bio2

UniProt ID: O59778
Organism: Schizosaccharomyces pombe 972h-
Review Status: DRAFT
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Gene Description

Biotin synthase (EC 2.8.1.6) of Schizosaccharomyces pombe (SPCC1235.02), a radical-SAM enzyme orthologous to S. cerevisiae Bio2 and E. coli BioB. It inserts sulfur into dethiobiotin to form the thiophane ring of biotin, the final step of biotin synthesis, using a [4Fe-4S] cluster to generate 5'-deoxyadenosyl radicals and a [2Fe-2S] cluster as the sulfur source. S. pombe bio2 complements a S. cerevisiae biotin synthase mutant. The protein is mitochondrial in the ORFeome localisation screen.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003824 catalytic activity
IEA
GO_REF:0000002 		MODIFY
Summary: InterPro2GO from generic radical-SAM signatures (IPR006638, IPR007197) to 'catalytic activity'. True but uninformative; bio2 is a biotin synthase (same correction as S. cerevisiae BIO2).
Proposed replacements: biotin synthase activity
Supporting Evidence:
file:SCHPO/bio2/bio2-uniprot.txt
FUNCTION: Catalyzes the last step of biotin biosynthesis, the
GO:0004076 biotin synthase activity
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA (PTN000540961) seeded by E. coli BioB, M. tuberculosis BioB, S. cerevisiae Bio2 and S. pombe bio2 itself. bio2's own appearance in the with/from reflects its IGI-supported experimental annotation, not circularity. Correct.
Supporting Evidence:
file:SCHPO/bio2/bio2-uniprot.txt
FUNCTION: Catalyzes the last step of biotin biosynthesis, the
PMID:10525840
Heterologous complementation experiment allowed the cloning and the characterization of a novel bio gene: bio2, encoding biotin synthase from Schizosaccharomyces pombe.
GO:0004076 biotin synthase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Combined IEA (InterPro IPR024177 biotin synthase, RHEA:22060, EC 2.8.1.6). Correct.
Supporting Evidence:
file:SCHPO/bio2/bio2-uniprot.txt
Reaction=(4R,5S)-dethiobiotin + (sulfur carrier)-SH + 2 reduced [2Fe-
GO:0004076 biotin synthase activity
IGI
PMID:10525840
Cloning of Schizosaccharomyces pombe bio2 by heterologous co... 		ACCEPT
Summary: S. pombe bio2 was cloned by complementing a S. cerevisiae bio2 (biotin synthase) transposon mutant, i.e. it restores the last step of biotin synthesis in vivo. Abstract-only cache; consistent with PomBase IGI with SGD BIO2. Accept.
Supporting Evidence:
PMID:10525840
Heterologous complementation experiment allowed the cloning and the characterization of a novel bio gene: bio2, encoding biotin synthase from Schizosaccharomyces pombe.
PMID:10525840
A Saccharomyces cerevisiae mutant affected in the last step of the biotin biosynthesis pathway was isolated
GO:0005739 mitochondrion
HDA
PMID:16823372
ORFeome cloning and global analysis of protein localization ... 		ACCEPT
Summary: Mitochondrial YFP signal in the S. pombe ORFeome screen. Consistent with the mitochondrial location of S. cerevisiae Bio2 and of biotin synthase in other eukaryotes. The PomBase GO-CAM (gomodel:67c10cc400002026) gives no occurs_in for the bio2 activity; this HDA could supply it.
Supporting Evidence:
PMID:16823372
we determined the localization of 4,431 proteins
GO:0009102 biotin biosynthetic process
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA for biotin biosynthesis (same node); biotin synthase performs the final step (dethiobiotin -> biotin). Correct.
Supporting Evidence:
file:SCHPO/bio2/bio2-uniprot.txt
PATHWAY: Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-
PMID:10525840
Heterologous complementation experiment allowed the cloning and the characterization of a novel bio gene: bio2, encoding biotin synthase from Schizosaccharomyces pombe.
GO:0009102 biotin biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: ARBA/InterPro/UniPathway (UPA00078) mapping to biotin biosynthesis. Correct; final step.
Supporting Evidence:
file:SCHPO/bio2/bio2-uniprot.txt
PATHWAY: Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-
GO:0009102 biotin biosynthetic process
IGI
PMID:10525840
Cloning of Schizosaccharomyces pombe bio2 by heterologous co... 		ACCEPT
Summary: Same complementation result supports participation in biotin biosynthesis (final step). Accept.
Supporting Evidence:
PMID:10525840
Heterologous complementation experiment allowed the cloning and the characterization of a novel bio gene: bio2, encoding biotin synthase from Schizosaccharomyces pombe.
PMID:10525840
A Saccharomyces cerevisiae mutant affected in the last step of the biotin biosynthesis pathway was isolated
GO:0051536 iron-sulfur cluster binding
IEA
GO_REF:0000002 		MODIFY
Summary: InterPro2GO (radical SAM signatures) to iron-sulfur cluster binding. bio2 binds a [4Fe-4S] radical-SAM cluster and a [2Fe-2S] cluster by similarity; correct but general (parent of the 2Fe-2S term).
Reason: Following the RADICAL_SAM project rule for the generic domain-derived rows (projects/RADICAL_SAM.md): correct but general, and TOO_GENERAL does not apply because no more specific cluster term is asserted elsewhere in this review for the radical SAM cluster itself. UniProt records both a [4Fe-4S] radical SAM cluster and an auxiliary [2Fe-2S] cluster, so both descendants are given; this matches ECOLI/bioB and PSEPK/bioB.
Supporting Evidence:
file:SCHPO/bio2/bio2-uniprot.txt
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
file:SCHPO/bio2/bio2-uniprot.txt
Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135; Evidence={ECO:0000250};
GO:0051537 2 iron, 2 sulfur cluster binding
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA from E. coli BioB, whose [2Fe-2S] cluster is the sacrificial sulfur donor for biotin. UniProt annotates the [2Fe-2S] cofactor for bio2 by similarity. Correct cofactor binding integral to the mechanism; accepted as for S. cerevisiae BIO2.
Supporting Evidence:
file:SCHPO/bio2/bio2-uniprot.txt
Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135; Evidence={ECO:0000250};
GO:1904047 S-adenosyl-L-methionine binding
IC
file:SCHPO/bio2/bio2-uniprot.txt 		NEW
Summary: bio2 binds S-adenosyl-L-methionine at the unique iron of its radical SAM [4Fe-4S] cluster and cleaves it to the 5'-deoxyadenosyl radical; two SAM are consumed per biotin formed.
Reason: Not in GOA. Added under the RADICAL_SAM treatment rule, which treats GO:1904047 as a core cosubstrate-binding function of every radical SAM enzyme whose catalysis is established. This is a molecular function the protein itself performs, so the participation test is met directly: bio2 binds SAM and cleaves it, rather than merely being required for a process that consumes it. UniProt's curated cofactor note records the exchangeable S-adenosyl-L-methionine on the radical SAM cluster and the entry's binding features name the 4Fe-4S-S-AdoMet ligand, so the claim rests on curated record content rather than on an electronic GO line. Coded IC because the inference is the reviewer's, drawn from that curated content and the established biotin synthase activity rather than from a SAM-binding assay on this protein. Comparator check, against GOA rather than against this project's own proposals: GOA does annotate GO:1904047 to radical SAM enzymes in exactly this role, by UniRule -- ECOLI/queE (UR000100349), ECOLI/moaA and PSEPK/moaA (UR000101305), METEA/pqqE and PSEPK/pqqE (UR000098303). So the absence here is patchy UniRule coverage, which rules happen to carry the term, not a GO convention against annotating a radical SAM enzyme's own cosubstrate. That is also why those five genes have an existing row to ACCEPT or MODIFY while this one needs a NEW row.
Supporting Evidence:
file:SCHPO/bio2/bio2-uniprot.txt
Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
file:SCHPO/bio2/bio2-uniprot.txt
cysteines and an exchangeable S-adenosyl-L-methionine
file:SCHPO/bio2/bio2-uniprot.txt
/ligand_note="4Fe-4S-S-AdoMet"

Core Functions

Radical-SAM biotin synthase that converts dethiobiotin to biotin, the final step of biotin synthesis, in mitochondria.

Molecular Function:
biotin synthase activity
Directly Involved In:
biotin biosynthetic process
Cellular Locations:
mitochondrion
Supporting Evidence:
  • file:SCHPO/bio2/bio2-uniprot.txt
    FUNCTION: Catalyzes the last step of biotin biosynthesis, the
  • file:SCHPO/bio2/bio2-uniprot.txt
    Reaction=(4R,5S)-dethiobiotin + (sulfur carrier)-SH + 2 reduced [2Fe-
  • PMID:10525840
    Heterologous complementation experiment allowed the cloning and the characterization of a novel bio gene: bio2, encoding biotin synthase from Schizosaccharomyces pombe.
  • PMID:16823372
    we determined the localization of 4,431 proteins

Binds the catalytic radical SAM [4Fe-4S] cluster through the CxxxCxxC motif; its unique iron coordinates the S-adenosyl-L-methionine that is reductively cleaved to the 5'-deoxyadenosyl radical starting every turnover of biotin synthase activity.

Molecular Function:
4 iron, 4 sulfur cluster binding
Supporting Evidence:
  • file:SCHPO/bio2/bio2-uniprot.txt
    Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
  • file:SCHPO/bio2/bio2-uniprot.txt
    cysteines and an exchangeable S-adenosyl-L-methionine

Binds the auxiliary [2Fe-2S] cluster that is the immediate source of the sulfur inserted into dethiobiotin and is destroyed in the course of a turnover, so biotin synthase activity depends on it as directly as on the radical SAM cluster.

Molecular Function:
2 iron, 2 sulfur cluster binding
Supporting Evidence:
  • file:SCHPO/bio2/bio2-uniprot.txt
    Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;

Binds S-adenosyl-L-methionine as the radical-generating cosubstrate at the unique iron of the [4Fe-4S] cluster: two SAM are consumed per biotin formed.

Molecular Function:
S-adenosyl-L-methionine binding
Supporting Evidence:
  • file:SCHPO/bio2/bio2-uniprot.txt
    cysteines and an exchangeable S-adenosyl-L-methionine
  • file:SCHPO/bio2/bio2-uniprot.txt
    /ligand_note="4Fe-4S-S-AdoMet"

References

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Suggested Questions for Experts

Q: Which upstream biotin biosynthesis steps (BioF, BioA, BioD equivalents) are present in S. pombe, i.e. can bio2 contribute to biotin prototrophy from dethiobiotin or only from supplied vitamers?

Q: Is S. pombe bio2 imported into the mitochondrial matrix, and does it depend on the mitochondrial ISC machinery for cluster assembly as in S. cerevisiae?

Suggested Experiments

Experiment: Test growth of wild-type and bio2-deleted S. pombe on dethiobiotin versus biotin, and localise endogenously tagged bio2 by mitochondrial fractionation.

Type: genetics and cell biology

📚 Additional Documentation

Notes

(bio2-notes.md)

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