FB2024_03 , released June 25, 2024
Physical Interaction report
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General Information
Interaction Type
Interacting Genes
FlyBase ID
FBig0000095777
Interaction Network
Interactions Browser links
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pum network
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Protein
RNA
Selected Interactor(s)
Common Interactor(s)
Reported Interactions
FBrf0080271-1.XL.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
hb 

NRE

bait

[32]P label

hb 
pum 

Pum

prey
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
hb 
NRE
sufficient binding region
AUUAUUUUGUUGUCGAAAAUUGUACAUAAGCC
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced and labeled by in vitro transcription; prey derived from wild-type adult female ovary extract.

The pum protein is detected as a 165 kDa band (close to its predicted 157.5 kDa size). Binding is absent in pum mutant extracts, and inhibited by pum antiserum.

Binding to the hb NRE by another unidentified 55 kDa factor (not nos or pum was observed).

FBrf0080271-2.XL.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
hb 

NRE

bait

[32]P label

hb 
pum 

Pum

prey
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
hb 
NRE
sufficient binding region
AUUAUUUUGUUGUCGAAAAUUGUACAUAAGCC
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced and labeled by in vitro transcription; prey produced by in vitro translation.

FBrf0100313-1.EMSA.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait

GST tag

pum 
hb 

hb

prey

[32]P label

hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
pum 
RBD
sufficient binding region
aa 1093-1426

coordinates relative to pum-PA

hb 
NRE
sufficient binding region
GUUGUCCAGAAUUGUA
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced as a recombinant fusion proteins in bacterial system; prey produced and labeled in vitro.

FBrf0103064-1.XL.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
hb 

hb

bait

[32]P label

hb 
pum 

Pum

prey
pum 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
hb 
NRE
sufficient binding region
GUUGUCGAAAAUUGUA
pum 
RNA-binding domain
sufficient binding region
aa 1092-1426

coordinates relative to pum-PA

Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced and labeled in vitro; prey produced and labeled by in vitro translation.

FBrf0112045-3.Y3H
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
hb 

hb NRE

bait

fused to MS2 stem loop

pum 

Pum

prey

fused to GAL4 activation domain

pum 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
pum 
RNA-binding domain
sufficient binding region
aa 1093-1426

coordinates relative to pum-PA

Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Source was yeast cell line; bait produced as transgenic fusion protein; prey produced as transgenic fusion protein (prey was previously cloned reagent).

Three-hybrid system: yeast LexA-BD/MS2-SL/GAL4-AD. LexA-BD fused to phage MS2 coat protein, which binds MS2-SL.

FBrf0112045-4.XL.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
hb 

hb

bait

[32]P label

hb 
pum 

Pum

prey
pum 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
hb 
NRE
sufficient binding region
GUUGUCGAAAAUUGUA
pum 
RNA-binding domain
sufficient binding region
aa 1093-1426

coordinates relative to pum-PA

Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced and labeled in vitro; prey derived from embryonic extract of wild-type fly line.

FBrf0135683-1.Y3H
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait

fused to GAL4 DNA-binding domain

pum 
pum 
pum 
pum 
pum 
pum 
hb 

hb NRE

prey

fused to MS2 stem loop

hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
pum 
Puf domain
sufficient binding region
aa 1092-1411

coordinates relative to pum-PA

pum 
Puf domain residue R1127
mutation disrupting interaction
aa 1127

R1127A, coordinates relative to pum-PA

pum 
Puf domain residue K1167
mutation disrupting interaction
aa 1167

K1167A, coordinates relative to pum-PA

pum 
Puf domain residue R1199
mutation disrupting interaction
aa 1199

R1199A, coordinates relative to pum-PA

pum 
Puf domain residue H1235
mutation disrupting interaction
aa 1235

H1235A, coordinates relative to pum-PA

pum 
Puf domain residue E1346
mutation disrupting interaction
aa 1346

E1346K, coordinates relative to pum-PA

hb 
NRE
sufficient binding region
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Source was yeast cell line; bait produced as transgenic fusion protein; prey produced as transgenic fusion protein (prey was previously cloned reagent).

Three-hybrid system: yeast GAL4-BD/MS2-SL/GAL4-AD. GAL4-AD fused to phage MS2 coat protein, which binds MS2-SL.

FBrf0135871-1.EMSA.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait
pum 
hb 

hunchback

prey
hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
pum 
Puf domain
sufficient binding region
aa 1093-1411

coordinates relative to pum-PA

hb 
NRE
sufficient binding region
UUUGUUGUCGAAAAUUGUACAUAA
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced as recombinant fusion protein in bacteria; prey produced and labeled by in vitro.

FBrf0180581-1.EMSA.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait

GST tag

pum 
hb 

hb

prey

[32]P label

hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
pum 
RBD
sufficient binding region
aa 1091-1433

coordinates relative to pum-PA

hb 
hb NRE
sufficient binding region
AUUAUUUUGUUGUCGAAAAUUGUACAUAAGCC
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced as a recombinant fusion proteins in bacterial system; prey produced and labeled in vitro.

Positive control.

FBrf0194692-1.EMSA.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait

His tag

pum 
hb 

hb

prey

[32]P label

hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
hb 
hb NRE
sufficient binding region
AUUAUUUUGUUGUCGAAAAUUGUACAUAAGCC
pum 
RBD
sufficient binding region
aa 1091-1433

coordinates relative to pum-PA

Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced as a recombinant fusion proteins in bacterial system; prey produced and labeled in vitro.

FBrf0210325-1.EMSA.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait

GST tag

pum 
hb 

hb

prey

[32]P label

hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
pum 
RBD
sufficient binding region
aa 1091-1533

coordinates relative to pum-PA

hb 
NRE2
sufficient binding region
AUUAUUUUGUUGUCGAAAAUUGUACAUAAGCC
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced as a recombinant fusion proteins in bacterial system; prey produced and labeled in vitro.

Positive control.

FBrf0215406-1.FPS
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait

His tag

pum 
hb 

NRE

prey

fluorescein label

hb 
hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
pum 
Puf domain
sufficient binding region
aa 1092-1411

coordinates relative to pum-PA

hb 
NRE1
sufficient binding region
UCAUAUAAUCGUUGUCCAGAAUUGUAUAUAUUCG
hb 
NRE2
sufficient binding region
ACAUUAUUUUGUUGUCGAAAAUUGUACAUAAGCC
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced as a recombinant fusion protein in bacterial system; prey oligonucleotide produced and labeled in vitro.

Cooperative binding of pum to hb NRE RNA element is best fit by a two-site model. Each hb NRE RNA element is composed of two pum binding sites: BoxA and BoxB.

FBrf0215406-2.EMSA.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait

His tag

pum 
hb 

NRE

prey

[32]P label

hb 
hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
pum 
Puf domain
sufficient binding region
aa 1092-1411

coordinates relative to pum-PA

hb 
NRE1
sufficient binding region
UCAUAUAAUCGUUGUCCAGAAUUGUAUAUAUUCG
hb 
NRE2
sufficient binding region
ACAUUAUUUUGUUGUCGAAAAUUGUACAUAAGCC
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced as a recombinant fusion protein in bacterial system; prey oligonucleotide produced and labeled in vitro.

Data are consistent with binding or one or two molecules of pum protein to each hb NRE RNA element. Two pum-NRE complexes are observed in gels - the higher molecular weight complex is not observed when one of the two NRE boxes is mutated.

FBrf0218126-1.Y3H
Reference
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait

fused to LexA DNA-binding domain

pum 
hb 

hb

prey

dimerized, fused to MS2 RNA-stem loop

hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
pum 
Puf region
sufficient binding region
aa 1093-1427
hb 
NRE
sufficient binding region
nt 2558-2565

coordinates relative to hb-RA isoform

Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

yeast LexA/GAL4-AD.

pum binds 3\' UTR NRE consensus sequences (UGUANAUA) in hb, Egfr, rl, Sos and drk, but not in phl (also known as raf).

FBrf0223419-7.PD.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
hb 

hb

bait

biotin tag

hb 
pum 

Pum

prey

[35]S label

pum 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
pum 
C-terminal region
sufficient binding region
aa 849–1533
hb 
three-prime UTR
sufficient binding region
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced and labeled by in vitro transcription; prey produced and labeled by in vitro translation.

Positive control.

FBrf0224581-3.EMSA.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

pum

bait
pum 
hb 

hb

prey

[32]P label

hb 
hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
hb 
3-prime UTR
sufficient binding region
nt 2834-2935
hb 
boxB
mutation disrupting interaction
AUUGUAUAU...AUUGUACAU

AUUGUAUAU...AUUGUACAU to AUGGGAUGG...AUGGGACGG

pum 
HD domain
sufficient binding region
aa 1093-1426

coordinates refer to pum-PA

Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced as a recombinant fusion protein in bacterial system; prey produced and labeled by in vitro transcription.

Binding of pum to hb mRNA facilitated by prebinding mRNA with brat.

FBrf0233303-3.XC
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pumilio

neutral component
pum 

Pumilio

neutral component
pum 
pum 

Pumilio

neutral component
pum 
hb 

hb

neutral component
hb 
hb 

hb

neutral component
hb 

hb

neutral component
hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
hb 
NRE2
sufficient binding region
AAAUUGUACAUAAGCC
pum 
RNA-binding domain
sufficient binding region
aa 1091-1426

coordinates relative to pum-PA

Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; protein produced as a recombinant fusion proteins in bacterial system; RNA synthesized in vitro.

Ternary complex of nos and pum proteins and hb RNA.

FBrf0233303-4.EMSA.A
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pumilio

bait
pum 
hb 

hb

prey

Cy5 label

hb 
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
hb 
NRE2
sufficient binding region
AAAUUGUACAUAAGCC
pum 
RNA-binding domain
sufficient binding region
aa 1091-1426

coordinates relative to pum-PA

Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Interaction in vitro; bait produced as a recombinant fusion proteins in bacterial system; prey synthesized in vitro.

Binding of hb NRE2 by pum protein is enhanced by nos protein. nos alone does not bind hb in this assay.

FBrf0242571-6.coIP.PCR
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait

Myc tag

hb 

Hb

prey
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Source was cell extract of S2 cell line; bait produced from tagged transgenic construct; prey produced from endogenous gene.

Positive control.

FBrf0247403-8.coIP.PCR
Description
physical association
Collection
Source/Stage
Cell line used
Participants
Corresponds to
Reported as
Role
Note
pum 

Pum

bait

HA tag

hb 

Hunchback

prey
Experimental entities
Corresponds to
Identifier
Reported
Role
Note
Subregions with role in interaction
Corresponds to
Description
Role
Coordinates
Note
Isoform-specific participants
Corresponds to
Description
Role
Note
Comments concerning this interaction

Source was cell extract of S2 cell line; bait produced from transfected construct; prey produced from endogenous gene.

External Crossreferences and Linkouts ( 1 )
Linkouts
MIST - An integrated Molecular Interaction Database
References (16)