPEUc; DNA Topoisomerase I (eukaryota)

cd03489
Location:370 → 582

Topoisomer_IB_N_LdtopoI_like; Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB ...

pfam01028
Location:585 → 780

Topoisom_I; Eukaryotic DNA topoisomerase I, catalytic core

pfam14370
Location:846 → 910

Topo_C_assoc; C-terminal topoisomerase domain
NM_001203615.1 → NP_001190544.1 DNA topoisomerase I alpha [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001190544.1

Status: REVIEWED

UniProtKB/TrEMBL

F4K3F5

Conserved Domains (2) summary

pfam01028
Location:297 → 428

Topoisom_I; Eukaryotic DNA topoisomerase I, catalytic core

pfam14370
Location:494 → 559

Topo_C_assoc; C-terminal topoisomerase domain