ArsR is the 117-residue transcriptional repressor of the chromosomal arsRBC arsenical resistance operon of Escherichia coli, a member of the ArsR/SmtB family of winged helix-turn-helix metalloregulators. ArsR binds as a homodimer to a 33-nucleotide operator overlapping the -35 element of the ars promoter, repressing its own transcription together with that of arsB (arsenite efflux permease) and arsC (arsenate reductase). Trivalent metalloids (arsenite and antimonite) are the inducers; by homology with the plasmid R773 repressor, As(III) is bound by the thiolates of the conserved Cys32/Cys34/Cys37 motif, and binding to Cys32 and Cys34 triggers the conformational change that releases ArsR from DNA. Derepression of the operon on arsenite exposure confers low-level resistance to arsenite and arsenate. Proteomic data suggest additional, possibly indirect, effects of ArsR on metabolic and redox proteins beyond the ars operon.
IDA PMID:9188467 Dimerization is essential for DNA binding and repression by ...
MODIFY
Summary: Gel mobility shift assays show purified dimeric ArsR binds the ars promoter. The binding is sequence-specific operator binding (a 33-nucleotide DNase I footprint over the -35 region, PMID:8576202).
Reason: DNA binding is correct but general. The evidence (this paper and the footprint in PMID:8576202) shows binding to a specific cis-regulatory region of the ars promoter, so the term is refined to its descendant GO:0000976 transcription cis-regulatory region binding.
The specific binding site, as determined by DNase I footprint analysis, spans 33 nucleotides in the promoter region, including the putative -35 promoter element.
Summary: InterPro2GO mapping from the ArsR-type HTH domain signatures. ArsR is a bona fide DNA-binding transcription factor, specifically a repressor whose DNA binding is relieved by binding of As(III)/Sb(III).
Reason: Correct but general. Experimental evidence shows ArsR is a trans-acting repressor whose operator binding is reversed by the metalloid inducer, so the term is refined to its descendant GO:0141096 ligand-modulated transcription repressor activity (is_a GO:0001217 DNA-binding transcription repressor activity and GO:0098531 ligand-modulated transcription factor activity).
binding to only two, the Cys-32 and Cys-34 thiolates, is required to produce the conformational change that results in release of the repressor from the DNA and induction
EXP PMID:8576202 The chromosomal arsR gene of Escherichia coli encodes a tran...
MODIFY
Summary: PMID:8576202 mapped the ars transcription start site and showed ArsR represses the operon in trans. ArsR does not carry out transcription; its experimentally shown role is negative regulation of transcription from the ars promoter.
Reason: The underlying observation (ArsR controls ars transcription) is sound, but DNA-templated transcription describes the act of RNA synthesis by RNA polymerase. The precise claim the paper supports is negative regulation of DNA-templated transcription (GO:0045892), which the curator's own IDA row for regulation (GO:0006355) also points to. This is a lateral correction, not a rejection of the curator's evidence.
it was shown that ArsR is a trans-acting repressor that regulates expression of the chromosomal ars operon
GO:0006355 regulation of DNA-templated transcription
IBA GO_REF:0000033
MODIFY
Summary: PAINT inference over the ArsR/SmtB metalloregulator family node; P37309 appears among the descendant evidence because it has its own experimental annotation, which is expected. The claim is true for ArsR.
Reason: Correct but general: ArsR is shown experimentally to be a repressor, so the term is refined to its descendant GO:0045892 negative regulation of DNA-templated transcription, matching the other GO:0006355 rows.
Propagation Review
Root cause:NO FAILURE CORE
Sources checked:
PANTHER:PTN002108422 · PANTHER:PTN002108422 SUPPORTS TRANSFER
ArsR lies within the ArsR/SmtB metalloregulator node; the transferred term is correct for ArsR and only refined here for specificity.
UniProtKB:P37309 · UniProtKB:P37309 SUPPORTS TRANSFER
The target's own experimental annotation, used as descendant evidence for the IBD; expected, not circular.
UniProtKB:Q9HW47 · UniProtKB:Q9HW47 SUPPORTS TRANSFER
Second family member with experimental evidence for transcription regulation, consistent with the family-level assertion.
negatively regulated by the trans-acting arsR gene product
GO:0006355 regulation of DNA-templated transcription
IDA PMID:8764681 Expression of the Escherichia coli chromosomal ars operon.
MODIFY
Summary: luxAB transcriptional fusions show the chromosomal ars operon is rapidly induced by arsenite and negatively regulated by the arsR product.
Reason: Correct but general; the paper shows negative regulation, so the term is refined to its descendant GO:0045892 negative regulation of DNA-templated transcription.
the operon was rapidly induced by sodium arsenite and negatively regulated by the trans-acting arsR gene product
GO:0006355 regulation of DNA-templated transcription
IEA GO_REF:0000002
MODIFY
Summary: InterPro2GO mapping from the ArsR-type HTH domain; true for ArsR.
Reason: Correct but general; refined to GO:0045892 negative regulation of DNA-templated transcription, consistent with the IBA and IDA rows for this term.
it was shown that ArsR is a trans-acting repressor that regulates expression of the chromosomal ars operon
GO:0046685 response to arsenic-containing substance
IDA PMID:7721697 An Escherichia coli chromosomal ars operon homolog is functi...
ACCEPT
Summary: The chromosomal arsRBC operon is induced by arsenite at low concentrations and is required for arsenite/arsenate resistance. ArsR is the arsenite-sensing component that couples arsenic exposure to derepression of the operon.
Reason: ArsR is the As(III) sensor of the ars system, so its role in the cellular response to arsenic is core. The broad term is appropriate because the operon responds to arsenite and is needed for resistance to both arsenite and arsenate; ArsR also responds to antimonite, which a narrower arsenite-ion term would not cover.
the operon was rapidly induced by sodium arsenite and negatively regulated by the trans-acting arsR gene product
Core Functions
Homodimeric As(III)/Sb(III)-responsive repressor of the arsRBC operon. ArsR binds the ars operator overlapping the -35 promoter element and represses transcription of its own gene and of arsB and arsC; binding of the trivalent metalloid to its Cys32/Cys34(/Cys37) site releases ArsR from DNA and derepresses the operon, so that arsenite exposure induces the arsenic detoxification genes.
binding to only two, the Cys-32 and Cys-34 thiolates, is required to produce the conformational change that results in release of the repressor from the DNA and induction
Sequence-specific binding to the ars operator, a 33-nucleotide region of the ars promoter that includes the -35 element.
The specific binding site, as determined by DNase I footprint analysis, spans 33 nucleotides in the promoter region, including the putative -35 promoter element.
Q: Does the chromosomal K-12 ArsR use the same Cys32/Cys34/Cys37 As(III) site as the R773 repressor, and does it respond to arsenate directly or only after ArsC reduces it to arsenite?
Q: Are the ArsR-dependent proteome changes reported in arsR-complemented strains direct (ArsR operator sites outside the ars operon) or secondary to ars operon expression and arsenic handling?
Experiment: Site-directed mutagenesis of Cys32, Cys34 and Cys37 in the chromosomal K-12 ArsR, with in vitro DNA-release assays and X-ray absorption spectroscopy, to confirm the metalloid-binding site directly in this protein.
Type: site-directed mutagenesis
Experiment: ChIP-seq of ArsR in K-12 with and without arsenite to determine whether ArsR binds any operators outside the arsRBC promoter, testing the proposed global regulatory role.
Type: ChIP-seq
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
NCBI PGAP made no GO or EC predictions for WP_000008957.1, so the predictions list is empty. PGAP takes a protein's GO terms only from the single evidence model that assigns its name. Here the name "As(III)-sensing metalloregulatory transcriptional repressor ArsR" comes from BlastRule NBR009015, and that rule carries no GO terms. The protein also matches the NCBIfam ArsR/SmtB family models NF007528 and NF033788 and the ArsR HTH domain model NF013209, each of which carries GO:0003700 DNA-binding transcription factor activity and GO:0006355 regulation of DNA-templated transcription, but because none of them named the protein their GO terms are discarded. Given the review of this gene, the absence is a recall failure. ArsR is an experimentally characterised DNA-binding repressor of the arsRBC operon (PMID:8576202, PMID:8764681), so both discarded family terms are true. They are general: the review refines them to GO:0141096 ligand-modulated transcription repressor activity and GO:0045892 negative regulation of DNA-templated transcription. Even so, passing them on would have given correct annotations at no precision cost, while the more specific naming rule (whose product name already states "transcriptional repressor" and "As(III)-sensing") has no GO terms at all. A GO mapping on NBR009015 to GO:0141096 (or at least GO:0001217 DNA-binding transcription repressor activity) and GO:0046685 response to arsenic-containing substance would recover the core function.